Starting phenix.real_space_refine on Fri Dec 8 20:08:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yae_33710/12_2023/7yae_33710_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yae_33710/12_2023/7yae_33710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yae_33710/12_2023/7yae_33710.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yae_33710/12_2023/7yae_33710.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yae_33710/12_2023/7yae_33710_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yae_33710/12_2023/7yae_33710_updated.pdb" } resolution = 3.37 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= -0.004 sd= 0.083 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 70 5.16 5 C 5779 2.51 5 N 1513 2.21 5 O 1669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S GLU 234": "OE1" <-> "OE2" Residue "E GLU 90": "OE1" <-> "OE2" Residue "E ARG 155": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9031 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1817 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 474 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 4, 'TRANS': 56} 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: "E" Number of atoms: 2219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2219 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 11, 'TRANS': 269} Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 71 Unusual residues: {'THO': 1} Classifications: {'peptide': 7, 'undetermined': 1} Modifications used: {'PEPT-D': 2} Link IDs: {'TRANS': 7} Chain: "E" 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: 5.37, per 1000 atoms: 0.59 Number of scatterers: 9031 At special positions: 0 Unit cell: (88.32, 121.44, 129.72, 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 70 16.00 O 1669 8.00 N 1513 7.00 C 5779 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Simple disulfide: pdb=" SG CYS E 115 " - pdb=" SG CYS E 193 " distance=2.03 Simple disulfide: pdb=" SG CYS D 2 " - pdb=" SG CYS D 7 " distance=2.02 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: 3.56 Conformation dependent library (CDL) restraints added in 1.8 seconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN D 1 " pdb=" CB DTR D 4 " Number of C-beta restraints generated: 2136 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 15 sheets defined 32.0% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 7 through 27 removed outlier: 3.537A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.679A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 286 Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.990A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 removed outlier: 4.381A pdb=" N GLN A 333 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE A 334 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS A 351 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.582A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 30 through 47 removed outlier: 4.814A pdb=" N LYS C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLU C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'E' and resid 43 through 71 Processing helix chain 'E' and resid 77 through 94 removed outlier: 4.026A pdb=" N TYR E 81 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU E 94 " --> pdb=" O GLU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 103 Processing helix chain 'E' and resid 112 through 145 removed outlier: 3.690A pdb=" N PHE E 127 " --> pdb=" O GLY E 123 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE E 130 " --> pdb=" O GLN E 126 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE E 131 " --> pdb=" O PHE E 127 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS E 132 " --> pdb=" O THR E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 175 removed outlier: 3.843A pdb=" N LEU E 175 " --> pdb=" O LEU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 180 No H-bonds generated for 'chain 'E' and resid 177 through 180' Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 218 through 240 removed outlier: 3.931A pdb=" N ILE E 240 " --> pdb=" O LYS E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 250 No H-bonds generated for 'chain 'E' and resid 247 through 250' Processing helix chain 'E' and resid 253 through 281 removed outlier: 3.509A pdb=" N TRP E 269 " --> pdb=" O PHE E 265 " (cutoff:3.500A) Proline