Starting phenix.real_space_refine on Tue Jan 14 06:34:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbx_38232/01_2025/8xbx_38232.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbx_38232/01_2025/8xbx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xbx_38232/01_2025/8xbx_38232.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbx_38232/01_2025/8xbx_38232.map" model { file = "/net/cci-nas-00/data/ceres_data/8xbx_38232/01_2025/8xbx_38232.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbx_38232/01_2025/8xbx_38232.cif" } resolution = 4.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 5.36, per 1000 atoms: 0.91 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: 1.76 Conformation dependent library (CDL) restraints added in 833.4 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: 2.11 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: 1.79 Time building geometry restraints manager: 1.71 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 1.490 1.557 -0.067 3.00e-02 1.11e+03 5.05e+00 bond pdb=" C1' DC J 1 " pdb=" N1 DC J 1 " ideal model delta sigma weight residual 1.490 1.557 -0.067 3.00e-02 1.11e+03 4.91e+00 bond pdb=" C1' DC I 154 " pdb=" N1 DC I 154 " ideal model delta sigma weight residual 1.490 1.556 -0.066 3.00e-02 1.11e+03 4.83e+00 bond pdb=" C1' DC I 155 " pdb=" N1 DC I 155 " ideal model delta sigma weight residual 1.490 1.556 -0.066 3.00e-02 1.11e+03 4.83e+00 bond pdb=" C1' DC I 152 " pdb=" N1 DC I 152 " ideal model delta sigma weight residual 1.490 1.556 -0.066 3.00e-02 1.11e+03 4.82e+00 ... (remaining 6027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 7855 1.60 - 3.20: 298 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: 546 0.030 - 0.060: 252 0.060 - 0.090: 91 0.090 - 0.120: 43 0.120 - 0.150: 18 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: 2.050 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: 2.010 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 18.510 Find NCS groups from input model: 0.400 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: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5805 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 : 0.005 0.067 6032 Z= 0.267 Angle : 0.898 8.000 8298 Z= 0.538 Chirality : 0.044 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (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 HIS 0.004 0.001 HIS M 294 PHE 0.009 0.002 PHE L 248 TYR 0.010 0.002 TYR K 178 ARG 0.015 0.002 ARG M 299 *********************** 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 : 0.481 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: 0.2068 time to fit residues: 9.3956 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 : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 34 optimal weight: 0.0370 chunk 27 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 39 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 overall best weight: 2.8464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.087601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.065754 restraints weight = 67110.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.068356 restraints weight = 22921.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.069246 restraints weight = 9844.126| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6032 Z= 0.199 Angle : 0.562 5.854 8298 Z= 0.310 Chirality : 0.041 0.167 950 Planarity : 0.004 0.030 944 Dihedral : 22.089 69.187 1144 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.32), residues: 651 helix: 0.67 (0.31), residues: 282 sheet: 0.84 (0.36), residues: 162 loop : -0.72 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS L 244 PHE 0.011 0.001 PHE M 126 TYR 0.014 0.002 TYR K 178 ARG 0.005 0.001 ARG M 170 *********************** 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 24 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.663 Fit side-chains REVERT: K 210 MET cc_start: 0.5853 (ptm) cc_final: 0.5492 (ptm) REVERT: L 326 MET cc_start: 0.4581 (tpp) cc_final: 0.4279 (mmm) REVERT: M 210 MET cc_start: 0.1510 (ppp) cc_final: 0.1269 (ppp) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1980 time to fit residues: 6.8667 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 : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 24 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 44 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 overall best weight: 5.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 114 GLN K 206 GLN ** M 101 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 = 0.4178 r_free = 0.4178 target = 0.081365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.059684 restraints weight = 71303.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.061627 restraints weight = 26530.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.062982 restraints weight = 12748.273| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 6032 Z= 0.310 Angle : 0.667 7.783 8298 Z= 0.368 Chirality : 0.044 0.146 950 Planarity : 0.004 0.037 944 Dihedral : 23.505 80.797 1144 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.30), residues: 651 helix: 0.21 (0.29), residues: 282 sheet: 1.14 (0.37), residues: 150 loop : -0.83 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS K 244 PHE 0.012 0.002 PHE M 259 TYR 0.024 0.002 TYR M 232 ARG 0.005 0.001 ARG M 170 *********************** 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: 0 poor density : 25 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: L 149 ASP cc_start: 0.8576 (t70) cc_final: 0.8353 (p0) REVERT: L 210 MET cc_start: 0.1287 (ppp) cc_final: 0.1010 (ppp) REVERT: L 326 MET cc_start: 0.4463 (tpp) cc_final: 0.4206 (mmm) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1688 time to fit residues: 6.3123 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 : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.5152 > 50: distance: 51 - 168: 11.415 distance: 54 - 165: 9.645 distance: 65 - 155: 18.755 distance: 68 - 152: 13.188 distance: 97 - 101: 8.133 distance: 101 - 102: 4.237 distance: 101 - 107: 21.506 distance: 102 - 103: 12.983 distance: 102 - 105: 15.684 distance: 103 - 104: 6.094 distance: 103 - 108: 13.799 distance: 105 - 106: 9.947 distance: 106 - 107: 16.278 distance: 108 - 109: 15.066 distance: 109 - 110: 17.759 distance: 109 - 112: 13.701 distance: 110 - 111: 12.029 distance: 110 - 114: 37.259 distance: 112 - 113: 61.515 distance: 114 - 115: 22.201 distance: 115 - 116: 15.284 distance: 115 - 118: 20.074 distance: 116 - 117: 22.253 distance: 116 - 122: 7.260 distance: 118 - 119: 5.991 distance: 119 - 120: 29.867 distance: 119 - 121: 28.892 distance: 122 - 123: 15.420 distance: 122 - 128: 21.992 distance: 123 - 124: 11.820 distance: 123 - 126: 12.835 distance: 124 - 125: 9.672 distance: 124 - 129: 11.492 distance: 126 - 127: 18.846 distance: 127 - 128: 21.595 distance: 129 - 130: 3.966 distance: 130 - 131: 4.303 distance: 130 - 133: 10.597 distance: 131 - 132: 13.323 distance: 131 - 138: 15.193 distance: 133 - 134: 5.191 distance: 134 - 135: 9.726 distance: 135 - 136: 18.065 distance: 135 - 137: 12.374 distance: 138 - 139: 5.813 distance: 139 - 140: 13.918 distance: 139 - 142: 10.857 distance: 140 - 141: 5.210 distance: 143 - 144: 10.000 distance: 144 - 145: 4.546 distance: 144 - 147: 7.361 distance: 145 - 146: 14.004 distance: 145 - 152: 7.226 distance: 147 - 148: 10.826 distance: 148 - 149: 7.534 distance: 149 - 150: 7.524 distance: 149 - 151: 14.981 distance: 152 - 153: 4.759 distance: 153 - 154: 6.510 distance: 153 - 156: 7.061 distance: 154 - 155: 23.472 distance: 154 - 157: 8.179 distance: 157 - 158: 5.812 distance: 158 - 159: 8.301 distance: 158 - 161: 8.557 distance: 159 - 165: 4.773 distance: 161 - 162: 17.455 distance: 162 - 163: 16.111 distance: 163 - 164: 8.202 distance: 165 - 166: 4.770 distance: 166 - 169: 8.443 distance: 167 - 168: 5.988 distance: 170 - 171: 6.718 distance: 171 - 173: 3.360 distance: 173 - 175: 4.004 distance: 174 - 175: 5.628