Starting phenix.real_space_refine on Thu Jul 2 02:32:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbx_38232/07_2026/8xbx_38232.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbx_38232/07_2026/8xbx_38232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xbx_38232/07_2026/8xbx_38232.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbx_38232/07_2026/8xbx_38232.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xbx_38232/07_2026/8xbx_38232.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbx_38232/07_2026/8xbx_38232.map" } resolution = 4.36 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 38 5.49 5 S 33 5.16 5 C 3543 2.51 5 N 1047 2.21 5 O 1212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5873 Number of models: 1 Model: "" Number of chains: 5 Chain: "I" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 389 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "J" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 390 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "K" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Chain: "L" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Chain: "M" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Time building chain proxies: 1.32, per 1000 atoms: 0.22 Number of scatterers: 5873 At special positions: 0 Unit cell: (109.18, 109.18, 85.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 38 15.00 O 1212 8.00 N 1047 7.00 C 3543 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 223.1 milliseconds 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1200 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 3 sheets defined 47.1% alpha, 20.8% beta 19 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'K' and resid 106 through 113 Processing helix chain 'K' and resid 132 through 144 removed outlier: 3.675A pdb=" N VAL K 142 " --> pdb=" O HIS K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 146 No H-bonds generated for 'chain 'K' and resid 145 through 146' Processing helix chain 'K' and resid 147 through 151 Processing helix chain 'K' and resid 167 through 178 Processing helix chain 'K' and resid 181 through 188 Processing helix chain 'K' and resid 196 through 214 removed outlier: 3.933A pdb=" N LEU K 204 " --> pdb=" O GLN K 200 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR K 205 " --> pdb=" O THR K 201 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN K 206 " --> pdb=" O GLN K 202 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA K 209 " --> pdb=" O TYR K 205 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL K 212 " --> pdb=" O SER K 208 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU K 213 " --> pdb=" O ALA K 209 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER K 214 " --> pdb=" O MET K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 231 removed outlier: 3.532A pdb=" N ARG K 229 " --> pdb=" O THR K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 260 Processing helix chain 'K' and resid 291 through 296 removed outlier: 3.879A pdb=" N ALA K 295 " --> pdb=" O ILE K 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 113 Processing helix chain 'L' and resid 132 through 144 removed outlier: 3.675A pdb=" N VAL L 142 " --> pdb=" O HIS L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 146 No H-bonds generated for 'chain 'L' and resid 145 through 146' Processing helix chain 'L' and resid 147 through 151 Processing helix chain 'L' and resid 167 through 178 Processing helix chain 'L' and resid 181 through 188 Processing helix chain 'L' and resid 196 through 214 removed outlier: 3.933A pdb=" N LEU L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR L 205 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN L 206 " --> pdb=" O GLN L 202 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA L 209 " --> pdb=" O TYR L 205 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL L 212 " --> pdb=" O SER L 208 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU L 213 " --> pdb=" O ALA L 209 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER L 214 " --> pdb=" O MET L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 231 removed outlier: 3.532A pdb=" N ARG L 229 " --> pdb=" O THR L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 260 Processing helix chain 'L' and resid 291 through 296 removed outlier: 3.879A pdb=" N ALA L 295 " --> pdb=" O ILE L 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 113 Processing helix chain 'M' and resid 132 through 144 removed outlier: 3.675A pdb=" N VAL M 142 " --> pdb=" O HIS M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 146 No H-bonds generated for 'chain 'M' and resid 145 through 146' Processing helix chain 'M' and resid 147 through 151 Processing helix chain 'M' and resid 167 through 178 Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 196 through 214 removed outlier: 3.933A pdb=" N LEU M 204 " --> pdb=" O GLN M 200 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR M 205 " --> pdb=" O THR M 201 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA M 209 " --> pdb=" O TYR M 205 