Starting phenix.real_space_refine on Wed Aug 5 14:42:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kwz_62622/08_2026/9kwz_62622.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kwz_62622/08_2026/9kwz_62622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kwz_62622/08_2026/9kwz_62622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kwz_62622/08_2026/9kwz_62622.map" model { file = "/net/cci-nas-00/data/ceres_data/9kwz_62622/08_2026/9kwz_62622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kwz_62622/08_2026/9kwz_62622.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 6314 2.51 5 N 1715 2.21 5 O 1941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10022 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1704 Classifications: {'peptide': 217} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 204} Chain: "B" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1695 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 203} Chain: "E" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1630 Classifications: {'peptide': 216} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 204} Chain: "F" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1629 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 205} Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1710 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "L" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1654 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Time building chain proxies: 2.04, per 1000 atoms: 0.20 Number of scatterers: 10022 At special positions: 0 Unit cell: (165.224, 143.484, 107.613, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1941 8.00 N 1715 7.00 C 6314 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 125 " distance=1.99 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 125 " distance=2.14 Simple disulfide: pdb=" SG CYS E 166 " - pdb=" SG CYS E 220 " distance=2.19 Simple disulfide: pdb=" SG CYS F 52 " - pdb=" SG CYS F 126 " distance=1.94 Simple disulfide: pdb=" SG CYS H 225 " - pdb=" SG CYS L 214 " distance=2.00 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.13 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.08 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: 0.89 Conformation dependent library (CDL) restraints added in 402.2 milliseconds 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2386 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 25 sheets defined 4.0% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.578A pdb=" N ASN A 120 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.508A pdb=" N PHE A 240 " --> pdb=" O PRO A 237 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET A 241 " --> pdb=" O GLU A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 237 through 241' Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'E' and resid 117 through 121 removed outlier: 3.549A pdb=" N ASP E 120 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER E 121 " --> pdb=" O ALA E 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 117 through 121' Processing helix chain 'E' and resid 239 through 243 removed outlier: 3.662A pdb=" N ARG E 243 " --> pdb=" O PRO E 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 238 through 242 removed outlier: 3.963A pdb=" N PHE F 241 " --> pdb=" O ALA F 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.886A pdb=" N ARG H 31 " --> pdb=" O ILE H 28 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 197 through 201 removed outlier: 3.592A pdb=" N THR H 200 " --> pdb=" O SER H 197 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN H 201 " --> pdb=" O LEU H 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 197 through 201' Processing helix chain 'H' and resid 211 through 214 removed outlier: 4.268A pdb=" N THR H 214 " --> pdb=" O PRO H 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 211 through 214' Processing helix chain 'L' and resid 123 through 127 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 removed outlier: 6.041A pdb=" N ILE A 39 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 63 " --> pdb=" O GLN A 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 50 Processing sheet with id=AA3, first strand: chain 'A' and resid 150 through 157 removed outlier: 5.187A pdb=" N ARG A 162 " --> pdb=" O ARG A 154 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS A 156 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLY A 160 " --> pdb=" O HIS A 156 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N GLU A 164 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL A 207 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE A 166 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N THR A 205 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ARG A 168 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL A 203 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 192 " --> pdb=" O THR A 204 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 179 Processing sheet with id=AA5, first strand: chain 'B' and resid 32 through 33 removed outlier: 3.676A pdb=" N HIS B 52 