Starting phenix.real_space_refine on Thu Mar 13 05:19:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yh6_39282/03_2025/8yh6_39282.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yh6_39282/03_2025/8yh6_39282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yh6_39282/03_2025/8yh6_39282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yh6_39282/03_2025/8yh6_39282.map" model { file = "/net/cci-nas-00/data/ceres_data/8yh6_39282/03_2025/8yh6_39282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yh6_39282/03_2025/8yh6_39282.cif" } resolution = 3.62 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= 0.005 sd= 1.069 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: 6 Type Number sf(0) Gaussians I 1 10.91 5 S 66 5.16 5 Cl 1 4.86 5 C 5570 2.51 5 N 1464 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8706 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} 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: "R" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2198 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1705 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 209} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'XS0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.32, per 1000 atoms: 0.61 Number of scatterers: 8706 At special positions: 0 Unit cell: (91.02, 123.21, 127.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) I 1 52.95 Cl 1 17.00 S 66 16.00 O 1604 8.00 N 1464 7.00 C 5570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 114 " distance=1.70 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.05 Simple disulfide: pdb=" SG CYS R 83 " - pdb=" SG CYS R 165 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 986.1 milliseconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 37.3% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.637A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.833A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 22 Processing helix chain 'G' and resid 33 through 44 removed outlier: 3.556A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.529A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.928A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'R' and resid 10 through 40 Processing helix chain 'R' and resid 41 through 44 Processing helix chain 'R' and resid 45 through 64 Processing helix chain 'R' and resid 64 through 75 Processing helix chain 'R' and resid 79 through 115 Processing helix chain 'R' and resid 116 through 122 removed outlier: 4.435A pdb=" N ARG R 120 " --> pdb=" O VAL R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 144 Processing helix chain 'R' and resid 145 through 148 Processing helix chain 'R' and resid 150 through 154 Processing helix chain 'R' and resid 166 through 171 removed outlier: 3.574A pdb=" N VAL R 170 " --> pdb=" O ARG R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 179 removed outlier: 3.570A pdb=" N MET R 176 " --> pdb=" O ARG R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 185 Processing helix chain 'R' and resid 185 through 207 Processing helix chain 'R' and resid 225 through 254 Proline residue: R 244 - end of helix Processing helix chain 'R' and resid 259 through 282 removed outlier: 3.824A pdb=" N MET R 275 " --> pdb=" O HIS R 271 " (cutoff:3.500A) Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 285 through 295 Processing helix chain 'A' and resid 6 through 31 removed outlier: 4.118A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 275 through 281 removed outlier: 3.886A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.615A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.994A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.673A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.301A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 5.007A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.517A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.912A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 276 removed outlier: 6.515A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.191A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 128 through 130 removed outlier: 3.636A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.143A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.270A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1170 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 2831 1.36 - 1.55: 5959 1.55 - 1.73: 0 1.73 - 1.92: 99 1.92 - 2.10: 1 Bond restraints: 8890 Sorted by residual: bond pdb=" C SER A 6 " pdb=" O SER A 6 " ideal model delta sigma weight residual 1.234 1.305 -0.071 1.35e-02 5.49e+03 2.77e+01 bond pdb=" C ASP A 200 " pdb=" O ASP A 200 " ideal model delta sigma weight residual 1.236 1.299 -0.063 1.22e-02 6.72e+03 2.67e+01 bond pdb=" C PHE A 307 " pdb=" O PHE A 307 