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL M 212 " --> pdb=" O SER M 208 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU M 213 " --> pdb=" O ALA M 209 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER M 214 " --> pdb=" O MET M 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 231 removed outlier: 3.533A pdb=" N ARG M 229 " --> pdb=" O THR M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 260 Processing helix chain 'M' and resid 291 through 296 removed outlier: 3.879A pdb=" N ALA M 295 " --> pdb=" O ILE M 291 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 189 through 193 removed outlier: 5.370A pdb=" N LYS K 156 " --> pdb=" O TYR K 216 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU K 218 " --> pdb=" O LYS K 156 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA K 217 " --> pdb=" O ALA K 262 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL K 264 " --> pdb=" O ALA K 217 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU K 219 " --> pdb=" O VAL K 264 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N THR K 266 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL K 221 " --> pdb=" O THR K 266 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N GLN K 268 " --> pdb=" O VAL K 221 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE K 265 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET K 125 " --> pdb=" O ILE K 265 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN K 267 " --> pdb=" O MET K 125 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY K 127 " --> pdb=" O ASN K 267 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE K 122 " --> pdb=" O THR K 298 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N LEU K 300 " --> pdb=" O ILE K 122 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU K 124 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU K 302 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE K 126 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N LYS K 304 " --> pdb=" O PHE K 126 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG K 299 " --> pdb=" O TYR K 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 189 through 193 removed outlier: 5.370A pdb=" N LYS L 156 " --> pdb=" O TYR L 216 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU L 218 " --> pdb=" O LYS L 156 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA L 217 " --> pdb=" O ALA L 262 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL L 264 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU L 219 " --> pdb=" O VAL L 264 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N THR L 266 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL L 221 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N GLN L 268 " --> pdb=" O VAL L 221 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE L 265 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET L 125 " --> pdb=" O ILE L 265 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN L 267 " --> pdb=" O MET L 125 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY L 127 " --> pdb=" O ASN L 267 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE L 122 " --> pdb=" O THR L 298 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N LEU L 300 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU L 124 " --> pdb=" O LEU L 300 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU L 302 " --> pdb=" O GLU L 124 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE L 126 " --> pdb=" O LEU L 302 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N LYS L 304 " --> pdb=" O PHE L 126 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG L 299 " --> pdb=" O TYR L 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 189 through 193 removed outlier: 5.370A pdb=" N LYS M 156 " --> pdb=" O TYR M 216 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU M 218 " --> pdb=" O LYS M 156 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA M 217 " --> pdb=" O ALA M 262 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL M 264 " --> pdb=" O ALA M 217 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU M 219 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N THR M 266 " --> pdb=" O LEU M 219 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL M 221 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N GLN M 268 " --> pdb=" O VAL M 221 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE M 265 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET M 125 " --> pdb=" O ILE M 265 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN M 267 " --> pdb=" O MET M 125 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY M 127 " --> pdb=" O ASN M 267 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE M 122 " --> pdb=" O THR M 298 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N LEU M 300 " --> pdb=" O ILE M 122 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU M 124 " --> pdb=" O LEU M 300 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU M 302 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE M 126 " --> pdb=" O LEU M 302 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N LYS M 304 " --> pdb=" O PHE M 126 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG M 299 " --> pdb=" O TYR M 315 " (cutoff:3.500A) 231 hydrogen bonds defined for protein. 