residue: E 271 - end of helix Processing helix chain 'E' and resid 288 through 312 removed outlier: 3.851A pdb=" N PHE E 296 " --> pdb=" O GLY E 292 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR E 301 " --> pdb=" O VAL E 297 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR E 302 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER E 305 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N CYS E 306 " --> pdb=" O TYR E 302 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA E 307 " --> pdb=" O ALA E 303 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN E 308 " --> pdb=" O ASN E 304 " (cutoff:3.500A) Proline residue: E 309 - end of helix Processing helix chain 'E' and resid 317 through 321 removed outlier: 3.525A pdb=" N LYS E 320 " --> pdb=" O ASP E 317 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 34 through 38 removed outlier: 3.628A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET A 198 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 187 " --> pdb=" O MET A 198 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 221 through 224 removed outlier: 4.010A pdb=" N ILE A 265 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE A 267 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.174A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.720A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 123 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.657A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 220 through 222 removed outlier: 3.806A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 7.267A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.794A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 327 through 329 removed outlier: 7.166A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.812A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 68 through 73 Processing sheet with id= L, first strand: chain 'S' and resid 92 through 94 Processing sheet with id= M, first strand: chain 'S' and resid 146 through 148 removed outlier: 7.357A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'S' and resid 155 through 160 removed outlier: 3.874A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR S 213 " --> pdb=" O SER S 206 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER S 206 " --> pdb=" O THR S 213 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR S 215 " --> pdb=" O SER S 204 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'S' and resid 226 through 231 removed outlier: 5.976A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 333 hydrogen bonds defined for protein. 906 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: 2.59 Time building geometry restraints manager: 3.84 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: 1455 1.32 - 1.44: 2520 1.44 - 1.57: 5148 1.57 - 1.69: 0 1.69 - 1.82: 102 Bond restraints: 9225 Sorted by residual: bond pdb=" C THO D 8 " pdb=" O THO D 8 " ideal model delta sigma weight residual 1.231 1.432 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" CA PHE D 3 " pdb=" C PHE D 3 " ideal model delta sigma weight residual 1.525 1.415 0.110 2.10e-02 2.27e+03 2.73e+01 bond pdb=" CA ARG E 241 " pdb=" C ARG E 241 " ideal model delta sigma weight residual 1.525 1.476 0.049 1.25e-02 6.40e+03 1.56e+01 bond pdb=" CD2 DTR D 4 " pdb=" CE2 DTR D 4 " ideal model delta sigma weight residual 1.409 1.470 -0.061 1.70e-02 3.46e+03 1.31e+01 bond pdb=" C ASN E 84 " pdb=" O ASN E 84 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.26e-02 6.30e+03 1.30e+01 ... (remaining 9220 not shown) Histogram of bond angle deviations from ideal: 97.78 - 105.22: 135 105.22 - 112.65: 4879 112.65 - 120.09: 3368 120.09 - 127.52: 4028 127.52 - 134.95: 85 Bond angle restraints: 12495 Sorted by residual: angle pdb=" N TYR S 101 " pdb=" CA TYR S 101 " pdb=" C TYR S 101 " ideal model delta sigma weight residual 108.58 121.63 -13.05 1.82e+00 3.02e-01 5.14e+01 angle pdb=" N ILE B 93 " pdb=" CA ILE B 93 " pdb=" C ILE B 93 " ideal model delta sigma weight residual 107.55 114.47 -6.92 9.90e-01 1.02e+00 4.88e+01 angle pdb=" CA THO D 8 " pdb=" C THO D 8 " pdb=" O THO D 8 " ideal model delta sigma weight residual 120.80 109.46 11.34 1.70e+00 3.46e-01 4.45e+01 angle pdb=" N GLU S 234 " pdb=" CA GLU S 234 " pdb=" C GLU S 234 " ideal model delta sigma weight residual 108.73 98.78 