Starting phenix.real_space_refine on Sat Aug 3 23:31:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7euo_31323/08_2024/7euo_31323.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7euo_31323/08_2024/7euo_31323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7euo_31323/08_2024/7euo_31323.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7euo_31323/08_2024/7euo_31323.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7euo_31323/08_2024/7euo_31323.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7euo_31323/08_2024/7euo_31323.cif" } resolution = 2.9 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= 0.072 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 64 5.16 5 C 5732 2.51 5 N 1511 2.21 5 O 1643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 54": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "R ARG 163": "NH1" <-> "NH2" Residue "R ARG 267": "NH1" <-> "NH2" Residue "R ARG 269": "NH1" <-> "NH2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S ARG 160": "NH1" <-> "NH2" Residue "S GLU 234": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8950 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2323 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 12, 'TRANS': 282} Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Classifications: {'peptide': 3} Modifications used: {'COO': 1} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.75, per 1000 atoms: 0.64 Number of scatterers: 8950 At special positions: 0 Unit cell: (88.4, 124.95, 123.25, 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 64 16.00 O 1643 8.00 N 1511 7.00 C 5732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 3.85 Conformation dependent library (CDL) restraints added in 1.6 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 38.5% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'R' and resid 22 through 53 removed outlier: 3.831A pdb=" N ASP R 26 " --> pdb=" O TYR R 22 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE R 27 " --> pdb=" O LEU R 23 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R 53 " --> pdb=" O TRP R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 77 Processing helix chain 'R' and resid 77 through 88 removed outlier: 4.519A pdb=" N PHE R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY R 88 " --> pdb=" O ARG R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 Processing helix chain 'R' and resid 131 through 136 removed outlier: 3.735A pdb=" N ASN R 135 " --> pdb=" O VAL R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 146 Processing helix chain 'R' and resid 146 through 163 removed outlier: 4.514A pdb=" N TRP R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 186 through 209 Processing helix chain 'R' and resid 210 through 232 Processing helix chain 'R' and resid 237 through 267 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 267 through 274 removed outlier: 3.882A pdb=" N GLN R 273 " --> pdb=" O ARG R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 302 removed outlier: 3.821A pdb=" N ASP R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N CYS R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 305 through 316 Processing helix chain 'A' and resid 8 through 31 removed outlier: 4.010A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.542A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.106A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.602A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.845A 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 328 through 351 Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.711A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.854A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.555A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.768A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 164 through 168 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.187A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.894A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.804A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.942A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.857A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.659A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.709A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.650A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.980A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.980A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG S 98 " --> pdb=" O PHE S 110 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.624A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1266 