675 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1849 1.34 - 1.46: 1254 1.46 - 1.57: 2801 1.57 - 1.69: 74 1.69 - 1.81: 54 Bond restraints: 6032 Sorted by residual: bond pdb=" C1' DC J 16 " pdb=" N1 DC J 16 " ideal model delta sigma weight residual 1.468 1.557 -0.089 1.40e-02 5.10e+03 4.08e+01 bond pdb=" C1' DC J 1 " pdb=" N1 DC J 1 " ideal model delta sigma weight residual 1.468 1.557 -0.089 1.40e-02 5.10e+03 4.00e+01 bond pdb=" C1' DC I 154 " pdb=" N1 DC I 154 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.95e+01 bond pdb=" C1' DC I 155 " pdb=" N1 DC I 155 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.94e+01 bond pdb=" C1' DC I 152 " pdb=" N1 DC I 152 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.94e+01 ... (remaining 6027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 7886 1.60 - 3.20: 267 3.20 - 4.80: 100 4.80 - 6.40: 3 6.40 - 8.00: 42 Bond angle restraints: 8298 Sorted by residual: angle pdb=" O3' DC J 10 " pdb=" P DG J 11 " pdb=" O5' DG J 11 " ideal model delta sigma weight residual 104.00 96.98 7.02 1.50e+00 4.44e-01 2.19e+01 angle pdb=" O3' DG J 2 " pdb=" P DT J 3 " pdb=" O5' DT J 3 " ideal model delta sigma weight residual 104.00 97.02 6.98 1.50e+00 4.44e-01 2.17e+01 angle pdb=" O3' DA I 153 " pdb=" P DC I 154 " pdb=" O5' DC I 154 " ideal model delta sigma weight residual 104.00 97.02 6.98 1.50e+00 4.44e-01 2.17e+01 angle pdb=" O3' DG J 4 " pdb=" P DG J 5 " pdb=" O5' DG J 5 " ideal model delta sigma weight residual 104.00 97.04 6.96 1.50e+00 4.44e-01 2.16e+01 angle pdb=" O3' DC I 151 " pdb=" P DC I 152 " pdb=" O5' DC I 152 " ideal model delta sigma weight residual 104.00 97.04 6.96 1.50e+00 4.44e-01 2.15e+01 ... (remaining 8293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.90: 2999 15.90 - 31.80: 311 31.80 - 47.69: 122 47.69 - 63.59: 79 63.59 - 79.49: 6 Dihedral angle restraints: 3517 sinusoidal: 1633 harmonic: 1884 Sorted by residual: dihedral pdb=" CA VAL L 334 " pdb=" C VAL L 334 " pdb=" N GLY L 335 " pdb=" CA GLY L 335 " ideal model delta harmonic sigma weight residual -180.00 -152.12 -27.88 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA VAL M 334 " pdb=" C VAL M 334 " pdb=" N GLY M 335 " pdb=" CA GLY M 335 " ideal model delta harmonic sigma weight residual -180.00 -152.14 -27.86 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA VAL K 334 " pdb=" C VAL K 334 " pdb=" N GLY K 335 " pdb=" CA GLY K 335 " ideal model delta harmonic sigma weight residual -180.00 -152.16 -27.84 0 5.00e+00 4.00e-02 3.10e+01 ... (remaining 3514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 582 0.030 - 0.060: 221 0.060 - 0.090: 67 0.090 - 0.120: 54 0.120 - 0.150: 26 Chirality restraints: 950 Sorted by residual: chirality pdb=" CA ILE M 311 " pdb=" N ILE M 311 " pdb=" C ILE M 311 " pdb=" CB ILE M 311 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ILE K 311 " pdb=" N ILE K 311 " pdb=" C ILE K 311 " pdb=" CB ILE K 311 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CA ILE L 311 " pdb=" N ILE L 311 " pdb=" C ILE L 311 " pdb=" CB ILE L 311 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 947 not shown) Planarity restraints: 944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE K 126 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C PHE K 126 " -0.030 2.00e-02 2.50e+03 pdb=" O PHE K 126 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY K 127 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE L 126 " -0.008 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C PHE L 126 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE L 126 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY L 127 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE M 126 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C PHE M 126 " -0.030 2.00e-02 2.50e+03 pdb=" O PHE M 126 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY M 127 " 0.010 2.00e-02 2.50e+03 ... (remaining 941 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1277 2.79 - 3.32: 5585 3.32 - 3.84: 10197 3.84 - 4.37: 12539 4.37 - 4.90: 19772 Nonbonded interactions: 49370 Sorted by model distance: nonbonded pdb=" N THR L 103 " pdb=" O GLY L 151 " model vdw 2.260 3.120 nonbonded pdb=" N THR K 103 " pdb=" O GLY K 151 " model vdw 2.260 3.120 nonbonded pdb=" N THR M 103 " pdb=" O GLY M 151 " model vdw 2.261 3.120 nonbonded pdb=" O ARG K 130 " pdb=" NH2 ARG K 310 " model vdw 2.354 3.120 nonbonded pdb=" O ARG M 130 " pdb=" NH2 ARG M 310 " model vdw 2.354 3.120 ... (remaining 49365 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 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.930 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5601 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 : 0.006 0.089 6032 Z= 0.477 Angle : 0.916 8.000 8298 Z= 0.655 Chirality : 0.045 0.150 950 Planarity : 0.006 0.059 944 Dihedral : 18.157 79.490 2317 