9.95 1.63e+00 3.76e-01 3.73e+01 angle pdb=" N PRO S 236 " pdb=" CA PRO S 236 " pdb=" C PRO S 236 " ideal model delta sigma weight residual 112.47 101.04 11.43 2.06e+00 2.36e-01 3.08e+01 ... (remaining 12490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 5009 17.59 - 35.17: 433 35.17 - 52.76: 96 52.76 - 70.35: 19 70.35 - 87.93: 10 Dihedral angle restraints: 5567 sinusoidal: 2250 harmonic: 3317 Sorted by residual: dihedral pdb=" C PHE D 3 " pdb=" N PHE D 3 " pdb=" CA PHE D 3 " pdb=" CB PHE D 3 " ideal model delta harmonic sigma weight residual -122.60 -109.38 -13.22 0 2.50e+00 1.60e-01 2.79e+01 dihedral pdb=" CA LEU E 105 " pdb=" C LEU E 105 " pdb=" N VAL E 106 " pdb=" CA VAL E 106 " ideal model delta harmonic sigma weight residual -180.00 -155.52 -24.48 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA TYR S 95 " pdb=" C TYR S 95 " pdb=" N CYS S 96 " pdb=" CA CYS S 96 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 5564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1241 0.065 - 0.129: 162 0.129 - 0.194: 10 0.194 - 0.259: 6 0.259 - 0.324: 3 Chirality restraints: 1422 Sorted by residual: chirality pdb=" C13 CLR E 401 " pdb=" C12 CLR E 401 " pdb=" C14 CLR E 401 " pdb=" C17 CLR E 401 " both_signs ideal model delta sigma weight residual False -2.93 -2.61 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CB VAL E 242 " pdb=" CA VAL E 242 " pdb=" CG1 VAL E 242 " pdb=" CG2 VAL E 242 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C13 CLR E 402 " pdb=" C12 CLR E 402 " pdb=" C14 CLR E 402 " pdb=" C17 CLR E 402 " both_signs ideal model delta sigma weight residual False -2.93 -2.64 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 1419 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 308 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO E 309 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 309 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 309 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU S 233 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" C LEU S 233 " 0.042 2.00e-02 2.50e+03 pdb=" O LEU S 233 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU S 234 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 303 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C ALA E 303 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA E 303 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN E 304 " -0.014 2.00e-02 2.50e+03 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 901 2.75 - 3.28: 8888 3.28 - 3.82: 14513 3.82 - 4.36: 16453 4.36 - 4.90: 28902 Nonbonded interactions: 69657 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.207 2.440 nonbonded pdb=" OH TYR B 264 " pdb=" O ASP B 298 " model vdw 2.243 2.440 nonbonded pdb=" OE2 GLU A 14 " pdb=" OG1 THR S 57 " model vdw 2.249 2.440 nonbonded pdb=" O ALA E 44 " pdb=" OG1 THR E 47 " model vdw 2.250 2.440 nonbonded pdb=" NE1 TRP E 197 " pdb=" O ALA E 203 " model vdw 2.284 2.520 ... (remaining 69652 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 3.970 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.220 Find NCS groups from input model: 0.230 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 9225 Z= 0.299 Angle : 0.738 13.053 12495 Z= 0.430 Chirality : 0.047 0.324 1422 Planarity : 0.004 0.062 1557 Dihedral : 14.545 87.934 3422 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.92 % Allowed : 1.33 % Favored : 97.76 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.25), residues: 1127 helix: 1.42 (0.29), residues: 366 sheet: -0.07 (0.35), residues: 242 loop : -1.42 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 258 HIS 0.003 0.001 HIS B 225 PHE 0.013 0.001 PHE A 274 TYR 0.016 0.001 TYR B 264 ARG 0.009 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 1.022 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 142 average time/residue: 0.2408 time to fit residues: 46.4014 Evaluate side-chains 100 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 0.983 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0979 time to fit residues: 1.7818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.3980 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 0.0870 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 0.0040 overall best weight: 0.2528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9225 Z= 0.157 Angle : 0.566 9.039 12495 Z= 0.296 Chirality : 0.042 0.221 1422 Planarity : 0.004 0.047 1557 Dihedral : 5.833 54.840 1372 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.02 % Allowed : 7.44 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.25), residues: 1127 helix: 1.66 (0.27), residues: 374 sheet: 0.48 (0.37), residues: 227 loop : -1.40 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.002 0.001 HIS B 225 PHE 0.019 0.001 PHE E 48 TYR 0.013 0.001 TYR E 205 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.084 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 118 average time/residue: 0.2303 time to fit residues: 37.3600 Evaluate side-chains 98 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0925 time to fit residues: 2.7966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 111 optimal weight: 0.1980 chunk 91 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9225 Z= 0.204 Angle : 0.572 10.192 12495 Z= 0.300 Chirality : 0.043 0.251 1422 Planarity : 0.004 0.053 1557 Dihedral : 5.548 48.622 1372 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.33 % Allowed : 10.81 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1127 helix: 1.62 (0.28), residues: 375 sheet: 0.08 (0.35), residues: 239 loop : -1.35 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 47 HIS 0.004 0.001 HIS B 62 PHE 0.032 0.002 PHE S 29 TYR 0.013 0.002 TYR S 173 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.006 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 109 average time/residue: 0.2455 time to fit residues: 36.6157 Evaluate side-chains 99 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0897 time to fit residues: 3.0769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 58.4519 > 50: distance: 39 - 61: 7.983 distance: 44 - 68: 26.029 distance: 48 - 53: 4.692 distance: 49 - 76: 13.354 distance: 53 - 54: 6.460 distance: 54 - 55: 7.097 distance: 54 - 57: 4.388 distance: 55 - 56: 12.787 distance: 55 - 61: 15.254 distance: 56 - 84: 20.974 distance: 57 - 58: 10.999 distance: 58 - 59: 18.178 distance: 58 - 60: 9.985 distance: 61 - 62: 19.052 distance: 62 - 63: 24.699 distance: 62 - 65: 15.271 distance: 63 - 64: 24.721 distance: 63 - 68: 58.452 distance: 64 - 90: 25.718 distance: 65 - 66: 13.714 distance: 65 - 67: 17.340 distance: 68 - 69: 35.472 distance: 69 - 70: 24.739 distance: 69 - 72: 31.045 distance: 70 - 71: 35.219 distance: 70 - 76: 33.803 distance: 71 - 98: 17.890 distance: 72 - 73: 24.382 distance: 72 - 74: 19.253 distance: 73 - 75: 14.328 distance: 76 - 77: 12.951 distance: 77 - 78: 17.068 distance: 77 - 80: 14.162 distance: 78 - 79: 21.455 distance: 78 - 84: 18.339 distance: 79 - 104: 27.047 distance: 80 - 81: 20.119 distance: 80 - 82: 21.531 distance: 81 - 83: 18.524 distance: 84 - 85: 10.211 distance: 85 - 86: 17.840 distance: 85 - 88: 15.316 distance: 86 - 87: 18.294 distance: 86 - 90: 16.155 distance: 87 - 116: 24.542 distance: 88 - 89: 28.508 distance: 90 - 91: 4.750 distance: 91 - 92: 16.296 distance: 91 - 94: 21.660 distance: 92 - 93: 9.425 distance: 92 - 98: 15.701 distance: 93 - 124: 21.920 distance: 94 - 95: 34.656 distance: 95 - 96: 23.662 distance: 95 - 97: 29.694 distance: 98 - 99: 21.074 distance: 99 - 100: 16.007 distance: 99 - 102: 21.479 distance: 100 - 101: 21.529 distance: 100 - 104: 34.274 distance: 101 - 135: 19.767 distance: 102 - 103: 29.380 distance: 104 - 105: 24.736 distance: 105 - 106: 11.608 distance: 105 - 108: 15.599 distance: 106 - 107: 14.951 distance: 106 - 116: 12.304 distance: 107 - 143: 10.609 distance: 108 - 109: 18.658 distance: 109 - 110: 15.970 distance: 109 - 111: 8.395 distance: 110 - 112: 8.005 distance: 111 - 113: 11.590 distance: 112 - 114: 7.811 distance: 113 - 114: 5.020 distance: 114 - 115: 10.498 distance: 116 - 117: 15.501 distance: 117 - 118: 4.543 distance: 117 - 120: 5.429 distance: 118 - 119: 7.977 distance: 118 - 124: 15.760 distance: 119 - 150: 3.006 distance: 120 - 121: 3.520 distance: 121 - 122: 7.778 distance: 121 - 123: 23.724 distance: 124 - 125: 11.464 distance: 125 - 126: 9.435 distance: 125 - 128: 8.254 distance: 126 - 127: 8.419 distance: 126 - 135: 7.639 distance: 127 - 158: 18.722 distance: 128 - 129: 6.301 distance: 129 - 130: 7.071 distance: 129 - 131: 10.151 distance: 130 - 132: 6.751 distance: 131 - 133: 22.642 distance: 132 - 134: 20.324 distance: 133 - 134: 20.915