Starting phenix.real_space_refine on Fri Jul 19 21:18:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfx_37207/07_2024/8kfx_37207.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfx_37207/07_2024/8kfx_37207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfx_37207/07_2024/8kfx_37207.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfx_37207/07_2024/8kfx_37207.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfx_37207/07_2024/8kfx_37207.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfx_37207/07_2024/8kfx_37207.cif" } resolution = 2.96 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= 0.001 sd= 0.024 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 66 5.16 5 C 5762 2.51 5 N 1506 2.21 5 O 1667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 67": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9001 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1812 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2342 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 5, 'TRANS': 282} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'OS9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.60, per 1000 atoms: 0.62 Number of scatterers: 9001 At special positions: 0 Unit cell: (89.44, 121.68, 130, 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 66 16.00 O 1667 8.00 N 1506 7.00 C 5762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.72 Conformation dependent library (CDL) restraints added in 1.3 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 39.4% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.534A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.666A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.962A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.727A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.663A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'R' and resid 31 through 62 Processing helix chain 'R' and resid 68 through 86 Processing helix chain 'R' and resid 87 through 97 Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 137 through 145 removed outlier: 3.749A pdb=" N LYS R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 170 Proline residue: R 167 - end of helix removed outlier: 3.777A pdb=" N VAL R 170 " --> pdb=" O ILE R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 205 removed outlier: 3.537A pdb=" N LYS R 195 " --> pdb=" O THR R 191 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET R 202 " --> pdb=" O THR R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 227 removed outlier: 3.523A pdb=" N ARG R 227 " --> pdb=" O HIS R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 266 Proline residue: R 253 - end of helix Processing helix chain 'R' and resid 271 through 291 Processing helix chain 'R' and resid 291 through 301 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 304 through 317 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.785A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.520A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.800A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.512A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.552A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.339A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.620A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.927A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.704A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.538A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.301A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.632A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 172 through 177 Processing sheet with id=AB1, first strand: chain 'S' and resid 6 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.814A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.843A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1320 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: 2.71 Time building geometry restraints manager: 4.00 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: 2861 1.34 - 1.46: 2235 1.46 - 1.58: 4001 1.58 - 1.70: 1 1.70 - 1.82: 95 Bond restraints: 9193 Sorted by residual: bond pdb=" N PRO S 224 " pdb=" CD PRO S 224 " ideal model delta sigma weight residual 1.473 1.624 -0.151 1.40e-02 5.10e+03 1.17e+02 bond pdb=" N ARG S 67 " pdb=" CA ARG S 67 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.24e-02 6.50e+03 7.06e+00 bond pdb=" N PHE R 290 " pdb=" CA PHE R 290 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.31e-02 5.83e+03 7.05e+00 bond pdb=" N THR R 291 " pdb=" CA THR R 291 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.29e-02 6.01e+03 6.69e+00 bond pdb=" N SER R 289 " pdb=" CA SER R 289 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.18e-02 7.18e+03 5.73e+00 ... (remaining 9188 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.89: 