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.19e-02 7.06e+03 2.19e+01 bond pdb=" N VAL R 170 " pdb=" CA VAL R 170 " ideal model delta sigma weight residual 1.459 1.498 -0.039 9.10e-03 1.21e+04 1.87e+01 bond pdb=" CA SER A 6 " pdb=" CB SER A 6 " ideal model delta sigma weight residual 1.528 1.462 0.066 1.61e-02 3.86e+03 1.69e+01 ... (remaining 8885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 10006 1.89 - 3.78: 1844 3.78 - 5.66: 168 5.66 - 7.55: 17 7.55 - 9.44: 6 Bond angle restraints: 12041 Sorted by residual: angle pdb=" N ILE R 248 " pdb=" CA ILE R 248 " pdb=" C ILE R 248 " ideal model delta sigma weight residual 110.42 100.98 9.44 9.60e-01 1.09e+00 9.67e+01 angle pdb=" N LYS A 210 " pdb=" CA LYS A 210 " pdb=" C LYS A 210 " ideal model delta sigma weight residual 112.92 103.60 9.32 1.23e+00 6.61e-01 5.74e+01 angle pdb=" N LEU A 268 " pdb=" CA LEU A 268 " pdb=" C LEU A 268 " ideal model delta sigma weight residual 108.54 100.39 8.15 1.41e+00 5.03e-01 3.34e+01 angle pdb=" C ASP R 255 " pdb=" N GLY R 256 " pdb=" CA GLY R 256 " ideal model delta sigma weight residual 122.27 116.74 5.53 9.90e-01 1.02e+00 3.12e+01 angle pdb=" CA ARG B 52 " pdb=" C ARG B 52 " pdb=" O ARG B 52 " ideal model delta sigma weight residual 121.58 115.15 6.43 1.16e+00 7.43e-01 3.07e+01 ... (remaining 12036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.67: 5132 30.67 - 61.35: 139 61.35 - 92.02: 7 92.02 - 122.70: 0 122.70 - 153.37: 4 Dihedral angle restraints: 5282 sinusoidal: 2077 harmonic: 3205 Sorted by residual: dihedral pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " pdb=" SG CYS B 114 " pdb=" CB CYS B 114 " ideal model delta sinusoidal sigma weight residual 93.00 19.91 73.09 1 1.00e+01 1.00e-02 6.81e+01 dihedral pdb=" CD ARG B 137 " pdb=" NE ARG B 137 " pdb=" CZ ARG B 137 " pdb=" NH1 ARG B 137 " ideal model delta sinusoidal sigma weight residual 0.00 51.93 -51.93 1 1.00e+01 1.00e-02 3.68e+01 dihedral pdb=" CA TYR S 223 " pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CA PRO S 224 " ideal model delta harmonic sigma weight residual 0.00 29.00 -29.00 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 5279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 497 0.051 - 0.103: 497 0.103 - 0.154: 272 0.154 - 0.206: 89 0.206 - 0.257: 22 Chirality restraints: 1377 Sorted by residual: chirality pdb=" CB VAL R 234 " pdb=" CA VAL R 234 " pdb=" CG1 VAL R 234 " pdb=" CG2 VAL R 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB ILE R 98 " pdb=" CA ILE R 98 " pdb=" CG1 ILE R 98 " pdb=" CG2 ILE R 98 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1374 not shown) Planarity restraints: 1501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 XS0 R 801 " 0.173 2.00e-02 2.50e+03 7.77e-02 1.81e+02 pdb=" C11 XS0 R 801 " -0.016 2.00e-02 2.50e+03 pdb=" C13 XS0 R 801 " -0.081 2.00e-02 2.50e+03 pdb=" C14 XS0 R 801 " -0.010 2.00e-02 2.50e+03 pdb=" C16 XS0 R 801 " -0.017 2.00e-02 2.50e+03 pdb=" C18 XS0 R 801 " -0.080 2.00e-02 2.50e+03 pdb=" N10 XS0 R 801 " -0.032 2.00e-02 2.50e+03 pdb=" N12 XS0 R 801 " -0.045 2.00e-02 2.50e+03 pdb=" N15 XS0 R 801 " 0.006 2.00e-02 2.50e+03 pdb=" N17 XS0 R 801 " -0.067 2.00e-02 2.50e+03 pdb=" N20 XS0 R 801 " 0.143 2.00e-02 2.50e+03 pdb="CL19 XS0 R 801 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 137 " -0.856 9.50e-02 1.11e+02 3.84e-01 8.93e+01 pdb=" NE ARG B 137 " 0.051 2.00e-02 2.50e+03 pdb=" CZ ARG B 137 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 137 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 137 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 205 " -0.726 9.50e-02 1.11e+02 3.25e-01 6.45e+01 pdb=" NE ARG A 205 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG A 205 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 205 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 205 " -0.024 2.00e-02 2.50e+03 ... (remaining 1498 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1312 2.76 - 3.31: 8871 3.31 - 3.86: 14990 3.86 - 4.41: 18911 4.41 - 4.96: 31539 Nonbonded interactions: 75623 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" OD1 ASP B 290 " model vdw 2.215 3.040 nonbonded pdb=" O MET G 21 " pdb=" CG1 ILE G 25 " model vdw 2.238 3.440 nonbonded pdb=" O LEU A 249 " pdb=" OG SER A 252 " model vdw 2.255 3.040 nonbonded pdb=" O GLY B 162 " pdb=" OD1 ASP B 186 " model vdw 2.258 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.279 3.040 ... (remaining 75618 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.580 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4927 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 : 0.012 0.071 8890 Z= 0.810 Angle : 1.430 9.438 12041 Z= 1.034 Chirality : 0.092 0.257 1377 Planarity : 0.028 0.384 1501 Dihedral : 14.434 153.370 3202 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.03 % Rotamer: Outliers : 0.94 % Allowed : 6.82 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.37 (0.23), residues: 1086 helix: -0.85 (0.24), residues: 374 sheet: -1.81 (0.30), residues: 239 loop : -1.92 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP S 36 HIS 0.013 0.003 HIS A 188 PHE 0.081 0.006 PHE A 199 TYR 0.039 0.005 TYR R 15 ARG 0.011 0.002 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 289 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 308 LEU cc_start: 0.7028 (mt) cc_final: 0.6653 (mt) REVERT: G 55 PRO cc_start: 0.5700 (Cg_exo) cc_final: 0.5484 (Cg_endo) outliers start: 9 outliers final: 2 residues processed: 294 average time/residue: 0.2333 time to fit residues: 91.5254 Evaluate side-chains 170 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 168 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 119 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 91 HIS ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 79 HIS A 22 ASN A 52 GLN A 213 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.163397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.141084 restraints weight = 25102.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.144131 restraints weight = 14948.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.146846 restraints weight = 10700.870| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5841 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8890 Z= 0.224 Angle : 0.702 14.127 12041 Z= 0.371 Chirality : 0.044 0.169 1377 Planarity : 0.005 0.042 1501 Dihedral : 9.336 131.046 1223 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.83 % Allowed : 16.05 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.29 (0.24), residues: 1086 helix: 0.50 (0.25), residues: 380 sheet: -1.27 (0.30), residues: 276 loop : -1.74 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 128 HIS 0.007 0.001 HIS A 188 PHE 0.012 0.002 PHE A 196 TYR 0.015 0.002 TYR B 105 ARG 0.007 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 CYS cc_start: 0.6253 (OUTLIER) cc_final: 0.5965 (p) REVERT: G 55 PRO cc_start: 0.5701 (Cg_exo) cc_final: 0.5466 (Cg_endo) REVERT: S 93 MET cc_start: 0.6941 (mpp) cc_final: 0.6181 (ptp) REVERT: S 182 ASN cc_start: 0.7219 (m-40) cc_final: 0.6915 (m-40) REVERT: S 218 MET cc_start: 0.3837 (ttp) cc_final: 0.3307 (tmm) REVERT: R 86 MET cc_start: 0.7264 (mmm) cc_final: 0.6945 (mtt) REVERT: R 99 MET cc_start: 0.7611 (mmt) cc_final: 0.7262 (mmp) REVERT: R 184 TRP cc_start: 0.5933 (m100) cc_final: 0.5611 (m100) REVERT: A 22 ASN cc_start: 0.6982 (m110) cc_final: 0.6519 (m110) REVERT: A 26 ASP cc_start: 0.7891 (p0) cc_final: 0.7491 (p0) REVERT: A 247 MET cc_start: 0.6462 (mmm) cc_final: 0.6210 (mmt) REVERT: A 256 ASN cc_start: 0.8378 (m110) cc_final: 0.7759 (m110) REVERT: A 345 LYS cc_start: 0.8494 (mttp) cc_final: 0.8014 (tmtt) outliers start: 27 outliers final: 11 residues processed: 220 average time/residue: 0.2120 time to fit residues: 63.4971 Evaluate side-chains 174 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 83 CYS Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain A residue 276 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.8848 > 50: distance: 44 - 113: 35.413 distance: 47 - 110: 31.295 distance: 58 - 102: 33.201 distance: 78 - 83: 34.444 distance: 83 - 84: 39.596 distance: 84 - 85: 51.745 distance: 84 - 87: 41.033 distance: 85 - 86: 6.641 distance: 85 - 94: 52.819 distance: 87 - 88: 69.832 distance: 90 - 91: 24.183 distance: 91 - 92: 16.132 distance: 91 - 93: 43.442 distance: 94 - 95: 43.202 distance: 95 - 96: 44.019 distance: 95 - 98: 21.141 distance: 96 - 97: 40.819 distance: 96 - 99: 40.532 distance: 101 - 102: 40.363 distance: 105 - 110: 22.482 distance: 107 - 108: 55.157 distance: 107 - 109: 56.397 distance: 110 - 111: 21.927 distance: 111 - 112: 26.928 distance: 111 - 114: 7.389 distance: 112 - 113: 5.785 distance: 112 - 118: 45.694 distance: 114 - 115: 32.803 distance: 115 - 116: 42.263 distance: 115 - 117: 39.131 distance: 118 - 119: 17.596 distance: 119 - 120: 49.846 distance: 119 - 122: 40.908 distance: 120 - 121: 41.728 distance: 120 - 123: 32.080 distance: 123 - 124: 40.413 distance: 124 - 125: 39.977 distance: 125 - 126: 56.466 distance: 125 - 127: 29.415 distance: 127 - 128: 10.143 distance: 129 - 130: 25.829 distance: 129 - 137: 19.453 distance: 131 - 132: 40.415 distance: 132 - 133: 9.030 distance: 132 - 134: 36.787 distance: 133 - 135: 10.197 distance: 135 - 136: 40.767 distance: 137 - 138: 38.415 distance: 138 - 139: 23.343 distance: 138 - 141: 16.333 distance: 141 - 142: 36.871 distance: 142 - 143: 40.645 distance: 142 - 144: 3.811 distance: 145 - 146: 6.365 distance: 146 - 147: 6.534 distance: 146 - 149: 51.463 distance: 147 - 148: 39.571 distance: 147 - 153: 33.038 distance: 150 - 151: 39.407