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 109 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AA7, first strand: chain 'B' and resid 150 through 157 removed outlier: 6.373A pdb=" N ILE B 151 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE B 166 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N MET B 153 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU B 164 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY B 155 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE B 201 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS B 190 " --> pdb=" O ALA B 206 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 185 through 186 removed outlier: 4.359A pdb=" N TRP B 178 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 33 through 34 removed outlier: 3.501A pdb=" N HIS E 53 " --> pdb=" O LEU E 34 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 40 through 43 removed outlier: 4.898A pdb=" N VAL E 78 " --> pdb=" O VAL E 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 190 through 191 removed outlier: 3.546A pdb=" N GLU E 203 " --> pdb=" O VAL E 195 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL E 195 " --> pdb=" O GLU E 203 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 190 through 191 removed outlier: 5.327A pdb=" N TYR E 202 " --> pdb=" O GLY E 170 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 186 through 187 removed outlier: 4.189A pdb=" N TRP E 179 " --> pdb=" O ILE E 187 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N VAL F 152 " --> pdb=" O THR E 232 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER E 234 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N VAL F 154 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER E 236 " --> pdb=" O VAL F 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 32 through 33 Processing sheet with id=AB6, first strand: chain 'F' and resid 40 through 41 removed outlier: 3.615A pdb=" N ILE F 40 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS F 142 " --> pdb=" O ILE F 40 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU F 65 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL F 78 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP F 67 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL F 78 " --> pdb=" O VAL F 85 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 128 through 130 Processing sheet with id=AB8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.800A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.675A pdb=" N CYS H 96 " --> pdb=" O TRP H 112 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TRP H 112 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG H 98 " --> pdb=" O ASP H 110 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 129 through 133 removed outlier: 4.254A pdb=" N GLY H 148 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL H 190 " --> pdb=" O HIS H 173 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS H 173 " --> pdb=" O VAL H 190 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 159 through 162 removed outlier: 3.616A pdb=" N THR H 160 " --> pdb=" O ASN H 208 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN H 208 " --> pdb=" O THR H 160 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.905A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.667A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 114 through 115 removed outlier: 3.654A pdb=" N SER L 114 " --> pdb=" O ASN L 137 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN L 137 " --> pdb=" O SER L 114 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU L 175 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER L 174 " --> pdb=" O THR L 164 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 154 through 155 319 hydrogen bonds defined for protein. 765 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: 1.58 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.30: 1904 1.30 - 1.46: 3621 1.46 - 1.62: 4603 1.62 - 1.79: 68 1.79 - 1.95: 45 Bond restraints: 10241 Sorted by residual: bond pdb=" ND1 HIS E 114 " pdb=" CE1 HIS E 114 " ideal model delta sigma weight residual 1.321 1.438 -0.117 1.00e-02 1.00e+04 1.36e+02 bond pdb=" CA GLN E 129 " pdb=" C GLN E 129 " ideal model delta sigma weight residual 1.520 1.635 -0.115 1.12e-02 7.97e+03 1.06e+02 bond pdb=" SD MET H 81 " pdb=" CE MET H 81 " ideal model delta sigma weight residual 1.791 1.535 0.256 2.50e-02 1.60e+03 1.05e+02 bond pdb=" ND1 HIS F 163 " pdb=" CE1 HIS F 163 " ideal model delta sigma weight residual 1.321 1.420 -0.099 1.00e-02 1.00e+04 9.72e+01 bond pdb=" CA ARG B 68 " pdb=" C ARG B 68 " ideal model delta sigma weight residual 1.527 1.409 0.118 1.21e-02 6.83e+03 9.47e+01 ... (remaining 10236 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 10303 2.83 - 5.65: 2455 5.65 - 8.48: 910 8.48 - 11.30: 184 11.30 - 14.13: 36 Bond angle restraints: 13888 Sorted by residual: angle pdb=" N LYS B 173 " pdb=" CA LYS B 173 " pdb=" C LYS B 173 " ideal model delta sigma weight residual 109.57 122.15 -12.58 1.23e+00 6.61e-01 1.05e+02 angle pdb=" N GLU A 60 " pdb=" CA GLU A 60 " pdb=" C GLU A 60 " ideal model delta sigma weight residual 113.02 100.84 12.18 1.20e+00 6.94e-01 1.03e+02 angle pdb=" N THR A 36 " pdb=" CA THR A 36 " pdb=" C THR A 36 " ideal model delta sigma weight residual 113.38 100.93 12.45 1.23e+00 6.61e-01 1.02e+02 angle pdb=" N PHE A 67 " pdb=" CA PHE A 67 " pdb=" C PHE A 67 " ideal model delta sigma weight residual 108.34 121.58 -13.24 1.31e+00 5.83e-01 1.02e+02 angle pdb=" CA LYS H 218 " pdb=" C LYS H 218 " pdb=" O LYS H 218 " ideal model delta sigma weight residual 121.33 110.99 10.34 1.08e+00 8.57e-01 9.17e+01 ... (remaining 13883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.06: 5787 19.06 - 38.12: 306 38.12 - 57.18: 47 57.18 - 76.23: 12 76.23 - 95.29: 6 Dihedral angle restraints: 6158 sinusoidal: 2422 harmonic: 3736 Sorted by residual: dihedral pdb=" CA TYR F 127 " pdb=" C TYR F 127 " pdb=" N PHE F 128 " pdb=" CA PHE F 128 " ideal model delta harmonic sigma weight residual 180.00 147.05 32.95 0 5.00e+00 4.00e-02 4.34e+01 dihedral pdb=" CA GLY A 130 " pdb=" C GLY A 130 " pdb=" N ARG A 131 " pdb=" CA ARG A 131 " ideal model delta harmonic sigma weight residual 180.00 149.52 30.48 0 5.00e+00 4.00e-02 3.72e+01 dihedral pdb=" CB CYS F 52 " pdb=" SG CYS F 52 " pdb=" SG CYS F 126 " pdb=" CB CYS F 126 " ideal model delta sinusoidal sigma weight residual 93.00 144.37 -51.37 1 1.00e+01 1.00e-02 3.61e+01 ... (remaining 6155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.307: 1354 0.307 - 0.613: 164 0.613 - 0.920: 14 0.920 - 1.226: 8 1.226 - 1.533: 2 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CG LEU B 200 " pdb=" CB LEU B 200 " pdb=" CD1 LEU B 200 " pdb=" CD2 LEU B 200 " both_signs ideal model delta sigma weight residual False -2.59 -1.06 -1.53 2.00e-01 2.50e+01 5.87e+01 chirality pdb=" CG LEU A 189 " pdb=" CB LEU A 189 " pdb=" CD1 LEU A 189 " pdb=" CD2 LEU A 189 " both_signs ideal model delta sigma weight residual False -2.59 -1.36 -1.23 2.00e-01 2.50e+01 3.78e+01 chirality pdb=" CB ILE H 28 " pdb=" CA ILE H 28 " pdb=" CG1 ILE H 28 " pdb=" CG2 ILE H 28 " both_signs ideal model delta sigma weight residual False 2.64 1.48 1.17 2.00e-01 2.50e+01 3.41e+01 ... (remaining 1539 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 178 " 0.031 2.00e-02 2.50e+03 8.31e-02 1.73e+02 pdb=" CG TRP B 178 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP B 178 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 178 " 0.032 2.00e-02 2.50e+03 pdb=" NE1 TRP B 178 " -0.145 2.00e-02 2.50e+03 pdb=" CE2 TRP B 178 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 178 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 178 " 0.163 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 178 " -0.118 2.00e-02 2.50e+03 pdb=" CH2 TRP B 178 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 163 " -0.010 2.00e-02 2.50e+03 8.19e-02 1.68e+02 pdb=" CG TRP H 163 " 0.111 2.00e-02 2.50e+03 pdb=" CD1 TRP H 163 " -0.136 2.00e-02 2.50e+03 pdb=" CD2 TRP H 163 " 0.075 2.00e-02 2.50e+03 pdb=" NE1 TRP H 163 " -0.060 2.00e-02 2.50e+03 pdb=" CE2 TRP H 163 " 0.077 2.00e-02 2.50e+03 pdb=" CE3 TRP H 163 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 163 " 0.078 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 163 " -0.120 2.00e-02 2.50e+03 pdb=" CH2 TRP H 163 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 66 " 0.009 2.00e-02 2.50e+03 7.31e-02 1.33e+02 pdb=" CG TRP A 66 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 66 " 0.100 2.00e-02 2.50e+03 pdb=" CD2 TRP A 66 " -0.081 2.00e-02 2.50e+03 pdb=" NE1 TRP A 66 " -0.059 2.00e-02 2.50e+03 pdb=" CE2 TRP A 66 " -0.093 2.00e-02 2.50e+03 pdb=" CE3 TRP A 66 " -0.082 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 66 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 66 " 0.032 2.00e-02 2.50e+03 pdb=" CH2 TRP A 66 " 0.114 2.00e-02 2.50e+03 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1596 2.76 - 3.30: 9099 3.30 - 3.83: 15264 3.83 - 4.37: 18394 4.37 - 4.90: 31915 Nonbonded interactions: 76268 Sorted by model distance: nonbonded pdb=" O THR H 174 " pdb=" CD1 PHE H 175 " model vdw 2.226 3.340 nonbonded pdb=" NH2 ARG A 68 " pdb=" O THR A 122 " model vdw 2.289 3.120 nonbonded pdb=" ND1 HIS E 151 " pdb=" OG SER F 234 " model vdw 2.300 3.120 nonbonded pdb=" CD1 LEU E 150 " pdb=" CD1 ILE E 222 " model vdw 2.309 3.880 nonbonded pdb=" CG1 VAL A 64 " pdb=" CE2 PHE A 127 " model vdw 2.315 3.760 ... (remaining 76263 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 30 through 245) selection = chain 'B' } ncs_group { reference = (chain 'E' and (resid 30 through 148 or resid 150 through 152 or resid 154 throu \ gh 157 or resid 159 through 181 or resid 183 through 188 or resid 190 through 20 \ 2 or resid 204 through 212 or resid 214 through 220 or resid 222 through 223 or \ resid 225 through 245)) selection = (chain 'F' and (resid 30 through 148 or resid 150 through 152 or resid 154 throu \ gh 157 or resid 159 through 181 or resid 183 through 188 or resid 190 through 20 \ 2 or resid 204 through 212 or resid 214 through 220 or resid 222 through 223 or \ resid 225 through 245)) } 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: 4.