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.30), residues: 651 helix: 0.12 (0.30), residues: 264 sheet: 0.76 (0.36), residues: 159 loop : -0.86 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG M 299 TYR 0.010 0.002 TYR K 178 PHE 0.009 0.002 PHE L 248 HIS 0.004 0.001 HIS M 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.48 ( 6032) covalent geometry : angle 0.91586 / 0.65 ( 8298) hydrogen bonds : bond 0.12930 / 13.55 ( 280) hydrogen bonds : angle 6.17028 / 8.28 ( 773) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.167 Fit side-chains REVERT: L 210 MET cc_start: 0.2434 (tmm) cc_final: 0.1427 (ppp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0639 time to fit residues: 2.9594 Evaluate side-chains 22 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 30.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 50.0000 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 30.0000 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 30.0000 chunk 27 optimal weight: 3.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 244 HIS ** 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 = 0.4279 r_free = 0.4279 target = 0.087147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.065561 restraints weight = 68709.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.068150 restraints weight = 20929.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.068997 restraints weight = 8927.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.069320 restraints weight = 6251.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.069320 restraints weight = 5608.257| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6032 Z= 0.260 Angle : 0.869 11.192 8298 Z= 0.452 Chirality : 0.056 0.244 950 Planarity : 0.005 0.037 944 Dihedral : 22.251 59.412 1144 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.31), residues: 651 helix: 0.32 (0.30), residues: 282 sheet: 0.44 (0.36), residues: 159 loop : -0.97 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 310 TYR 0.033 0.002 TYR K 216 PHE 0.015 0.002 PHE M 126 HIS 0.006 0.002 HIS K 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.26 ( 6032) covalent geometry : angle 0.86887 / 0.45 ( 8298) hydrogen bonds : bond 0.14271 / 16.20 ( 280) hydrogen bonds : angle 5.24237 / 6.90 ( 773) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.159 Fit side-chains REVERT: K 158 MET cc_start: 0.8792 (mmp) cc_final: 0.8529 (mpp) REVERT: K 210 MET cc_start: 0.5922 (ptm) cc_final: 0.5649 (ptm) REVERT: L 210 MET cc_start: 0.1831 (tmm) cc_final: 0.1602 (ppp) REVERT: L 326 MET cc_start: 0.4523 (tpp) cc_final: 0.4247 (mmt) REVERT: M 210 MET cc_start: 0.1216 (ppp) cc_final: 0.1014 (ppp) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0614 time to fit residues: 2.1061 Evaluate side-chains 21 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 64 optimal weight: 0.0010 chunk 14 optimal weight: 9.9990 chunk 40 optimal weight: 50.0000 chunk 12 optimal weight: 5.9990 chunk 21 optimal weight: 40.0000 chunk 45 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 23 optimal weight: 40.0000 overall best weight: 5.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.068697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.063284 restraints weight = 70531.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.057559 restraints weight = 100768.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.056750 restraints weight = 137897.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.056728 restraints weight = 173536.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.056719 restraints weight = 158001.583| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5455 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6032 Z= 0.174 Angle : 0.651 7.778 8298 Z= 0.346 Chirality : 0.048 0.250 950 Planarity : 0.004 0.028 944 Dihedral : 23.721 77.708 1144 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.19 % Allowed : 2.07 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.31), residues: 651 helix: 0.47 (0.30), residues: 282 sheet: 0.62 (0.36), residues: 162 loop : -1.00 (0.38), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 310 TYR 0.025 0.002 TYR L 232 PHE 0.013 0.001 PHE M 126 HIS 0.004 0.001 HIS M 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 ( 6032) covalent geometry : angle 0.65050 / 0.35 ( 8298) hydrogen bonds : bond 0.05293 / 5.53 ( 280) hydrogen bonds : angle 4.67140 / 6.14 ( 773) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: K 210 MET cc_start: 0.6818 (ptm) cc_final: 0.6417 (ptm) REVERT: L 125 MET cc_start: 0.7484 (mpp) cc_final: 0.7240 (mpp) REVERT: L 326 MET cc_start: 0.3483 (tpp) cc_final: 0.2944 (mmm) outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.0649 time to fit residues: 2.4386 Evaluate side-chains 23 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 30.0000 chunk 48 optimal weight: 40.0000 chunk 22 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 chunk 28 optimal weight: 8.9990 chunk 65 optimal weight: 50.0000 chunk 7 optimal weight: 30.0000 chunk 46 optimal weight: 10.0000 chunk 51 optimal weight: 30.0000 chunk 52 optimal weight: 9.9990 overall best weight: 11.