Starting phenix.real_space_refine on Wed Feb 4 10:50:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kwz_62622/02_2026/9kwz_62622.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kwz_62622/02_2026/9kwz_62622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kwz_62622/02_2026/9kwz_62622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kwz_62622/02_2026/9kwz_62622.map" model { file = "/net/cci-nas-00/data/ceres_data/9kwz_62622/02_2026/9kwz_62622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kwz_62622/02_2026/9kwz_62622.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 6314 2.51 5 N 1715 2.21 5 O 1941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10022 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1704 Classifications: {'peptide': 217} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 204} Chain: "B" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1695 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 203} Chain: "E" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1630 Classifications: {'peptide': 216} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 204} Chain: "F" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1629 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 205} Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1710 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "L" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1654 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Time building chain proxies: 2.47, per 1000 atoms: 0.25 Number of scatterers: 10022 At special positions: 0 Unit cell: (165.224, 143.484, 107.613, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1941 8.00 N 1715 7.00 C 6314 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 125 " distance=1.99 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 125 " distance=2.14 Simple disulfide: pdb=" SG CYS E 166 " - pdb=" SG CYS E 220 " distance=2.19 Simple disulfide: pdb=" SG CYS F 52 " - pdb=" SG CYS F 126 " distance=1.94 Simple disulfide: pdb=" SG CYS H 225 " - pdb=" SG CYS L 214 " distance=2.00 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.13 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.08 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 476.0 milliseconds 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2386 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 25 sheets defined 4.0% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.578A pdb=" N ASN A 120 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.508A pdb=" N PHE A 240 " --> pdb=" O PRO A 237 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET A 241 " --> pdb=" O GLU A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 237 through 241' Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'E' and resid 117 through 121 removed outlier: 3.549A pdb=" N ASP E 120 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER E 121 " --> pdb=" O ALA E 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 117 through 121' Processing helix chain 'E' and resid 239 through 243 removed outlier: 3.662A pdb=" N ARG E 243 " --> pdb=" O PRO E 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 238 through 242 removed outlier: 3.963A pdb=" N PHE F 241 " --> pdb=" O ALA F 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.886A pdb=" N ARG H 31 " --> pdb=" O ILE H 28 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 197 through 201 removed outlier: 3.592A pdb=" N THR H 200 " --> pdb=" O SER H 197 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN H 201 " --> pdb=" O LEU H 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 197 through 201' Processing helix chain 'H' and resid 211 through 214 removed outlier: 4.268A pdb=" N THR H 214 " --> pdb=" O PRO H 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 211 through 214' Processing helix chain 'L' and resid 123 through 127 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 removed outlier: 6.041A pdb=" N ILE A 39 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 63 " --> pdb=" O GLN A 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 50 Processing sheet with id=AA3, first strand: chain 'A' and resid 150 through 