122 105.89 - 112.94: 4988 112.94 - 119.98: 3075 119.98 - 127.02: 4169 127.02 - 134.07: 90 Bond angle restraints: 12444 Sorted by residual: angle pdb=" N THR R 291 " pdb=" CA THR R 291 " pdb=" C THR R 291 " ideal model delta sigma weight residual 112.34 107.46 4.88 1.30e+00 5.92e-01 1.41e+01 angle pdb=" CA GLN A 52 " pdb=" CB GLN A 52 " pdb=" CG GLN A 52 " ideal model delta sigma weight residual 114.10 121.50 -7.40 2.00e+00 2.50e-01 1.37e+01 angle pdb=" C GLU S 222 " pdb=" N TYR S 223 " pdb=" CA TYR S 223 " ideal model delta sigma weight residual 121.80 113.02 8.78 2.44e+00 1.68e-01 1.29e+01 angle pdb=" CA PHE R 290 " pdb=" CB PHE R 290 " pdb=" CG PHE R 290 " ideal model delta sigma weight residual 113.80 117.11 -3.31 1.00e+00 1.00e+00 1.10e+01 angle pdb=" CA LEU R 205 " pdb=" CB LEU R 205 " pdb=" CG LEU R 205 " ideal model delta sigma weight residual 116.30 127.73 -11.43 3.50e+00 8.16e-02 1.07e+01 ... (remaining 12439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4718 17.91 - 35.82: 558 35.82 - 53.73: 162 53.73 - 71.65: 22 71.65 - 89.56: 5 Dihedral angle restraints: 5465 sinusoidal: 2151 harmonic: 3314 Sorted by residual: dihedral pdb=" CA TYR S 223 " pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CA PRO S 224 " ideal model delta harmonic sigma weight residual 180.00 134.90 45.10 0 5.00e+00 4.00e-02 8.14e+01 dihedral pdb=" CA ARG S 179 " pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 159.86 20.14 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 5462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 821 0.028 - 0.057: 354 0.057 - 0.085: 154 0.085 - 0.114: 71 0.114 - 0.142: 14 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CB ILE S 70 " pdb=" CA ILE S 70 " pdb=" CG1 ILE S 70 " pdb=" CG2 ILE S 70 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA ILE S 177 " pdb=" N ILE S 177 " pdb=" C ILE S 177 " pdb=" CB ILE S 177 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA PHE R 41 " pdb=" N PHE R 41 " pdb=" C PHE R 41 " pdb=" CB PHE R 41 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 1411 not shown) Planarity restraints: 1558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " 0.040 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO S 224 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 186 " -0.011 2.00e-02 2.50e+03 1.64e-02 4.71e+00 pdb=" CG PHE R 186 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE R 186 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE R 186 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE R 186 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 186 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE R 186 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 170 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" CG ASP B 170 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP B 170 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP B 170 " -0.012 2.00e-02 2.50e+03 ... (remaining 1555 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 554 2.73 - 3.27: 8901 3.27 - 3.82: 15392 3.82 - 4.36: 18481 4.36 - 4.90: 31911 Nonbonded interactions: 75239 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.189 2.440 nonbonded pdb=" O LEU R 50 " pdb=" OG SER R 54 " model vdw 2.204 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.208 2.440 nonbonded pdb=" ND1 HIS B 54 " pdb=" OG SER B 74 " model vdw 2.252 2.520 nonbonded pdb=" N GLU A 297 " pdb=" OE1 GLU A 297 " model vdw 2.267 2.520 ... (remaining 75234 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.740 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 : 0.004 0.151 9193 Z= 0.253 Angle : 0.613 11.433 12444 Z= 0.329 Chirality : 0.042 0.142 1414 Planarity : 0.004 0.058 1558 Dihedral : 16.545 89.558 3318 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.51 % Allowed : 30.16 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 0.90 (0.25), residues: 1125 helix: 2.18 (0.27), residues: 398 sheet: 0.30 (0.30), residues: 286 loop : -0.64 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 251 HIS 0.005 0.001 HIS S 35 PHE 0.037 0.002 PHE R 186 TYR 0.016 0.001 TYR R 94 ARG 0.013 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 252 time to evaluate : 0.978 Fit side-chains REVERT: A 231 ASP cc_start: 0.7629 (t0) cc_final: 0.7403 (t0) REVERT: A 340 THR cc_start: 0.8656 (m) cc_final: 0.8351 (t) REVERT: B 19 ARG cc_start: 0.7572 (ttp80) cc_final: 0.7279 (mtm110) REVERT: B 61 MET cc_start: 0.8231 (tmm) cc_final: 0.7993 (ppp) REVERT: R 117 PHE cc_start: 0.8151 (t80) cc_final: 0.7919 (t80) REVERT: R 121 MET cc_start: 0.8187 (tpp) cc_final: 0.7617 (mpp) REVERT: R 216 PHE cc_start: 0.8045 (t80) cc_final: 0.7738 (t80) outliers start: 5 outliers final: 4 residues processed: 256 average time/residue: 1.0837 time to fit residues: 296.7339 Evaluate side-chains 246 