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.950 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 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 : 0.038 0.256 10248 Z= 2.368 Angle : 2.952 14.129 13902 Z= 1.891 Chirality : 0.219 1.533 1542 Planarity : 0.024 0.134 1796 Dihedral : 12.372 95.292 3751 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.27 % Allowed : 0.90 % Favored : 98.82 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.09 (0.21), residues: 1292 helix: -4.93 (0.39), residues: 18 sheet: -1.25 (0.22), residues: 552 loop : -2.71 (0.19), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.090 0.012 ARG E 223 TYR 0.118 0.026 TYR L 173 PHE 0.115 0.026 PHE H 107 TRP 0.163 0.041 TRP B 178 HIS 0.071 0.015 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.03793 / 2.37 (10241) covalent geometry : angle 2.94687 / 1.89 (13888) SS BOND : bond 0.09282 / 4.40 ( 7) SS BOND : angle 6.28573 / 3.80 ( 14) hydrogen bonds : bond 0.16232 / 10.85 ( 310) hydrogen bonds : angle 9.16774 / 6.11 ( 765) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 215 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.4728 (OUTLIER) cc_final: 0.3819 (mmp-170) REVERT: A 202 MET cc_start: 0.5121 (ptt) cc_final: 0.4459 (ptt) REVERT: B 231 GLU cc_start: 0.6842 (tm-30) cc_final: 0.6369 (tm-30) REVERT: F 99 ILE cc_start: 0.6399 (mm) cc_final: 0.6110 (mt) REVERT: H 103 ASP cc_start: 0.7702 (m-30) cc_final: 0.7439 (m-30) REVERT: L 3 GLN cc_start: 0.7871 (pp30) cc_final: 0.7552 (pp30) REVERT: L 4 MET cc_start: 0.8485 (mtp) cc_final: 0.8221 (mtp) outliers start: 3 outliers final: 1 residues processed: 218 average time/residue: 0.0960 time to fit residues: 29.0659 Evaluate side-chains 162 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain E residue 150 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 HIS A 228 GLN B 46 ASN B 58 ASN F 151 HIS ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.183104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.172958 restraints weight = 16375.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.170236 restraints weight = 21148.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 80)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.168923 restraints weight = 23344.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.169197 restraints weight = 22560.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.169548 restraints weight = 18033.159| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10248 Z= 0.166 Angle : 0.709 8.496 13902 Z= 0.366 Chirality : 0.047 0.182 1542 Planarity : 0.006 0.067 1796 Dihedral : 6.314 56.630 1419 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.72 % Allowed : 6.06 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.22), residues: 1292 helix: -4.71 (0.62), residues: 18 sheet: -0.79 (0.22), residues: 553 loop : -2.23 (0.20), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 162 TYR 0.016 0.002 TYR A 171 PHE 0.020 0.003 PHE B 127 TRP 0.032 0.003 TRP F 67 HIS 0.007 0.001 HIS H 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (10241) covalent geometry : angle 0.70789 / 0.37 (13888) SS BOND : bond 0.00553 / 0.22 ( 7) SS BOND : angle 1.30617 / 0.86 ( 14) hydrogen bonds : bond 0.03483 / 2.31 ( 310) hydrogen bonds : angle 7.05445 / 4.69 ( 765) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.5526 (OUTLIER) cc_final: 0.4982 (mmp80) REVERT: A 92 TYR cc_start: 0.3862 (m-80) cc_final: 0.3340 (m-80) REVERT: B 58 ASN cc_start: 0.7392 (m-40) cc_final: 0.7172 (m-40) REVERT: E 167 ARG cc_start: 0.5867 (ptp90) cc_final: 0.5579 (ptm-80) REVERT: H 109 MET cc_start: 0.8260 (mtt) cc_final: 0.7727 (mtt) outliers start: 19 outliers final: 14 residues processed: 191 average time/residue: 0.0960 time to fit residues: 25.1880 Evaluate side-chains 179 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain E residue 52 CYS Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain F residue 168 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 145 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 0.5980 chunk 40 optimal weight: 0.0980 chunk 79 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 69.8891 > 50:) chunk 126 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 42 optimal weight: 0.0170 chunk 101 optimal weight: 0.5980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 129 GLN F 186 ASN ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.185390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.174085 restraints weight = 16373.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 84)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.171355 restraints weight = 23547.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.171167 restraints weight = 22512.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.171567 restraints weight = 19067.