Starting phenix.real_space_refine on Sat Aug 3 19:22:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyb_32890/08_2024/7wyb_32890_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyb_32890/08_2024/7wyb_32890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyb_32890/08_2024/7wyb_32890.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyb_32890/08_2024/7wyb_32890.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyb_32890/08_2024/7wyb_32890_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyb_32890/08_2024/7wyb_32890_neut.cif" } resolution = 2.97 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= 0.019 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 5587 2.51 5 N 1476 2.21 5 O 1628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 248": "OE1" <-> "OE2" Residue "R PHE 1027": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 8757 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1812 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Chain: "C" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "R" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2123 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 3, 'TRANS': 258} Chain breaks: 1 Time building chain proxies: 5.03, per 1000 atoms: 0.57 Number of scatterers: 8757 At special positions: 0 Unit cell: (92.4, 122.1, 130.9, 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 1628 8.00 N 1476 7.00 C 5587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 231 " distance=2.04 Simple disulfide: pdb=" SG CYS R1008 " - pdb=" SG CYS R1080 " 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: 3.07 Conformation dependent library (CDL) restraints added in 1.7 seconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 35.3% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'B' and resid 8 through 30 removed outlier: 3.551A pdb=" N ALA B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 207 through 212 removed outlier: 4.407A pdb=" N TRP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE B 212 " --> pdb=" O ARG B 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 207 through 212' Processing helix chain 'B' and resid 213 through 216 removed outlier: 3.736A pdb=" N GLU B 216 " --> pdb=" O HIS B 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 213 through 216' Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.842A pdb=" N ALA B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 removed outlier: 3.777A pdb=" N PHE B 259 " --> pdb=" O ASN B 256 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 260' Processing helix chain 'B' and resid 271 through 279 Processing helix chain 'B' and resid 295 through 309 removed outlier: 3.654A pdb=" N ALA B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 332 through 348 Processing helix chain 'C' and resid 3 through 26 removed outlier: 3.774A pdb=" N ALA C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 33 Processing helix chain 'D' and resid 6 through 24 Processing helix chain 'D' and resid 29 through 43 Processing helix chain 'D' and resid 44 through 48 removed outlier: 3.521A pdb=" N GLU D 47 " --> pdb=" O HIS D 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.957A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.034A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 924 through 929 Processing helix chain 'R' and resid 940 through 956 Processing helix chain 'R' and resid 958 through 970 removed outlier: 3.821A pdb=" N ILE R 962 " --> pdb=" O VAL R 958 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE R 970 " --> pdb=" O THR R 966 " (cutoff:3.500A) Processing helix chain 'R' and resid 971 through 974 removed outlier: 3.656A pdb=" N GLN R 974 " --> pdb=" O ARG R 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 971 through 974' Processing helix chain 'R' and resid 975 through 999 removed outlier: 3.597A pdb=" N ILE R 999 " --> pdb=" O PHE R 995 " (cutoff:3.500A) Processing helix chain 'R' and resid 1007 through 1038 removed outlier: 3.930A pdb=" N PHE R1011 " --> pdb=" O ALA R1007 " (cutoff:3.500A) Processing helix chain 'R' and resid 1047 through 1070 removed outlier: 3.762A pdb=" N PHE R1051 " --> pdb=" O ARG R1047 " (cutoff:3.500A) Proline residue: R1059 - end of helix Processing helix chain 'R' and resid 1088 through 1091 Processing helix chain 'R' and resid 1092 through 1099 removed outlier: 3.658A pdb=" N ALA R1096 " --> pdb=" O PHE R1092 " (cutoff:3.500A) Processing helix chain 'R' and resid 1099 through 1117 removed outlier: 4.131A pdb=" N ILE R1105 " --> pdb=" O