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 242 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain S residue 130 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 311 ASN B 75 GLN R 203 ASN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9193 Z= 0.412 Angle : 0.600 10.213 12444 Z= 0.319 Chirality : 0.044 0.175 1414 Planarity : 0.004 0.062 1558 Dihedral : 5.715 49.780 1276 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.76 % Allowed : 24.90 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 0.79 (0.25), residues: 1125 helix: 2.08 (0.26), residues: 398 sheet: 0.33 (0.30), residues: 295 loop : -0.80 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 169 HIS 0.005 0.001 HIS S 35 PHE 0.028 0.002 PHE R 290 TYR 0.016 0.002 TYR A 320 ARG 0.006 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 250 time to evaluate : 1.010 Fit side-chains REVERT: A 49 ILE cc_start: 0.6737 (OUTLIER) cc_final: 0.5933 (mp) REVERT: A 186 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6391 (tm-30) REVERT: A 193 ASP cc_start: 0.7760 (m-30) cc_final: 0.7556 (t0) REVERT: A 231 ASP cc_start: 0.7685 (t0) cc_final: 0.7419 (t0) REVERT: A 269 ASN cc_start: 0.8216 (m-40) cc_final: 0.8001 (m110) REVERT: A 310 LEU cc_start: 0.8645 (mt) cc_final: 0.8417 (mp) REVERT: B 22 ARG cc_start: 0.7138 (mtt180) cc_final: 0.6845 (mtp180) REVERT: B 197 ARG cc_start: 0.7279 (mpt-90) cc_final: 0.7030 (mtt-85) REVERT: B 219 ARG cc_start: 0.7960 (mtp85) cc_final: 0.7699 (mtt-85) REVERT: B 234 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8410 (m-80) REVERT: B 258 ASP cc_start: 0.7803 (t0) cc_final: 0.7141 (t0) REVERT: R 37 LEU cc_start: 0.7302 (tp) cc_final: 0.6869 (tm) REVERT: R 41 PHE cc_start: 0.7726 (m-80) cc_final: 0.7247 (m-80) REVERT: R 46 PHE cc_start: 0.7736 (t80) cc_final: 0.7411 (t80) REVERT: R 51 LEU cc_start: 0.8323 (mt) cc_final: 0.8116 (mt) REVERT: R 55 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8066 (tt) REVERT: R 95 LEU cc_start: 0.8524 (mt) cc_final: 0.8289 (mm) REVERT: R 105 MET cc_start: 0.7218 (mmm) cc_final: 0.6871 (tmm) REVERT: R 113 TYR cc_start: 0.8654 (t80) cc_final: 0.8110 (t80) REVERT: S 39 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7956 (tp40) REVERT: S 87 ARG cc_start: 0.7595 (pmm-80) cc_final: 0.7148 (ptt90) REVERT: S 223 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.7816 (t80) outliers start: 47 outliers final: 21 residues processed: 276 average time/residue: 1.0901 time to fit residues: 322.2875 Evaluate side-chains 273 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 247 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.231 > 50: distance: 25 - 46: 37.008 distance: 29 - 57: 35.120 distance: 35 - 65: 28.341 distance: 41 - 46: 34.535 distance: 42 - 72: 37.324 distance: 46 - 47: 39.926 distance: 47 - 48: 38.742 distance: 47 - 50: 68.711 distance: 48 - 49: 55.284 distance: 48 - 57: 39.742 distance: 49 - 78: 64.762 distance: 50 - 51: 41.309 distance: 51 - 53: 39.806 distance: 52 - 54: 40.304 distance: 55 - 56: 56.739 distance: 57 - 58: 4.931 distance: 58 - 59: 5.922 distance: 58 - 61: 57.505 distance: 59 - 60: 31.706 distance: 59 - 65: 43.724 distance: 60 - 86: 40.376 distance: 61 - 62: 40.553 distance: 62 - 63: 57.834 distance: 62 - 64: 55.345 distance: 65 - 66: 45.749 distance: 66 - 67: 17.887 distance: 66 - 69: 40.468 distance: 67 - 68: 19.703 distance: 67 - 72: 40.353 distance: 68 - 96: 13.093 distance: 69 - 70: 43.307 distance: 69 - 71: 68.087 distance: 72 - 73: 33.328 distance: 73 - 74: 25.986 distance: 73 - 76: 25.224 distance: 74 - 75: 39.515 distance: 74 - 78: 21.298 distance: 75 - 102: 17.399 distance: 76 - 77: 41.241 distance: 78 - 79: 34.565 distance: 79 - 80: 48.304 distance: 79 - 82: 44.150 distance: 80 - 81: 57.231 distance: 80 - 86: 40.377 distance: 82 - 83: 66.790 distance: 83 - 84: 40.362 distance: 86 - 87: 40.520 distance: 87 - 90: 40.249 distance: 88 - 96: 56.279 distance: 91 - 92: 23.869 distance: 92 - 94: 22.393 distance: 97 - 100: 57.515 distance: 98 - 99: 40.013 distance: 98 - 102: 52.027 distance: 100 - 101: 45.096 distance: 102 - 103: 9.716 distance: 103 - 104: 31.890 distance: 103 - 106: 39.191 distance: 104 - 105: 30.569 distance: 104 - 110: 28.929 distance: 106 - 107: 21.538 distance: 107 - 108: 52.810 distance: 108 - 109: 45.382 distance: 110 - 111: 39.430 distance: 111 - 112: 40.116 distance: 111 - 114: 39.529 distance: 112 - 113: 40.526 distance: 112 - 120: 40.178 distance: 114 - 115: 40.047 distance: 115 - 116: 59.928 distance: 115 - 117: 39.417 distance: 116 - 118: 42.469 distance: 117 - 119: 39.027 distance: 118 - 119: 40.179 distance: 120 - 121: 48.185 distance: 121 - 122: 25.629 distance: 121 - 124: 14.053 distance: 122 - 123: 21.575 distance: 122 - 128: 34.155 distance: 124 - 125: 41.442 distance: 124 - 126: 30.549 distance: 125 - 127: 69.764