Starting phenix.real_space_refine on Fri Aug 22 19:11:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eib_31145/08_2025/7eib_31145.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eib_31145/08_2025/7eib_31145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7eib_31145/08_2025/7eib_31145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eib_31145/08_2025/7eib_31145.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eib_31145/08_2025/7eib_31145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eib_31145/08_2025/7eib_31145.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.028 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 37 5.16 5 C 4628 2.51 5 N 1253 2.21 5 O 1286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7204 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2419 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Chain: "D" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 5} Chain: "B" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1880 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2478 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 5, 'GLN:plan1': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 91 Chain: "E" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 1.96, per 1000 atoms: 0.27 Number of scatterers: 7204 At special positions: 0 Unit cell: (91.8, 82.08, 125.28, 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 37 16.00 O 1286 8.00 N 1253 7.00 C 4628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 189 " distance=2.04 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: 0.79 Conformation dependent library (CDL) restraints added in 517.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1762 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 9 sheets defined 48.9% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 30 through 64 removed outlier: 3.592A pdb=" N ASP A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Proline residue: A 41 - end of helix Processing helix chain 'A' and resid 70 through 89 removed outlier: 3.505A pdb=" N TYR A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.829A pdb=" N TRP A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 141 removed outlier: 3.795A pdb=" N ASN A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 149 through 168 removed outlier: 3.670A pdb=" N GLN A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 175 Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.672A pdb=" N PHE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 239 removed outlier: 4.013A pdb=" N THR A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 278 removed outlier: 3.757A pdb=" N VAL A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Proline residue: A 265 - end of helix Processing helix chain 'A' and resid 283 through 302 removed outlier: 3.717A pdb=" N GLN A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.982A pdb=" N SER A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 316 through 325 Processing helix chain 'B' and resid 6 through 33 removed outlier: 3.842A pdb=" N GLN B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 29 " --> pdb=" O LYS B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 57 Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.596A pdb=" N ASN B 216 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP B 217 " --> pdb=" O CYS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 246 removed outlier: 3.903A pdb=" N GLN B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 250 removed outlier: 3.661A pdb=" N ARG B 250 " --> pdb=" O ARG B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 250' Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 298 through 320 removed outlier: 3.893A pdb=" N SER B 319 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 358 Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'E' and resid 12 through 24 removed outlier: 3.562A pdb=" N GLU E 17 " --> pdb=" O ARG E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 180 Processing sheet with id=AA2, first strand: chain 'B' and resid 184 through 191 removed outlier: 6.197A pdb=" N LEU B 34 " --> pdb=" O HIS B 197 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N PHE B 199 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU B 36 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N VAL B 201 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N LEU B 38 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE B 222 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU B 39 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ASP B 226 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE B 221 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE B 257 