MET R1101 " (cutoff:3.500A) Processing helix chain 'R' and resid 1144 through 1154 removed outlier: 3.652A pdb=" N CYS R1152 " --> pdb=" O ILE R1148 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU R1153 " --> pdb=" O ALA R1149 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU R1154 " --> pdb=" O LEU R1150 " (cutoff:3.500A) Processing helix chain 'R' and resid 1155 through 1162 Processing helix chain 'R' and resid 1169 through 1181 removed outlier: 3.801A pdb=" N ALA R1173 " --> pdb=" O THR R1169 " (cutoff:3.500A) Processing helix chain 'R' and resid 1182 through 1193 removed outlier: 4.024A pdb=" N VAL R1193 " --> pdb=" O ILE R1189 " (cutoff:3.500A) Processing helix chain 'R' and resid 1195 through 1206 Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191 removed outlier: 6.355A pdb=" N VAL B 34 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE B 199 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU B 36 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 7.155A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.808A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.284A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153 removed outlier: 3.807A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER C 161 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 191 removed outlier: 6.829A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 277 removed outlier: 3.691A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 6.545A pdb=" N GLY E 16 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.739A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 142 through 144 Processing sheet with id=AB3, first strand: chain 'E' and resid 149 through 150 removed outlier: 3.898A pdb=" N GLU E 248 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU E 180 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU E 189 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR E 192 " --> pdb=" O ASN E 196 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN E 196 " --> pdb=" O TYR E 192 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1104 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: 3.20 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2808 1.35 - 1.47: 2259 1.47 - 1.59: 3778 1.59 - 1.71: 0 1.71 - 1.83: 96 Bond restraints: 8941 Sorted by residual: bond pdb=" N THR E 212 " pdb=" CA THR E 212 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.32e-02 5.74e+03 7.61e+00 bond pdb=" N GLU E 236 " pdb=" CA GLU E 236 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.18e-02 7.18e+03 7.46e+00 bond pdb=" CA ALA C 299 " pdb=" C ALA C 299 " ideal model delta sigma weight residual 1.523 1.479 0.044 1.80e-02 3.09e+03 6.01e+00 bond pdb=" N TYR E 237 " pdb=" CA TYR E 237 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.41e-02 5.03e+03 5.99e+00 bond pdb=" C GLN C 44 " pdb=" N MET C 45 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.31e-02 5.83e+03 5.87e+00 ... (remaining 8936 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.15: 150 106.15 - 113.13: 4805 113.13 - 120.11: 3197 120.11 - 127.09: 3855 127.09 - 134.07: 92 Bond angle restraints: 12099 Sorted by residual: angle pdb=" N SER R1168 " pdb=" CA SER R1168 " pdb=" C SER R1168 " ideal model delta sigma weight residual 113.23 107.67 5.56 1.22e+00 6.72e-01 2.08e+01 angle pdb=" N LYS B 349 " pdb=" CA LYS B 349 " pdb=" C LYS B 349 " ideal model delta sigma weight residual 114.04 108.94 5.10 1.24e+00 6.50e-01 1.69e+01 angle pdb=" C PRO E 14 " pdb=" CA PRO E 14 " pdb=" CB PRO E 14 " ideal model delta sigma weight residual 111.39 116.45 -5.06 1.28e+00 6.10e-01 1.57e+01 angle pdb=" N PHE R 970 " pdb=" CA PHE R 970 " pdb=" C PHE R 970 " ideal model delta sigma weight residual 109.15 114.77 -5.62 1.44e+00 4.82e-01 1.52e+01 angle pdb=" C LEU C 55 " pdb=" CA LEU C 55 " pdb=" CB LEU C 55 " ideal model delta sigma weight residual 109.65 103.09 6.56 1.68e+00 3.54e-01 1.52e+01 ... (remaining 12094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 4853 17.55 - 35.10: 360 35.10 - 52.65: 52 52.65 - 70.20: 3 70.20 - 87.75: 6 Dihedral angle restraints: 5274 sinusoidal: 2047 harmonic: 3227 Sorted by residual: dihedral pdb=" CB CYS E 161 " pdb=" SG CYS E 161 " pdb=" SG CYS E 231 " pdb=" CB CYS E 231 " ideal model delta sinusoidal sigma weight residual 93.00 135.64 -42.64 1 1.00e+01 1.00e-02 2.54e+01 dihedral pdb=" CB CYS R1008 " pdb=" SG CYS R1008 " pdb=" SG CYS R1080 " pdb=" CB CYS R1080 " ideal model delta sinusoidal sigma weight residual -86.00 -47.47 -38.53 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" CA ARG E 193 " pdb=" C ARG E 193 " pdb=" N MET E 194 " pdb=" CA MET E 194 " ideal model delta harmonic sigma weight residual 180.00 160.55 19.45 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 5271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1023 0.051 - 0.102: 282 0.102 - 0.153: 56 0.153 - 0.204: 6 0.204 - 0.255: 2 Chirality restraints: 1369 Sorted by residual: chirality pdb=" CA LEU R 928 " pdb=" N LEU R 928 " pdb=" C LEU R 928 " pdb=" CB LEU R 928 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA GLU B 216 " pdb=" N GLU B 216 " pdb=" C GLU B 216 " pdb=" CB GLU B 216 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ALA C 56 " pdb=" N ALA C 56 " pdb=" C ALA C 56 " pdb=" CB ALA C 56 " both_signs ideal model delta sigma weight residual False 2.48 2.68 -0.20 2.00e-01 2.50e+01 9.81e-01 ... (remaining 1366 not shown) Planarity restraints: 1525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 182 " -0.050 5.00e-02 4.00e+02 7.57e-02 9.18e+00 pdb=" N PRO E 183 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO E 183 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 183 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER E 210 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C SER E 210 " 0.032 2.00e-02 2.50e+03 pdb=" O SER E 210 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY E 211 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 222 " -0.007 2.00e-02 2.50e+03 1.37e-02 3.29e+00 pdb=" CG PHE C 222 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 222 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE C 222 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 222 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE C 222 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 222 " 0.002 2.00e-02 2.50e+03 ... (remaining 1522 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 447 2.72 - 3.27: 8475 3.27 - 3.81: 13324 3.81 - 4.36: 16117 4.36 - 4.90: 28133 Nonbonded interactions: 66496 Sorted by model distance: nonbonded pdb=" O GLY E 211 " pdb=" OG1 THR E 212 " model vdw 2.176 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.258 3.040 nonbonded pdb=" O ALA B 41 " pdb=" OG SER B 44 " model vdw 2.259 3.040 nonbonded pdb=" O GLU R1167 " pdb=" OG SER R1168 " model vdw 2.276 3.040 nonbonded pdb=" O ARG C 314 " pdb=" OG SER C 331 " model vdw 2.293 3.040 ... (remaining 66491 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: 1.820 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.960 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:13.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5858 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 0.053 8941 Z= 0.354 Angle : 0.803 9.493 12099 Z= 0.464 Chirality : 0.049 0.255 1369 Planarity : 0.005 0.076 1525 Dihedral : 12.351 87.746 3188 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.33 (0.25), residues: 1099 helix: 0.32 (0.29), residues: 348 sheet: -0.19 (0.32), residues: 276 loop : -2.27 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 82 HIS 0.008 0.001 HIS R1016 PHE 0.028 0.003 PHE C 222 TYR 0.031 0.002 TYR C 105 ARG 0.006 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.923 Fit side-chains REVERT: B 308 GLU cc_start: 0.6288 (mt-10) cc_final: 0.6083 (mt-10) REVERT: C 101 MET cc_start: 0.5505 (mtt) cc_final: 0.5283 (ttm) REVERT: E 246 LYS cc_start: 0.7146 (ttmm) cc_final: 0.6845 (ttmm) REVERT: R 1180 ASN cc_start: 0.7186 (m-40) cc_final: 0.6938 (m110) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.9848 time to fit residues: 124.8416 Evaluate side-chains 105 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 0.0570 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS B 255 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5837 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8941 Z= 0.240 Angle : 0.635 9.867 12099 Z= 0.338 Chirality : 0.043 0.194 1369 Planarity : 0.004 0.056 1525 Dihedral : 5.248 46.413 1201 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.58 % Allowed : 8.19 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.82 (0.25), residues: 1099 helix: 0.75 (0.29), residues: 348 sheet: 0.12 (0.32), residues: 275 loop : -1.98 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 211 HIS 0.005 0.001 HIS R1016 PHE 0.018 0.002 PHE C 253 TYR 0.021 0.002 TYR C 105 ARG 0.004 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: B 184 ILE cc_start: 0.8066 (mt) cc_final: 0.7856 (mt) REVERT: B 240 MET cc_start: 