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.171638 restraints weight = 16215.021| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10248 Z= 0.115 Angle : 0.612 8.254 13902 Z= 0.318 Chirality : 0.045 0.157 1542 Planarity : 0.005 0.054 1796 Dihedral : 5.445 54.179 1417 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.44 % Allowed : 9.50 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.22), residues: 1292 helix: -4.62 (1.16), residues: 12 sheet: -0.47 (0.23), residues: 529 loop : -1.89 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 162 TYR 0.016 0.001 TYR L 140 PHE 0.015 0.002 PHE L 209 TRP 0.032 0.002 TRP L 35 HIS 0.005 0.001 HIS E 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (10241) covalent geometry : angle 0.61160 / 0.32 (13888) SS BOND : bond 0.00392 / 0.16 ( 7) SS BOND : angle 1.17981 / 0.77 ( 14) hydrogen bonds : bond 0.03020 / 2.02 ( 310) hydrogen bonds : angle 6.51739 / 4.36 ( 765) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.4281 (OUTLIER) cc_final: 0.4038 (tt) REVERT: A 68 ARG cc_start: 0.5312 (OUTLIER) cc_final: 0.4597 (mmp80) REVERT: A 92 TYR cc_start: 0.3627 (m-80) cc_final: 0.3248 (m-80) REVERT: H 103 ASP cc_start: 0.7759 (m-30) cc_final: 0.7509 (m-30) REVERT: H 109 MET cc_start: 0.8251 (mtt) cc_final: 0.7972 (mtt) REVERT: H 175 PHE cc_start: 0.7427 (m-10) cc_final: 0.7139 (m-10) outliers start: 27 outliers final: 19 residues processed: 183 average time/residue: 0.1046 time to fit residues: 26.3180 Evaluate side-chains 177 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 52 CYS Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain F residue 168 SER Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 25 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 63 optimal weight: 0.0020 chunk 50 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 87 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 89 GLN F 186 ASN ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.181829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.170144 restraints weight = 16381.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.168792 restraints weight = 23588.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.169583 restraints weight = 19938.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.169253 restraints weight = 16946.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.169473 restraints weight = 14926.286| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10248 Z= 0.150 Angle : 0.623 8.187 13902 Z= 0.324 Chirality : 0.046 0.155 1542 Planarity : 0.005 0.050 1796 Dihedral : 5.541 56.503 1417 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.99 % Allowed : 10.50 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.23), residues: 1292 helix: -4.62 (1.16), residues: 12 sheet: -0.42 (0.23), residues: 543 loop : -1.88 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 124 TYR 0.018 0.001 TYR L 140 PHE 0.019 0.002 PHE A 235 TRP 0.031 0.002 TRP L 35 HIS 0.006 0.001 HIS E 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (10241) covalent geometry : angle 0.62105 / 0.32 (13888) SS BOND : bond 0.00448 / 0.19 ( 7) SS BOND : angle 1.60573 / 1.07 ( 14) hydrogen bonds : bond 0.03137 / 2.09 ( 310) hydrogen bonds : angle 6.55020 / 4.38 ( 765) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.4562 (OUTLIER) cc_final: 0.4298 (tt) REVERT: A 68 ARG cc_start: 0.5124 (OUTLIER) cc_final: 0.4585 (mmp80) REVERT: A 92 TYR cc_start: 0.3817 (m-80) cc_final: 0.3369 (m-80) REVERT: B 65 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7701 (ptp90) REVERT: H 12 LYS cc_start: 0.8101 (mmtt) cc_final: 0.7777 (mmmt) REVERT: H 103 ASP cc_start: 0.7826 (m-30) cc_final: 0.7576 (m-30) REVERT: H 175 PHE cc_start: 0.7467 (m-10) cc_final: 0.7150 (m-10) REVERT: L 209 PHE cc_start: -0.0437 (OUTLIER) cc_final: -0.0651 (p90) outliers start: 33 outliers final: 24 residues processed: 187 average time/residue: 0.0973 time to fit residues: 24.9523 Evaluate side-chains 188 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 52 CYS Chi-restraints excluded: chain E residue 55 PHE Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain F residue 168 SER Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 209 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 61 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 chunk 44 optimal weight: 0.1980 chunk 111 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 100 optimal weight: 0.0170 chunk 74 optimal weight: 4.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 GLN F 89 GLN F 186 ASN ** H 180 GLN ** 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 = 0.4150 r_free = 0.4150 target = 0.180563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.170726 restraints weight = 16243.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 115)---------------| | r_work = 0.4013 r_free = 0.4013 target = 0.168492 restraints weight = 20475.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 114)---------------| | r_work = 0.3997 r_free = 0.3997 target = 0.167460 restraints weight = 19918.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.167492 restraints weight = 17253.