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE B 223 " --> pdb=" O PHE B 257 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN B 259 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL B 225 " --> pdb=" O ASN B 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 51 Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.571A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.902A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 153 removed outlier: 3.749A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.739A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.917A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.849A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) 404 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: 1.21 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1165 1.31 - 1.44: 2056 1.44 - 1.57: 4097 1.57 - 1.69: 0 1.69 - 1.82: 48 Bond restraints: 7366 Sorted by residual: bond pdb=" CA PRO D 4 " pdb=" C PRO D 4 " ideal model delta sigma weight residual 1.520 1.458 0.062 1.24e-02 6.50e+03 2.48e+01 bond pdb=" N CYS B 332 " pdb=" CA CYS B 332 " ideal model delta sigma weight residual 1.454 1.402 0.052 1.23e-02 6.61e+03 1.78e+01 bond pdb=" C PRO D 8 " pdb=" O PRO D 8 " ideal model delta sigma weight residual 1.238 1.186 0.052 1.36e-02 5.41e+03 1.44e+01 bond pdb=" C PHE D 6 " pdb=" O PHE D 6 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.28e-02 6.10e+03 1.42e+01 bond pdb=" CA SER D 7 " pdb=" CB SER D 7 " ideal model delta sigma weight residual 1.533 1.477 0.056 1.49e-02 4.50e+03 1.40e+01 ... (remaining 7361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 9849 2.64 - 5.29: 154 5.29 - 7.93: 15 7.93 - 10.58: 1 10.58 - 13.22: 2 Bond angle restraints: 10021 Sorted by residual: angle pdb=" C PRO D 3 " pdb=" N PRO D 4 " pdb=" CA PRO D 4 " ideal model delta sigma weight residual 120.14 109.58 10.56 1.06e+00 8.90e-01 9.92e+01 angle pdb=" CA PRO B 295 " pdb=" N PRO B 295 " pdb=" CD PRO B 295 " ideal model delta sigma weight residual 112.00 100.07 11.93 1.40e+00 5.10e-01 7.26e+01 angle pdb=" N VAL B 334 " pdb=" CA VAL B 334 " pdb=" C VAL B 334 " ideal model delta sigma weight residual 110.62 115.36 -4.74 1.02e+00 9.61e-01 2.16e+01 angle pdb=" CA PRO D 8 " pdb=" C PRO D 8 " pdb=" O PRO D 8 " ideal model delta sigma weight residual 120.03 113.31 6.72 1.45e+00 4.76e-01 2.14e+01 angle pdb=" C VAL B 334 " pdb=" CA VAL B 334 " pdb=" CB VAL B 334 " ideal model delta sigma weight residual 112.14 106.19 5.95 1.35e+00 5.49e-01 1.94e+01 ... (remaining 10016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 3991 16.96 - 33.92: 287 33.92 - 50.88: 34 50.88 - 67.84: 15 67.84 - 84.80: 7 Dihedral angle restraints: 4334 sinusoidal: 1628 harmonic: 2706 Sorted by residual: dihedral pdb=" CA ILE A 97 " pdb=" C ILE A 97 " pdb=" N TRP A 98 " pdb=" CA TRP A 98 " ideal model delta harmonic sigma weight residual 180.00 150.12 29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA LEU A 326 " pdb=" C LEU A 326 " pdb=" N TYR A 327 " pdb=" CA TYR A 327 " ideal model delta harmonic sigma weight residual 180.00 150.71 29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA ASN C 295 " pdb=" C ASN C 295 " pdb=" N VAL C 296 " pdb=" CA VAL C 296 " ideal model delta harmonic sigma weight residual -180.00 -152.46 -27.54 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 4331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 930 0.063 - 0.125: 196 0.125 - 0.188: 23 0.188 - 0.251: 2 0.251 - 0.313: 1 Chirality restraints: 1152 Sorted by residual: chirality pdb=" CA PRO D 8 " pdb=" N PRO D 8 " pdb=" C PRO D 8 " pdb=" CB PRO D 8 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA PHE D 9 " pdb=" N PHE D 9 " pdb=" C PHE D 9 " pdb=" CB PHE D 9 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB VAL A 128 " pdb=" CA VAL A 128 " pdb=" CG1 VAL A 128 " pdb=" CG2 VAL A 128 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 1149 not shown) Planarity restraints: 1276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 326 " 0.059 2.00e-02 2.50e+03 1.17e-01 1.36e+02 pdb=" C LEU A 326 " -0.202 2.00e-02 2.50e+03 pdb=" O LEU A 326 " 0.077 2.00e-02 2.50e+03 pdb=" N TYR A 327 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 206 " 0.024 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" C LEU A 206 " -0.081 2.00e-02 2.50e+03 pdb=" O LEU A 206 " 0.030 2.00e-02 2.50e+03 pdb=" N ASN A 207 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 208 " -0.022 2.00e-02 2.50e+03 4.39e-02 1.92e+01 pdb=" C ILE A 208 " 0.076 2.00e-02 2.50e+03 pdb=" O ILE A 208 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU A 209 " -0.026 2.00e-02 2.50e+03 ... (remaining 1273 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 