0.5166 (tmm) cc_final: 0.4902 (pp-130) REVERT: C 239 ASN cc_start: 0.6683 (m-40) cc_final: 0.6252 (t0) REVERT: D 21 MET cc_start: 0.0245 (mtm) cc_final: -0.0240 (mtm) REVERT: E 76 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6767 (mtpp) REVERT: E 246 LYS cc_start: 0.7124 (ttmm) cc_final: 0.6833 (ttmm) REVERT: R 1026 MET cc_start: 0.4546 (mtt) cc_final: 0.4341 (mtt) outliers start: 15 outliers final: 6 residues processed: 115 average time/residue: 1.0941 time to fit residues: 135.6250 Evaluate side-chains 114 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain R residue 1058 MET Chi-restraints excluded: chain R residue 1178 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS B 255 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5876 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8941 Z= 0.299 Angle : 0.648 10.430 12099 Z= 0.345 Chirality : 0.044 0.215 1369 Planarity : 0.004 0.051 1525 Dihedral : 5.262 46.208 1201 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.00 % Allowed : 11.76 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.76 (0.25), residues: 1099 helix: 0.73 (0.29), residues: 354 sheet: 0.08 (0.31), residues: 295 loop : -1.94 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R1143 HIS 0.008 0.001 HIS R1016 PHE 0.020 0.002 PHE C 199 TYR 0.028 0.002 TYR C 105 ARG 0.004 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: B 53 MET cc_start: 0.5522 (OUTLIER) cc_final: 0.5202 (ppp) REVERT: B 309 ASP cc_start: 0.5638 (m-30) cc_final: 0.5383 (m-30) REVERT: C 239 ASN cc_start: 0.6677 (m-40) cc_final: 0.6239 (t0) REVERT: D 21 MET cc_start: 0.0221 (mtm) cc_final: -0.0307 (mtm) REVERT: E 246 LYS cc_start: 0.7095 (ttmm) cc_final: 0.6823 (ttmm) outliers start: 19 outliers final: 10 residues processed: 116 average time/residue: 1.0859 time to fit residues: 135.6126 Evaluate side-chains 119 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain R residue 1058 MET Chi-restraints excluded: chain R residue 1109 ILE Chi-restraints excluded: chain R residue 1178 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 65.3883 > 50: distance: 52 - 64: 29.801 distance: 64 - 65: 6.635 distance: 65 - 66: 27.206 distance: 65 - 68: 40.134 distance: 66 - 67: 20.212 distance: 66 - 72: 40.937 distance: 68 - 69: 20.123 distance: 69 - 70: 12.805 distance: 69 - 71: 11.849 distance: 72 - 73: 21.129 distance: 73 - 74: 37.736 distance: 73 - 76: 26.562 distance: 74 - 75: 23.270 distance: 74 - 83: 19.532 distance: 76 - 77: 9.201 distance: 77 - 78: 8.145 distance: 78 - 79: 4.370 distance: 79 - 80: 5.636 distance: 83 - 84: 13.768 distance: 84 - 85: 3.025 distance: 84 - 87: 15.364 distance: 85 - 86: 8.444 distance: 85 - 91: 18.429 distance: 87 - 88: 8.752 distance: 88 - 89: 9.255 distance: 88 - 90: 6.144 distance: 91 - 92: 14.786 distance: 92 - 93: 6.658 distance: 92 - 95: 3.322 distance: 93 - 94: 4.421 distance: 93 - 99: 9.966 distance: 95 - 96: 3.684 distance: 96 - 97: 4.152 distance: 99 - 100: 11.757 distance: 100 - 101: 20.655 distance: 100 - 103: 18.198 distance: 101 - 102: 16.789 distance: 101 - 106: 39.960 distance: 103 - 104: 10.854 distance: 103 - 105: 13.671 distance: 106 - 107: 47.042 distance: 107 - 108: 42.855 distance: 107 - 110: 49.196 distance: 108 - 109: 19.183 distance: 108 - 118: 52.014 distance: 110 - 111: 26.002 distance: 111 - 112: 13.353 distance: 111 - 113: 13.202 distance: 112 - 114: 4.889 distance: 114 - 116: 5.913 distance: 115 - 116: 5.616 distance: 118 - 119: 36.802 distance: 119 - 120: 12.713 distance: 119 - 122: 23.856 distance: 120 - 121: 7.195 distance: 120 - 129: 24.842 distance: 121 - 151: 26.244 distance: 122 - 123: 12.661 distance: 123 - 124: 8.700 distance: 123 - 125: 9.335 distance: 124 - 126: 8.237 distance: 125 - 127: 7.602 distance: 126 - 128: 7.220 distance: 127 - 128: 6.183 distance: 129 - 130: 52.229 distance: 130 - 131: 23.262 distance: 130 - 133: 65.388 distance: 131 - 132: 12.482 distance: 131 - 137: 36.759 distance: 133 - 134: 39.484 distance: 133 - 135: 40.813 distance: 134 - 136: 13.495 distance: 137 - 138: 24.562 distance: 138 - 139: 22.324 distance: 138 - 141: 28.108 distance: 139 - 140: 13.297 distance: 139 - 151: 19.026 distance: 141 - 142: 9.785 distance: 142 - 143: 6.282 distance: 143 - 145: 7.441 distance: 144 - 146: 8.840 distance: 144 - 147: 4.448 distance: 145 - 146: 6.001 distance: 147 - 149: 6.238 distance: 151 - 152: 20.590 distance: 152 - 153: 30.390 distance: 152 - 155: 13.749 distance: 153 - 154: 14.654 distance: 153 - 157: 9.784 distance: 155 - 156: 22.511