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.167747 restraints weight = 15192.577| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10248 Z= 0.160 Angle : 0.631 8.174 13902 Z= 0.330 Chirality : 0.046 0.157 1542 Planarity : 0.005 0.048 1796 Dihedral : 5.631 58.039 1417 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.44 % Allowed : 11.67 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.23), residues: 1292 helix: -4.57 (1.21), residues: 12 sheet: -0.43 (0.23), residues: 546 loop : -1.85 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 162 TYR 0.022 0.002 TYR L 140 PHE 0.016 0.002 PHE L 73 TRP 0.037 0.002 TRP L 35 HIS 0.007 0.001 HIS E 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (10241) covalent geometry : angle 0.62901 / 0.33 (13888) SS BOND : bond 0.00584 / 0.24 ( 7) SS BOND : angle 1.64569 / 1.09 ( 14) hydrogen bonds : bond 0.03166 / 2.09 ( 310) hydrogen bonds : angle 6.62044 / 4.43 ( 765) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.4899 (OUTLIER) cc_final: 0.4648 (tt) REVERT: A 68 ARG cc_start: 0.5228 (OUTLIER) cc_final: 0.4770 (tpm170) REVERT: A 92 TYR cc_start: 0.3951 (m-80) cc_final: 0.3521 (m-80) REVERT: B 65 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7681 (ptp90) REVERT: H 103 ASP cc_start: 0.7873 (m-30) cc_final: 0.7631 (m-30) REVERT: H 175 PHE cc_start: 0.7663 (m-80) cc_final: 0.7305 (m-10) outliers start: 38 outliers final: 29 residues processed: 193 average time/residue: 0.0968 time to fit residues: 25.9905 Evaluate side-chains 199 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 52 CYS Chi-restraints excluded: chain E residue 55 PHE Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain F residue 168 SER Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 168 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 89 GLN F 186 ASN ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.180516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.171202 restraints weight = 16345.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.170038 restraints weight = 23608.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.169435 restraints weight = 21885.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.169227 restraints weight = 21719.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.169593 restraints weight = 17102.345| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10248 Z= 0.149 Angle : 0.623 8.136 13902 Z= 0.325 Chirality : 0.046 0.165 1542 Planarity : 0.004 0.045 1796 Dihedral : 5.592 59.756 1417 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.53 % Allowed : 12.49 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.23), residues: 1292 helix: -4.60 (1.18), residues: 12 sheet: -0.44 (0.23), residues: 545 loop : -1.83 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 101 TYR 0.025 0.002 TYR L 140 PHE 0.023 0.002 PHE A 235 TRP 0.039 0.002 TRP L 35 HIS 0.006 0.001 HIS E 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (10241) covalent geometry : angle 0.62119 / 0.32 (13888) SS BOND : bond 0.00622 / 0.25 ( 7) SS BOND : angle 1.60126 / 1.05 ( 14) hydrogen bonds : bond 0.03111 / 2.05 ( 310) hydrogen bonds : angle 6.59501 / 4.41 ( 765) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.4933 (OUTLIER) cc_final: 0.4717 (tt) REVERT: A 68 ARG cc_start: 0.5212 (OUTLIER) cc_final: 0.4886 (tpm170) REVERT: A 92 TYR cc_start: 0.3878 (m-80) cc_final: 0.3496 (m-80) REVERT: A 236 ILE cc_start: 0.5079 (mt) cc_final: 0.4767 (mt) REVERT: B 65 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7700 (ptp90) REVERT: F 89 GLN cc_start: 0.2376 (tp-100) cc_final: 0.1987 (tp40) REVERT: H 103 ASP cc_start: 0.7858 (m-30) cc_final: 0.7589 (m-30) REVERT: H 175 PHE cc_start: 0.7611 (m-80) cc_final: 0.7370 (m-10) outliers start: 39 outliers final: 33 residues processed: 190 average time/residue: 0.0920 time to fit residues: 24.2204 Evaluate side-chains 195 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 52 CYS Chi-restraints excluded: chain E residue 55 PHE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain F residue 168 SER Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 168 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 10 optimal weight: 4.9990 chunk 100 optimal weight: 0.0170 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 186 ASN ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.183311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.4062 r_free = 0.4062 target = 0.172651 restraints weight = 16223.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 116)---------------| | r_work = 0.4028 r_free = 0.4028 target = 0.170055 restraints weight = 20425.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 82)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.168934 restraints weight = 19723.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.169823 restraints weight = 15579.