157 removed outlier: 5.187A pdb=" N ARG A 162 " --> pdb=" O ARG A 154 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS A 156 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLY A 160 " --> pdb=" O HIS A 156 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N GLU A 164 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL A 207 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE A 166 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N THR A 205 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ARG A 168 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL A 203 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 192 " --> pdb=" O THR A 204 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 179 Processing sheet with id=AA5, first strand: chain 'B' and resid 32 through 33 removed outlier: 3.676A pdb=" N HIS B 52 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 109 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AA7, first strand: chain 'B' and resid 150 through 157 removed outlier: 6.373A pdb=" N ILE B 151 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE B 166 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N MET B 153 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU B 164 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY B 155 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE B 201 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS B 190 " --> pdb=" O ALA B 206 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 185 through 186 removed outlier: 4.359A pdb=" N TRP B 178 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 33 through 34 removed outlier: 3.501A pdb=" N HIS E 53 " --> pdb=" O LEU E 34 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 40 through 43 removed outlier: 4.898A pdb=" N VAL E 78 " --> pdb=" O VAL E 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 190 through 191 removed outlier: 3.546A pdb=" N GLU E 203 " --> pdb=" O VAL E 195 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL E 195 " --> pdb=" O GLU E 203 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 190 through 191 removed outlier: 5.327A pdb=" N TYR E 202 " --> pdb=" O GLY E 170 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 186 through 187 removed outlier: 4.189A pdb=" N TRP E 179 " --> pdb=" O ILE E 187 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N VAL F 152 " --> pdb=" O THR E 232 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER E 234 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N VAL F 154 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER E 236 " --> pdb=" O VAL F 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 32 through 33 Processing sheet with id=AB6, first strand: chain 'F' and resid 40 through 41 removed outlier: 3.615A pdb=" N ILE F 40 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS F 142 " --> pdb=" O ILE F 40 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU F 65 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL F 78 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP F 67 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL F 78 " --> pdb=" O VAL F 85 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 128 through 130 Processing sheet with id=AB8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.800A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.675A pdb=" N CYS H 96 " --> pdb=" O TRP H 112 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TRP H 112 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG H 98 " --> pdb=" O ASP H 110 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 129 through 133 removed outlier: 4.254A pdb=" N GLY H 148 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL H 190 " --> pdb=" O HIS H 173 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS H 173 " --> pdb=" O VAL H 190 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 159 through 162 removed outlier: 3.616A pdb=" N THR H 160 " --> pdb=" O ASN H 208 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN H 208 " --> pdb=" O THR H 160 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.905A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.667A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 114 through 115 removed outlier: 3.654A pdb=" N SER L 114 " --> pdb=" O ASN L 137 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN L 137 " --> pdb=" O SER L 114 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU L 175 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER L 174 " --> pdb=" O THR L 164 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 154 through 155 319 hydrogen bonds defined for protein. 