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: 3.04 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1444 1.32 - 1.44: 2509 1.44 - 1.57: 5095 1.57 - 1.70: 1 1.70 - 1.82: 95 Bond restraints: 9144 Sorted by residual: bond pdb=" CA SER B 281 " pdb=" C SER B 281 " ideal model delta sigma weight residual 1.522 1.474 0.047 1.31e-02 5.83e+03 1.29e+01 bond pdb=" C ILE R 204 " pdb=" O ILE R 204 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.23e-02 6.61e+03 1.29e+01 bond pdb=" CA SER B 281 " pdb=" CB SER B 281 " ideal model delta sigma weight residual 1.533 1.479 0.054 1.60e-02 3.91e+03 1.13e+01 bond pdb=" N ILE R 207 " pdb=" CA ILE R 207 " ideal model delta sigma weight residual 1.459 1.418 0.041 1.25e-02 6.40e+03 1.08e+01 bond pdb=" CA ARG R 201 " pdb=" C ARG R 201 " ideal model delta sigma weight residual 1.524 1.484 0.039 1.26e-02 6.30e+03 9.74e+00 ... (remaining 9139 not shown) Histogram of bond angle deviations from ideal: 98.03 - 105.23: 149 105.23 - 112.43: 4733 112.43 - 119.63: 2896 119.63 - 126.83: 4493 126.83 - 134.04: 124 Bond angle restraints: 12395 Sorted by residual: angle pdb=" N ARG R 201 " pdb=" CA ARG R 201 " pdb=" C ARG R 201 " ideal model delta sigma weight residual 111.14 107.05 4.09 1.08e+00 8.57e-01 1.44e+01 angle pdb=" O ILE R 203 " pdb=" C ILE R 203 " pdb=" N ILE R 204 " ideal model delta sigma weight residual 121.83 118.40 3.43 1.03e+00 9.43e-01 1.11e+01 angle pdb=" N LEU R 78 " pdb=" CA LEU R 78 " pdb=" C LEU R 78 " ideal model delta sigma weight residual 109.81 116.69 -6.88 2.21e+00 2.05e-01 9.68e+00 angle pdb=" CA PRO A 282 " pdb=" N PRO A 282 " pdb=" CD PRO A 282 " ideal model delta sigma weight residual 112.00 107.84 4.16 1.40e+00 5.10e-01 8.83e+00 angle pdb=" C ILE R 207 " pdb=" N ILE R 208 " pdb=" CA ILE R 208 " ideal model delta sigma weight residual 122.35 118.85 3.50 1.18e+00 7.18e-01 8.78e+00 ... (remaining 12390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4983 17.93 - 35.87: 430 35.87 - 53.80: 70 53.80 - 71.74: 11 71.74 - 89.67: 7 Dihedral angle restraints: 5501 sinusoidal: 2219 harmonic: 3282 Sorted by residual: dihedral pdb=" CA GLU B 215 " pdb=" C GLU B 215 " pdb=" N GLY B 216 " pdb=" CA GLY B 216 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual -180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA TYR S 101 " pdb=" C TYR S 101 " pdb=" N TYR S 102 " pdb=" CA TYR S 102 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1346 0.097 - 0.195: 66 0.195 - 0.292: 3 0.292 - 0.389: 2 0.389 - 0.486: 2 Chirality restraints: 1419 Sorted by residual: chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.80 0.49 2.00e-01 2.50e+01 5.91e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.80 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" C10 CLR R 402 " pdb=" C1 CLR R 402 " pdb=" C5 CLR R 402 " pdb=" C9 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.85 -2.49 -0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 1416 not shown) Planarity restraints: 1550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 203 " -0.015 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C ILE R 203 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE R 203 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE R 204 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 280 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" C LYS B 280 " 0.049 2.00e-02 2.50e+03 pdb=" O LYS B 280 " -0.018 2.00e-02 2.50e+03 pdb=" N SER B 281 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 281 " 0.040 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO A 282 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " 0.032 5.00e-02 4.00e+02 ... (remaining 1547 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 706 2.74 - 3.28: 8682 3.28 - 3.82: 13883 3.82 - 4.36: 16034 4.36 - 4.90: 29453 Nonbonded interactions: 68758 Sorted by model distance: nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.198 3.040 nonbonded pdb=" NH1 ARG B 251 " pdb=" OE2 GLU B 260 " model vdw 2.270 3.120 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.274 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.276 3.040 nonbonded pdb=" OD2 ASP R 186 " pdb=" NZ LYS R 188 " model vdw 2.282 3.120 ... (remaining 68753 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 ========== 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.390 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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: 0.020 Load rotamer database and sin/cos tables:15.