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.170003 restraints weight = 14199.103| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10248 Z= 0.124 Angle : 0.598 8.111 13902 Z= 0.312 Chirality : 0.045 0.155 1542 Planarity : 0.004 0.043 1796 Dihedral : 5.374 58.396 1417 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.26 % Allowed : 13.03 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.23), residues: 1292 helix: -4.60 (1.18), residues: 12 sheet: -0.39 (0.23), residues: 535 loop : -1.67 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 101 TYR 0.025 0.001 TYR L 140 PHE 0.015 0.002 PHE L 73 TRP 0.023 0.001 TRP L 35 HIS 0.006 0.001 HIS E 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (10241) covalent geometry : angle 0.59655 / 0.31 (13888) SS BOND : bond 0.00457 / 0.19 ( 7) SS BOND : angle 1.43551 / 0.94 ( 14) hydrogen bonds : bond 0.02906 / 1.92 ( 310) hydrogen bonds : angle 6.41309 / 4.30 ( 765) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.5253 (OUTLIER) cc_final: 0.4775 (tpp-160) REVERT: A 92 TYR cc_start: 0.3856 (m-80) cc_final: 0.3447 (m-80) REVERT: A 236 ILE cc_start: 0.5124 (mt) cc_final: 0.4793 (mt) REVERT: B 65 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7718 (ptp90) REVERT: E 243 ARG cc_start: 0.6150 (ttp-170) cc_final: 0.5892 (ptm160) REVERT: F 89 GLN cc_start: 0.2276 (tp-100) cc_final: 0.1818 (tp40) REVERT: F 99 ILE cc_start: 0.6870 (mm) cc_final: 0.6559 (mt) REVERT: H 103 ASP cc_start: 0.7792 (m-30) cc_final: 0.7536 (m-30) outliers start: 36 outliers final: 29 residues processed: 188 average time/residue: 0.0957 time to fit residues: 25.1164 Evaluate side-chains 193 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 52 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 168 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 53 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 96 optimal weight: 0.0980 chunk 121 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 122 optimal weight: 0.0770 chunk 104 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.183925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.174735 restraints weight = 16128.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.173201 restraints weight = 22760.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.172555 restraints weight = 22878.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.172780 restraints weight = 20414.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.172928 restraints weight = 16841.378| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10248 Z= 0.113 Angle : 0.599 8.107 13902 Z= 0.311 Chirality : 0.045 0.157 1542 Planarity : 0.004 0.041 1796 Dihedral : 5.241 56.497 1417 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.08 % Allowed : 14.12 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.23), residues: 1292 helix: -4.57 (1.21), residues: 12 sheet: -0.32 (0.23), residues: 528 loop : -1.64 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 131 TYR 0.026 0.001 TYR L 140 PHE 0.023 0.002 PHE A 235 TRP 0.050 0.002 TRP L 35 HIS 0.005 0.001 HIS E 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (10241) covalent geometry : angle 0.59783 / 0.31 (13888) SS BOND : bond 0.00433 / 0.17 ( 7) SS BOND : angle 1.31547 / 0.87 ( 14) hydrogen bonds : bond 0.02830 / 1.88 ( 310) hydrogen bonds : angle 6.30310 / 4.24 ( 765) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.5303 (OUTLIER) cc_final: 0.4672 (tpt90) REVERT: A 92 TYR cc_start: 0.3792 (m-80) cc_final: 0.3510 (m-80) REVERT: A 236 ILE cc_start: 0.5202 (mt) cc_final: 0.4917 (mt) REVERT: B 65 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7695 (ptp90) REVERT: E 243 ARG cc_start: 0.6095 (ttp-170) cc_final: 0.5881 (ptm160) REVERT: F 89 GLN cc_start: 0.2261 (tp-100) cc_final: 0.1795 (tp40) REVERT: H 103 ASP cc_start: 0.7776 (m-30) cc_final: 0.7467 (m-30) outliers start: 34 outliers final: 29 residues processed: 186 average time/residue: 0.0926 time to fit residues: 23.9652 Evaluate side-chains 189 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 52 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 168 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 15 optimal weight: 0.0170 chunk 7 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 173 HIS ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.182920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.172275 restraints weight = 16182.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 162)---------------| | r_work = 0.4034 r_free = 0.4034 target = 0.170365 restraints weight = 19828.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 91)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.169435 restraints weight = 21639.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.169500 restraints weight = 18732.