765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.58 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.30: 1904 1.30 - 1.46: 3621 1.46 - 1.62: 4603 1.62 - 1.79: 68 1.79 - 1.95: 45 Bond restraints: 10241 Sorted by residual: bond pdb=" ND1 HIS E 114 " pdb=" CE1 HIS E 114 " ideal model delta sigma weight residual 1.321 1.438 -0.117 1.00e-02 1.00e+04 1.36e+02 bond pdb=" CA GLN E 129 " pdb=" C GLN E 129 " ideal model delta sigma weight residual 1.520 1.635 -0.115 1.12e-02 7.97e+03 1.06e+02 bond pdb=" SD MET H 81 " pdb=" CE MET H 81 " ideal model delta sigma weight residual 1.791 1.535 0.256 2.50e-02 1.60e+03 1.05e+02 bond pdb=" ND1 HIS F 163 " pdb=" CE1 HIS F 163 " ideal model delta sigma weight residual 1.321 1.420 -0.099 1.00e-02 1.00e+04 9.72e+01 bond pdb=" CA ARG B 68 " pdb=" C ARG B 68 " ideal model delta sigma weight residual 1.527 1.409 0.118 1.21e-02 6.83e+03 9.47e+01 ... (remaining 10236 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 10303 2.83 - 5.65: 2455 5.65 - 8.48: 910 8.48 - 11.30: 184 11.30 - 14.13: 36 Bond angle restraints: 13888 Sorted by residual: angle pdb=" N LYS B 173 " pdb=" CA LYS B 173 " pdb=" C LYS B 173 " ideal model delta sigma weight residual 109.57 122.15 -12.58 1.23e+00 6.61e-01 1.05e+02 angle pdb=" N GLU A 60 " pdb=" CA GLU A 60 " pdb=" C GLU A 60 " ideal model delta sigma weight residual 113.02 100.84 12.18 1.20e+00 6.94e-01 1.03e+02 angle pdb=" N THR A 36 " pdb=" CA THR A 36 " pdb=" C THR A 36 " ideal model delta sigma weight residual 113.38 100.93 12.45 1.23e+00 6.61e-01 1.02e+02 angle pdb=" N PHE A 67 " pdb=" CA PHE A 67 " pdb=" C PHE A 67 " ideal model delta sigma weight residual 108.34 121.58 -13.24 1.31e+00 5.83e-01 1.02e+02 angle pdb=" CA LYS H 218 " pdb=" C LYS H 218 " pdb=" O LYS H 218 " ideal model delta sigma weight residual 121.33 110.99 10.34 1.08e+00 8.57e-01 9.17e+01 ... (remaining 13883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.06: 5787 19.06 - 38.12: 306 38.12 - 57.18: 47 57.18 - 76.23: 12 76.23 - 95.29: 6 Dihedral angle restraints: 6158 sinusoidal: 2422 harmonic: 3736 Sorted by residual: dihedral pdb=" CA TYR F 127 " pdb=" C TYR F 127 " pdb=" N PHE F 128 " pdb=" CA PHE F 128 " ideal model delta harmonic sigma weight residual 180.00 147.05 32.95 0 5.00e+00 4.00e-02 4.34e+01 dihedral pdb=" CA GLY A 130 " pdb=" C GLY A 130 " pdb=" N ARG A 131 " pdb=" CA ARG A 131 " ideal model delta harmonic sigma weight residual 180.00 149.52 30.48 0 5.00e+00 4.00e-02 3.72e+01 dihedral pdb=" CB CYS F 52 " pdb=" SG CYS F 52 " pdb=" SG CYS F 126 " pdb=" CB CYS F 126 " ideal model delta sinusoidal sigma weight residual 93.00 144.37 -51.37 1 1.00e+01 1.00e-02 3.61e+01 ... (remaining 6155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.307: 1354 0.307 - 0.613: 164 0.613 - 0.920: 14 0.920 - 1.226: 8 1.226 - 1.533: 2 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CG LEU B 200 " pdb=" CB LEU B 200 " pdb=" CD1 LEU B 200 " pdb=" CD2 LEU B 200 " both_signs ideal model delta sigma weight residual False -2.59 -1.06 -1.53 2.00e-01 2.50e+01 5.87e+01 chirality pdb=" CG LEU A 189 " pdb=" CB LEU A 189 " pdb=" CD1 LEU A 189 " pdb=" CD2 LEU A 189 " both_signs ideal model delta sigma weight residual False -2.59 -1.36 -1.23 2.00e-01 2.50e+01 3.78e+01 chirality pdb=" CB ILE H 28 " pdb=" CA ILE H 28 " pdb=" CG1 ILE H 28 " pdb=" CG2 ILE H 28 " both_signs ideal model delta sigma weight residual False 2.64 1.48 1.17 2.00e-01 2.50e+01 3.41e+01 ... (remaining 1539 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 178 " 0.031 2.00e-02 2.50e+03 8.31e-02 1.73e+02 pdb=" CG TRP B 178 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP B 178 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 178 " 0.032 2.00e-02 