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 114 GLN K 206 GLN ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.079039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.057487 restraints weight = 72438.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.059748 restraints weight = 25968.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.060688 restraints weight = 11260.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.060808 restraints weight = 7421.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.060808 restraints weight = 7046.981| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 6032 Z= 0.370 Angle : 1.066 13.365 8298 Z= 0.546 Chirality : 0.065 0.375 950 Planarity : 0.006 0.058 944 Dihedral : 24.265 80.153 1144 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 38.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.30), residues: 651 helix: -0.49 (0.29), residues: 285 sheet: 0.56 (0.38), residues: 153 loop : -1.38 (0.37), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 170 TYR 0.026 0.003 TYR M 315 PHE 0.022 0.003 PHE M 126 HIS 0.014 0.003 HIS K 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.37 ( 6032) covalent geometry : angle 1.06624 / 0.55 ( 8298) hydrogen bonds : bond 0.21652 / 23.75 ( 280) hydrogen bonds : angle 5.90473 / 7.53 ( 773) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.200 Fit side-chains REVERT: L 210 MET cc_start: 0.2902 (ppp) cc_final: 0.2690 (ppp) REVERT: L 326 MET cc_start: 0.4341 (tpp) cc_final: 0.4134 (mmt) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0588 time to fit residues: 2.1285 Evaluate side-chains 22 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 13 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 66 optimal weight: 0.0040 chunk 36 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 overall best weight: 4.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.064024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.051678 restraints weight = 68953.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 14)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.051677 restraints weight = 74955.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.051677 restraints weight = 74973.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.051677 restraints weight = 74973.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.051677 restraints weight = 74973.613| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5845 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6032 Z= 0.161 Angle : 0.684 8.654 8298 Z= 0.361 Chirality : 0.048 0.261 950 Planarity : 0.004 0.037 944 Dihedral : 24.435 81.946 1144 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.30), residues: 651 helix: -0.30 (0.29), residues: 285 sheet: 0.52 (0.39), residues: 153 loop : -1.28 (0.38), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 310 TYR 0.017 0.002 TYR L 232 PHE 0.011 0.002 PHE M 126 HIS 0.003 0.001 HIS K 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 ( 6032) covalent geometry : angle 0.68363 / 0.36 ( 8298) hydrogen bonds : bond 0.07059 / 7.70 ( 280) hydrogen bonds : angle 4.98780 / 6.45 ( 773) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.151 Fit side-chains REVERT: L 326 MET cc_start: 0.4215 (tpp) cc_final: 0.3814 (mmp) REVERT: M 211 MET cc_start: 0.0478 (ttt) cc_final: 0.0088 (ttt) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0620 time to fit residues: 2.2093 Evaluate side-chains 22 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 40.0000 chunk 29 optimal weight: 40.0000 chunk 6 optimal weight: 40.0000 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 18 optimal weight: 30.0000 chunk 4 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.081809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.060592 restraints weight = 69588.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.062796 restraints weight = 26028.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.063541 restraints weight = 11121.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.064322 restraints weight = 7971.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.064514 restraints weight = 6233.124| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6068 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6032 Z= 0.146 Angle : 0.638 7.916 8298 Z= 0.337 Chirality : 0.046 0.258 950 Planarity : 0.003 0.034 944 Dihedral : 24.206 84.501 1144 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.31), residues: 651 helix: -0.07 (0.29), residues: 285 sheet: 0.53 (0.40), residues: 150 loop : -1.04 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 170 TYR 0.012 0.001 TYR L 232 PHE 0.010 0.002 PHE M 126 HIS 0.006 0.001 HIS K 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 ( 6032) covalent geometry : angle 0.63801 / 0.34 ( 8298) hydrogen bonds : bond 0.07621 / 8.19 ( 280) hydrogen bonds : angle 4.63656 / 6.01 ( 773) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.204 Fit side-chains REVERT: K 251 MET cc_start: 0.4620 (mtm) cc_final: 0.4311 (mmm) REVERT: L 210 MET cc_start: 0.3814 (ppp) cc_final: 0.3519 (ppp) REVERT: L 326 MET cc_start: 0.4322 (tpp) cc_final: 0.4100 (mmp) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0694 time to fit residues: 2.4861 Evaluate side-chains 22 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 50.0000 chunk 65 optimal weight: 40.0000 chunk 50 optimal weight: 0.1980 chunk 10 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 49 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 62 optimal weight: 40.0000 overall best weight: 5.