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.169418 restraints weight = 17484.006| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10248 Z= 0.125 Angle : 0.611 8.260 13902 Z= 0.315 Chirality : 0.045 0.157 1542 Planarity : 0.004 0.042 1796 Dihedral : 5.232 55.380 1417 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.26 % Allowed : 13.94 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.23), residues: 1292 helix: -4.55 (1.23), residues: 12 sheet: -0.33 (0.23), residues: 528 loop : -1.64 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 131 TYR 0.026 0.001 TYR L 140 PHE 0.015 0.002 PHE L 73 TRP 0.042 0.002 TRP L 35 HIS 0.006 0.001 HIS E 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (10241) covalent geometry : angle 0.60928 / 0.31 (13888) SS BOND : bond 0.00480 / 0.19 ( 7) SS BOND : angle 1.36216 / 0.90 ( 14) hydrogen bonds : bond 0.02837 / 1.89 ( 310) hydrogen bonds : angle 6.31266 / 4.25 ( 765) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.5381 (OUTLIER) cc_final: 0.4746 (tpm170) REVERT: A 92 TYR cc_start: 0.3787 (m-80) cc_final: 0.3513 (m-80) REVERT: A 236 ILE cc_start: 0.5346 (mt) cc_final: 0.5053 (mt) REVERT: B 62 MET cc_start: 0.7920 (mmp) cc_final: 0.7293 (mmp) REVERT: B 65 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7722 (ptp90) REVERT: B 70 GLN cc_start: 0.8417 (pm20) cc_final: 0.8182 (pm20) REVERT: E 243 ARG cc_start: 0.6058 (ttp-170) cc_final: 0.5853 (ptm160) REVERT: F 89 GLN cc_start: 0.2199 (tp-100) cc_final: 0.1720 (tp40) REVERT: H 103 ASP cc_start: 0.7818 (m-30) cc_final: 0.7532 (m-30) outliers start: 36 outliers final: 32 residues processed: 181 average time/residue: 0.0912 time to fit residues: 23.0583 Evaluate side-chains 189 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 52 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 168 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 0.2980 chunk 16 optimal weight: 0.0470 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.183581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 133)---------------| | r_work = 0.4064 r_free = 0.4064 target = 0.172725 restraints weight = 16038.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 117)---------------| | r_work = 0.4033 r_free = 0.4033 target = 0.170312 restraints weight = 21723.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.168781 restraints weight = 21034.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.169408 restraints weight = 17956.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.169408 restraints weight = 15971.247| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10248 Z= 0.120 Angle : 0.615 8.148 13902 Z= 0.315 Chirality : 0.045 0.156 1542 Planarity : 0.004 0.041 1796 Dihedral : 5.185 54.612 1417 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.08 % Allowed : 14.39 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.23), residues: 1292 helix: -4.58 (1.20), residues: 12 sheet: -0.34 (0.23), residues: 536 loop : -1.70 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 131 TYR 0.026 0.001 TYR L 140 PHE 0.024 0.002 PHE A 235 TRP 0.047 0.002 TRP L 35 HIS 0.005 0.001 HIS E 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (10241) covalent geometry : angle 0.61418 / 0.31 (13888) SS BOND : bond 0.00480 / 0.19 ( 7) SS BOND : angle 1.21370 / 0.84 ( 14) hydrogen bonds : bond 0.02837 / 1.90 ( 310) hydrogen bonds : angle 6.24551 / 4.20 ( 765) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.5364 (OUTLIER) cc_final: 0.4804 (tpm170) REVERT: A 92 TYR cc_start: 0.3720 (m-80) cc_final: 0.3486 (m-80) REVERT: A 236 ILE cc_start: 0.5328 (mt) cc_final: 0.5054 (mt) REVERT: B 62 MET cc_start: 0.7815 (mmp) cc_final: 0.7388 (mmp) REVERT: B 65 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7746 (ptp90) REVERT: F 89 GLN cc_start: 0.2186 (tp-100) cc_final: 0.1709 (tp40) REVERT: H 103 ASP cc_start: 0.7776 (m-30) cc_final: 0.7486 (m-30) outliers start: 34 outliers final: 31 residues processed: 189 average time/residue: 0.0935 time to fit residues: 24.8278 Evaluate side-chains 196 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 52 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 168 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 90 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 0.0060 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.183836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.173495 restraints weight = 16360.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 100)---------------| | r_work = 0.4049 r_free = 0.4049 target = 0.170801 restraints weight = 22974.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.170997 restraints weight = 21202.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.171234 restraints weight = 18127.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.171305 restraints weight = 15935.673| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10248 Z= 0.116 Angle : 0.617 8.135 13902 Z= 0.313 Chirality : 0.045 0.153 1542 Planarity : 0.004 0.041 1796 Dihedral : 5.119 53.620 1417 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.90 % Allowed : 14.75 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.23), residues: 1292 helix: -4.54 (1.24), residues: 12 sheet: -0.32 (0.23), residues: 541 loop : -1.70 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 101 TYR 0.026 0.001 TYR L 140 PHE 0.020 0.001 PHE H 64 TRP 0.045 0.002 TRP L 35 HIS 0.005 0.001 HIS E 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (10241) covalent geometry : angle 0.61574 / 0.31 (13888) SS BOND : bond 0.00415 / 0.17 ( 7) SS BOND : angle 1.22742 / 0.82 ( 14) hydrogen bonds : bond 0.02771 / 1.85 ( 310) hydrogen bonds : angle 6.19492 / 4.16 ( 765) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2010.37 seconds wall clock time: 35 minutes 24.48 seconds (2124.48 seconds total)