2.50e+03 pdb=" NE1 TRP B 178 " -0.145 2.00e-02 2.50e+03 pdb=" CE2 TRP B 178 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 178 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 178 " 0.163 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 178 " -0.118 2.00e-02 2.50e+03 pdb=" CH2 TRP B 178 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 163 " -0.010 2.00e-02 2.50e+03 8.19e-02 1.68e+02 pdb=" CG TRP H 163 " 0.111 2.00e-02 2.50e+03 pdb=" CD1 TRP H 163 " -0.136 2.00e-02 2.50e+03 pdb=" CD2 TRP H 163 " 0.075 2.00e-02 2.50e+03 pdb=" NE1 TRP H 163 " -0.060 2.00e-02 2.50e+03 pdb=" CE2 TRP H 163 " 0.077 2.00e-02 2.50e+03 pdb=" CE3 TRP H 163 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 163 " 0.078 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 163 " -0.120 2.00e-02 2.50e+03 pdb=" CH2 TRP H 163 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 66 " 0.009 2.00e-02 2.50e+03 7.31e-02 1.33e+02 pdb=" CG TRP A 66 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 66 " 0.100 2.00e-02 2.50e+03 pdb=" CD2 TRP A 66 " -0.081 2.00e-02 2.50e+03 pdb=" NE1 TRP A 66 " -0.059 2.00e-02 2.50e+03 pdb=" CE2 TRP A 66 " -0.093 2.00e-02 2.50e+03 pdb=" CE3 TRP A 66 " -0.082 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 66 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 66 " 0.032 2.00e-02 2.50e+03 pdb=" CH2 TRP A 66 " 0.114 2.00e-02 2.50e+03 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1596 2.76 - 3.30: 9099 3.30 - 3.83: 15264 3.83 - 4.37: 18394 4.37 - 4.90: 31915 Nonbonded interactions: 76268 Sorted by model distance: nonbonded pdb=" O THR H 174 " pdb=" CD1 PHE H 175 " model vdw 2.226 3.340 nonbonded pdb=" NH2 ARG A 68 " pdb=" O THR A 122 " model vdw 2.289 3.120 nonbonded pdb=" ND1 HIS E 151 " pdb=" OG SER F 234 " model vdw 2.300 3.120 nonbonded pdb=" CD1 LEU E 150 " pdb=" CD1 ILE E 222 " model vdw 2.309 3.880 nonbonded pdb=" CG1 VAL A 64 " pdb=" CE2 PHE A 127 " model vdw 2.315 3.760 ... (remaining 76263 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 30 through 245) selection = chain 'B' } ncs_group { reference = (chain 'E' and (resid 30 through 148 or resid 150 through 152 or resid 154 throu \ gh 157 or resid 159 through 181 or resid 183 through 188 or resid 190 through 20 \ 2 or resid 204 through 212 or resid 214 through 220 or resid 222 through 223 or \ resid 225 through 245)) selection = (chain 'F' and (resid 30 through 148 or resid 150 through 152 or resid 154 throu \ gh 157 or resid 159 through 181 or resid 183 through 188 or resid 190 through 20 \ 2 or resid 204 through 212 or resid 214 through 220 or resid 222 through 223 or \ resid 225 through 245)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.600 Find NCS groups from input model: 0.140 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.038 0.256 10248 Z= 2.368 Angle : 2.952 14.129 13902 Z= 1.891 Chirality : 0.219 1.533 1542 Planarity : 0.024 0.134 1796 Dihedral : 12.372 95.292 3751 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.27 % Allowed : 0.90 % Favored : 98.82 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.21), residues: 1292 helix: -4.93 (0.39), residues: 18 sheet: -1.25 (0.22), residues: 552 loop : -2.71 (0.19), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.090 0.012 ARG E 223 TYR 0.118 0.026 TYR L 173 PHE 0.115 0.026 PHE H 107 TRP 0.163 0.041 TRP B 178 HIS 0.071 0.015 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.03793 (10241) covalent geometry : angle 2.94687 (13888) SS BOND : bond 0.09282 ( 7) SS BOND : angle 6.28573 ( 14) hydrogen bonds : bond 0.16232 ( 310) hydrogen bonds : angle 9.16774 ( 765) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 215 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.4728 (OUTLIER) cc_final: 0.3819 (mmp-170) REVERT: A 202 MET cc_start: 0.5121 (ptt) cc_final: 0.4459 (ptt) REVERT: B 231 GLU cc_start: 0.6842 (tm-30) cc_final: 0.6369 (tm-30) REVERT: F 99 ILE cc_start: 0.6399 (mm) cc_final: 0.6110 (mt) REVERT: H 103 ASP cc_start: 0.7702 (m-30) cc_final: 0.7439 (m-30) REVERT: L 3 GLN cc_start: 0.7871 (pp30) cc_final: 0.7552 (pp30) REVERT: L 4 MET cc_start: 0.8485 (mtp) cc_final: 0.8221 (mtp) outliers start: 3 outliers final: 1 residues processed: 218 average time/residue: 0.1116 time to fit residues: 33.2787 Evaluate side-chains 162 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain E residue 150 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS A 228 GLN B 46 ASN B 58 ASN F 151 HIS ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.183104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.172958 restraints weight = 16375.