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 0.090 9144 Z= 0.258 Angle : 0.648 8.155 12395 Z= 0.355 Chirality : 0.051 0.486 1419 Planarity : 0.004 0.059 1550 Dihedral : 13.715 89.671 3374 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.21 (0.25), residues: 1119 helix: 1.83 (0.27), residues: 387 sheet: -0.53 (0.29), residues: 286 loop : -1.65 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 211 HIS 0.013 0.001 HIS S 35 PHE 0.010 0.001 PHE A 189 TYR 0.013 0.001 TYR S 190 ARG 0.003 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8604 (m170) cc_final: 0.8366 (m-70) REVERT: A 193 ASP cc_start: 0.8488 (m-30) cc_final: 0.8254 (m-30) REVERT: A 242 ARG cc_start: 0.7965 (mmt90) cc_final: 0.7757 (mmt90) REVERT: G 58 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8320 (mp0) REVERT: S 160 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7360 (ttm110) REVERT: S 234 GLU cc_start: 0.7925 (pt0) cc_final: 0.7262 (pp20) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 1.1306 time to fit residues: 203.5638 Evaluate side-chains 119 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 0.0770 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 0.1980 overall best weight: 2.6544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS B 268 ASN S 142 GLN S 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9144 Z= 0.368 Angle : 0.639 7.190 12395 Z= 0.338 Chirality : 0.045 0.145 1419 Planarity : 0.004 0.038 1550 Dihedral : 5.884 79.935 1356 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.37 % Allowed : 10.84 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.09 (0.25), residues: 1119 helix: 1.95 (0.26), residues: 388 sheet: -0.46 (0.30), residues: 287 loop : -1.63 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.010 0.001 HIS S 35 PHE 0.016 0.002 PHE B 235 TYR 0.018 0.001 TYR S 190 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 117 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 306 GLN cc_start: 0.7774 (tp40) cc_final: 0.7520 (mm-40) REVERT: A 193 ASP cc_start: 0.8518 (m-30) cc_final: 0.8275 (m-30) REVERT: A 309 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: B 217 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6851 (ptp) REVERT: G 46 LYS cc_start: 0.9162 (mppt) cc_final: 0.8788 (mtmm) REVERT: G 47 GLU cc_start: 0.8314 (mp0) cc_final: 0.8012 (mp0) REVERT: G 58 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8341 (mp0) REVERT: S 160 ARG cc_start: 0.7987 (ttp80) cc_final: 0.7515 (ttm110) REVERT: S 234 GLU cc_start: 0.8042 (pt0) cc_final: 0.7382 (pp20) outliers start: 23 outliers final: 12 residues processed: 126 average time/residue: 1.3455 time to fit residues: 180.7350 Evaluate side-chains 124 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.9933 > 50: distance: 9 - 13: 5.993 distance: 13 - 14: 5.184 distance: 14 - 15: 11.974 distance: 14 - 17: 12.316 distance: 15 - 16: 7.217 distance: 17 - 18: 13.943 distance: 19 - 20: 4.048 distance: 20 - 21: 13.341 distance: 20 - 23: 13.929 distance: 21 - 22: 8.640 distance: 21 - 25: 11.511 distance: 23 - 24: 18.314 distance: 25 - 26: 7.742 distance: 26 - 27: 3.441 distance: 26 - 29: 15.349 distance: 27 - 28: 3.835 distance: 27 - 33: 13.830 distance: 29 - 30: 27.899 distance: 30 - 31: 14.490 distance: 30 - 32: 23.606 distance: 33 - 34: 15.367 distance: 34 - 35: 24.289 distance: 34 - 37: 13.714 distance: 35 - 36: 13.962 distance: 35 - 41: 12.015 distance: 37 - 38: 8.815 distance: 37 - 39: 16.974 distance: 38 - 40: 32.956 distance: 41 - 42: 10.017 distance: 42 - 43: 4.610 distance: 42 - 45: 6.826 distance: 43 - 48: 10.205 distance: 45 - 46: 19.198 distance: 45 - 47: 8.894 distance: 48 - 49: 12.067 distance: 49 - 50: 7.806 distance: 49 - 52: 19.838 distance: 50 - 51: 13.711 distance: 50 - 56: 20.271 distance: 52 - 53: 12.529 distance: 53 - 54: 21.404 distance: 54 - 55: 21.848 distance: 56 - 57: 30.343 distance: 56 - 108: 20.392 distance: 57 - 58: 18.289 distance: 57 - 60: 18.552 distance: 58 - 59: 13.649 distance: 58 - 63: 7.191 distance: 59 - 105: 22.305 distance: 60 - 61: 8.460 distance: 60 - 62: 11.659 distance: 63 - 64: 11.065 distance: 64 - 65: 9.802 distance: 64 - 67: 14.807 distance: 65 - 66: 22.641 distance: 65 - 72: 10.337 distance: 67 - 68: 17.619 distance: 68 - 69: 21.849 distance: 69 - 70: 18.366 distance: 69 - 71: 6.437 distance: 72 - 73: 12.868 distance: 73 - 74: 14.115 distance: 73 - 76: 18.867 distance: 74 - 75: 26.799 distance: 74 - 77: 11.550 distance: 77 - 78: 5.717 distance: 78 - 79: 8.615 distance: 78 - 81: 24.668 distance: 79 - 80: 29.823 distance: 79 - 84: 22.264 distance: 81 - 83: 25.188