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 244 HIS L 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.062316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.056571 restraints weight = 71538.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.055010 restraints weight = 124087.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.054194 restraints weight = 134577.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.053771 restraints weight = 164142.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.053527 restraints weight = 135789.508| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5335 moved from start: 0.5959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6032 Z= 0.200 Angle : 0.714 8.750 8298 Z= 0.374 Chirality : 0.049 0.261 950 Planarity : 0.004 0.032 944 Dihedral : 24.189 84.564 1144 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 24.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.31), residues: 651 helix: -0.12 (0.29), residues: 285 sheet: 0.39 (0.42), residues: 141 loop : -1.05 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 170 TYR 0.014 0.002 TYR L 232 PHE 0.015 0.002 PHE L 259 HIS 0.006 0.001 HIS K 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.20 ( 6032) covalent geometry : angle 0.71376 / 0.37 ( 8298) hydrogen bonds : bond 0.10721 / 11.81 ( 280) hydrogen bonds : angle 4.83625 / 6.24 ( 773) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.195 Fit side-chains REVERT: K 251 MET cc_start: 0.4628 (mtm) cc_final: 0.4035 (mmp) REVERT: L 125 MET cc_start: 0.8035 (mpp) cc_final: 0.7773 (mpp) REVERT: L 326 MET cc_start: 0.3838 (tpp) cc_final: 0.3313 (mmm) REVERT: M 326 MET cc_start: 0.7950 (tpt) cc_final: 0.7690 (tpp) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0588 time to fit residues: 2.1166 Evaluate side-chains 22 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 53 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 50.0000 chunk 58 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.062745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.050849 restraints weight = 70367.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.050835 restraints weight = 91033.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.050835 restraints weight = 90377.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.050835 restraints weight = 90384.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.050835 restraints weight = 90384.473| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 moved from start: 0.6292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6032 Z= 0.160 Angle : 0.665 8.576 8298 Z= 0.348 Chirality : 0.047 0.259 950 Planarity : 0.003 0.034 944 Dihedral : 24.172 86.548 1144 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.31), residues: 651 helix: -0.13 (0.29), residues: 285 sheet: 0.40 (0.46), residues: 117 loop : -1.27 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 170 TYR 0.013 0.001 TYR L 232 PHE 0.010 0.001 PHE M 126 HIS 0.002 0.001 HIS M 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.16 ( 6032) covalent geometry : angle 0.66491 / 0.35 ( 8298) hydrogen bonds : bond 0.07287 / 7.72 ( 280) hydrogen bonds : angle 4.76351 / 6.23 ( 773) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.195 Fit side-chains REVERT: K 211 MET cc_start: 0.2446 (tpt) cc_final: 0.2240 (tpt) REVERT: K 251 MET cc_start: 0.4751 (mtm) cc_final: 0.4295 (mmp) REVERT: L 210 MET cc_start: 0.3425 (ppp) cc_final: 0.2990 (ppp) REVERT: L 326 MET cc_start: 0.4025 (tpp) cc_final: 0.3632 (tpp) REVERT: M 211 MET cc_start: -0.0080 (ttt) cc_final: -0.0658 (ttt) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0598 time to fit residues: 2.1680 Evaluate side-chains 22 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 25 optimal weight: 30.0000 chunk 40 optimal weight: 20.0000 chunk 48 optimal weight: 40.0000 chunk 59 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 66 optimal weight: 0.0000 chunk 4 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 41 optimal weight: 0.0170 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.1826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.062963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.056572 restraints weight = 70281.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.049938 restraints weight = 120218.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.049938 restraints weight = 128299.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.049938 restraints weight = 128298.