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.170236 restraints weight = 21148.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 80)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.168923 restraints weight = 23344.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.169197 restraints weight = 22560.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.169548 restraints weight = 18033.159| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10248 Z= 0.166 Angle : 0.709 8.496 13902 Z= 0.366 Chirality : 0.047 0.182 1542 Planarity : 0.006 0.067 1796 Dihedral : 6.314 56.630 1419 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.72 % Allowed : 6.06 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.22), residues: 1292 helix: -4.71 (0.62), residues: 18 sheet: -0.79 (0.22), residues: 553 loop : -2.23 (0.20), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 162 TYR 0.016 0.002 TYR A 171 PHE 0.020 0.003 PHE B 127 TRP 0.032 0.003 TRP F 67 HIS 0.007 0.001 HIS H 209 Details of bonding type rmsd covalent geometry : bond 0.00383 (10241) covalent geometry : angle 0.70789 (13888) SS BOND : bond 0.00553 ( 7) SS BOND : angle 1.30617 ( 14) hydrogen bonds : bond 0.03483 ( 310) hydrogen bonds : angle 7.05445 ( 765) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.5526 (OUTLIER) cc_final: 0.4982 (mmp80) REVERT: A 92 TYR cc_start: 0.3862 (m-80) cc_final: 0.3340 (m-80) REVERT: B 58 ASN cc_start: 0.7392 (m-40) cc_final: 0.7172 (m-40) REVERT: E 167 ARG cc_start: 0.5867 (ptp90) cc_final: 0.5579 (ptm-80) REVERT: H 109 MET cc_start: 0.8260 (mtt) cc_final: 0.7727 (mtt) outliers start: 19 outliers final: 14 residues processed: 191 average time/residue: 0.1145 time to fit residues: 29.9284 Evaluate side-chains 179 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain E residue 52 CYS Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain F residue 168 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 145 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.8891 > 50: distance: 23 - 28: 7.701 distance: 28 - 29: 18.077 distance: 29 - 30: 10.438 distance: 29 - 32: 22.668 distance: 30 - 31: 24.679 distance: 30 - 35: 33.561 distance: 32 - 33: 15.119 distance: 32 - 34: 31.378 distance: 35 - 36: 12.721 distance: 36 - 37: 28.548 distance: 36 - 39: 16.855 distance: 37 - 38: 11.483 distance: 37 - 42: 21.326 distance: 39 - 40: 28.097 distance: 39 - 41: 41.317 distance: 42 - 43: 47.906 distance: 43 - 44: 26.025 distance: 43 - 46: 30.720 distance: 44 - 45: 21.752 distance: 44 - 51: 4.944 distance: 46 - 47: 35.648 distance: 47 - 48: 48.727 distance: 48 - 49: 11.045 distance: 48 - 50: 25.318 distance: 51 - 52: 31.734 distance: 52 - 53: 63.152 distance: 52 - 55: 39.661 distance: 53 - 54: 21.350 distance: 53 - 56: 40.804 distance: 56 - 57: 21.663 distance: 56 - 62: 26.846 distance: 57 - 58: 30.218 distance: 57 - 60: 11.439 distance: 58 - 59: 23.040 distance: 58 - 63: 17.152 distance: 60 - 61: 24.843 distance: 61 - 62: 28.101 distance: 63 - 64: 7.912 distance: 64 - 65: 34.035 distance: 64 - 67: 52.616 distance: 65 - 66: 7.559 distance: 65 - 70: 47.249 distance: 67 - 68: 4.046 distance: 67 - 69: 39.502 distance: 70 - 71: 22.491 distance: 71 - 72: 51.786 distance: 71 - 74: 29.361 distance: 72 - 73: 45.394 distance: 72 - 77: 53.724 distance: 74 - 75: 34.814 distance: 74 - 76: 32.714 distance: 77 - 78: 18.636 distance: 78 - 79: 23.294 distance: 78 - 81: 22.142 distance: 79 - 80: 14.103 distance: 79 - 82: 26.536 distance: 82 - 83: 17.919 distance: 83 - 84: 13.195 distance: 83 - 86: 28.283 distance: 84 - 85: 3.266 distance: 84 - 90: 4.062 distance: 86 - 87: 18.601 distance: 87 - 88: 18.106 distance: 87 - 89: 23.994 distance: 90 - 91: 39.514 distance: 91 - 92: 13.283 distance: 92 - 93: 17.201 distance: 92 - 94: 18.092