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.049938 restraints weight = 128298.574| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 0.6309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6032 Z= 0.126 Angle : 0.630 7.841 8298 Z= 0.331 Chirality : 0.046 0.251 950 Planarity : 0.003 0.027 944 Dihedral : 24.149 87.381 1144 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.31), residues: 651 helix: -0.07 (0.29), residues: 288 sheet: 0.16 (0.40), residues: 156 loop : -0.75 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 229 TYR 0.032 0.001 TYR K 159 PHE 0.015 0.001 PHE K 166 HIS 0.007 0.001 HIS M 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.13 ( 6032) covalent geometry : angle 0.63022 / 0.33 ( 8298) hydrogen bonds : bond 0.06099 / 6.41 ( 280) hydrogen bonds : angle 4.55156 / 5.93 ( 773) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.197 Fit side-chains REVERT: K 211 MET cc_start: 0.2601 (tpt) cc_final: 0.2300 (tpt) REVERT: K 251 MET cc_start: 0.4654 (mtm) cc_final: 0.4079 (mmm) REVERT: L 125 MET cc_start: 0.8507 (mpp) cc_final: 0.8279 (mpp) REVERT: L 210 MET cc_start: 0.4189 (ppp) cc_final: 0.3548 (ppp) REVERT: L 326 MET cc_start: 0.3899 (tpp) cc_final: 0.3478 (tpp) REVERT: M 211 MET cc_start: 0.1274 (ttt) cc_final: 0.0738 (ttt) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0607 time to fit residues: 2.3062 Evaluate side-chains 24 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 44 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 206 GLN M 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.060391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.054438 restraints weight = 74667.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.054438 restraints weight = 172792.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.054438 restraints weight = 165583.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.054438 restraints weight = 165583.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.054438 restraints weight = 165583.442| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5508 moved from start: 0.6866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6032 Z= 0.193 Angle : 0.702 8.777 8298 Z= 0.370 Chirality : 0.049 0.243 950 Planarity : 0.004 0.028 944 Dihedral : 24.195 87.641 1144 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 25.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.31), residues: 651 helix: -0.24 (0.29), residues: 288 sheet: 0.42 (0.40), residues: 150 loop : -0.96 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 170 TYR 0.023 0.002 TYR L 216 PHE 0.010 0.002 PHE M 126 HIS 0.005 0.001 HIS M 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.19 ( 6032) covalent geometry : angle 0.70219 / 0.37 ( 8298) hydrogen bonds : bond 0.11400 / 12.51 ( 280) hydrogen bonds : angle 4.82673 / 6.20 ( 773) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.199 Fit side-chains REVERT: K 211 MET cc_start: 0.2509 (tpt) cc_final: 0.2094 (tpt) REVERT: K 251 MET cc_start: 0.4657 (mtm) cc_final: 0.4151 (mmp) REVERT: L 125 MET cc_start: 0.8344 (mpp) cc_final: 0.8080 (mpp) REVERT: L 326 MET cc_start: 0.3890 (tpp) cc_final: 0.3409 (tpp) REVERT: M 326 MET cc_start: 0.7482 (tpt) cc_final: 0.7240 (tpp) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0511 time to fit residues: 1.9624 Evaluate side-chains 23 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 28 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 15 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 63 optimal weight: 30.0000 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 206 GLN ** M 244 HIS ** 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 = 0.3848 r_free = 0.3848 target = 0.060632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.048810 restraints weight = 76244.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.048810 restraints weight = 81372.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.048810 restraints weight = 81317.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.048810 restraints weight = 81317.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.048810 restraints weight = 81317.849| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5890 moved from start: 0.7318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6032 Z= 0.176 Angle : 0.693 9.099 8298 Z= 0.365 Chirality : 0.047 0.204 950 Planarity : 0.004 0.031 944 Dihedral : 24.206 88.046 1144 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 24.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.31), residues: 651 helix: -0.35 (0.29), residues: 288 sheet: 0.26 (0.40), residues: 150 loop : -0.94 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 170 TYR 0.015 0.002 TYR L 232 PHE 0.011 0.002 PHE M 248 HIS 0.010 0.001 HIS M 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.18 ( 6032) covalent geometry : angle 0.69327 / 0.37 ( 8298) hydrogen bonds : bond 0.08876 / 9.42 ( 280) hydrogen bonds : angle 4.93311 / 6.29 ( 773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1392.04 seconds wall clock time: 24 minutes 44.30 seconds (1484.30 seconds total)