2122 2.82 - 3.34: 7243 3.34 - 3.86: 12557 3.86 - 4.38: 14516 4.38 - 4.90: 24893 Nonbonded interactions: 61331 Sorted by model distance: nonbonded pdb=" OD2 ASP A 134 " pdb=" OH TYR B 358 " model vdw 2.306 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.306 3.040 nonbonded pdb=" NH2 ARG B 208 " pdb=" OD1 ASP B 239 " model vdw 2.309 3.120 nonbonded pdb=" NH1 ARG C 251 " pdb=" OE1 GLU C 260 " model vdw 2.316 3.120 nonbonded pdb=" NH1 ARG A 176 " pdb=" O GLY D 5 " model vdw 2.333 3.120 ... (remaining 61326 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: 0.530 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: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.290 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 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 0.071 7367 Z= 0.286 Angle : 0.856 13.224 10023 Z= 0.530 Chirality : 0.051 0.313 1152 Planarity : 0.010 0.117 1276 Dihedral : 12.654 84.801 2569 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.27 % Allowed : 1.48 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.26), residues: 914 helix: -0.34 (0.22), residues: 412 sheet: 0.23 (0.35), residues: 195 loop : -0.05 (0.38), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.055 0.008 ARG B 205 TYR 0.026 0.006 TYR C 289 PHE 0.026 0.003 PHE C 235 TRP 0.043 0.003 TRP B 211 HIS 0.005 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00537 ( 7366) covalent geometry : angle 0.85511 (10021) SS BOND : bond 0.00449 ( 1) SS BOND : angle 2.31838 ( 2) hydrogen bonds : bond 0.13296 ( 404) hydrogen bonds : angle 6.85076 ( 1170) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 205 time to evaluate : 0.275 Fit side-chains REVERT: A 47 ILE cc_start: 0.8050 (mt) cc_final: 0.7846 (mp) REVERT: A 84 LEU cc_start: 0.8250 (tp) cc_final: 0.8028 (tt) REVERT: A 102 ASN cc_start: 0.7763 (t0) cc_final: 0.7396 (t0) REVERT: A 111 ARG cc_start: 0.7887 (mtt-85) cc_final: 0.7584 (mtt180) REVERT: A 298 ASN cc_start: 0.7450 (t0) cc_final: 0.7175 (t0) REVERT: D 9 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.6943 (m-80) REVERT: B 188 LYS cc_start: 0.8085 (mtmm) cc_final: 0.7786 (mttm) REVERT: B 195 ASN cc_start: 0.7521 (m-40) cc_final: 0.7255 (m110) REVERT: B 252 ILE cc_start: 0.8191 (mt) cc_final: 0.7904 (mm) REVERT: B 253 SER cc_start: 0.8193 (m) cc_final: 0.7800 (t) REVERT: B 300 ARG cc_start: 0.8164 (mtm180) cc_final: 0.7936 (mtm180) REVERT: B 348 ASP cc_start: 0.7714 (t70) cc_final: 0.7180 (t0) REVERT: C 111 TYR cc_start: 0.8262 (m-80) cc_final: 0.7889 (m-80) REVERT: C 153 ASP cc_start: 0.6985 (t70) cc_final: 0.6744 (t70) REVERT: C 186 ASP cc_start: 0.7128 (m-30) cc_final: 0.6879 (m-30) REVERT: C 204 CYS cc_start: 0.7830 (m) cc_final: 0.7624 (m) REVERT: C 212 ASP cc_start: 0.6803 (t0) cc_final: 0.6410 (t70) REVERT: C 239 ASN cc_start: 0.7246 (m-40) cc_final: 0.6715 (m-40) REVERT: C 295 ASN cc_start: 0.6557 (p0) cc_final: 0.6351 (p0) REVERT: C 303 ASP cc_start: 0.6614 (t0) cc_final: 0.6285 (m-30) outliers start: 2 outliers final: 1 residues processed: 207 average time/residue: 0.5661 time to fit residues: 123.6148 Evaluate side-chains 173 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain D residue 9 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 308 ASN B 246 ASN B 259 ASN B 359 ASN C 110 ASN C 119 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.137465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.117880 restraints weight = 9671.032| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.06 r_work: 0.3369 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7367 Z= 0.189 Angle : 0.656 6.965 10023 Z= 0.353 Chirality : 0.046 0.190 1152 Planarity : 0.005 0.046 1276 Dihedral : 6.109 51.672 1006 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.75 % Allowed : 12.10 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.28), residues: 914 helix: 1.34 (0.25), residues: 412 sheet: 0.24 (0.35), residues: 193 loop : 0.37 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 68 TYR 0.021 0.002 TYR A 75 PHE 0.014 0.002 PHE A 173 TRP 0.026 0.003 TRP C 82 HIS 0.006 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 7366) covalent geometry : angle 0.65591 (10021) SS BOND : bond 0.00768 ( 1) SS BOND : angle 2.02289 ( 2) hydrogen bonds : bond 0.04779 ( 404) hydrogen bonds : angle 5.29292 ( 1170) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 111 ARG cc_start: 0.8092 (mtt-85) cc_final: 0.7806 (mtt180) REVERT: A 176 ARG cc_start: 0.8486 (tpp-160) cc_final: 0.8071 (ttt180) REVERT: A 232 ARG cc_start: 0.7373 (ttt-90) cc_final: 0.7037 (ttt180) REVERT: A 298 ASN cc_start: 0.7846 (t0) cc_final: 0.7641 (t160) REVERT: B 188 LYS cc_start: 0.8706 (mtmm) cc_final: 0.8420 (mttm) REVERT: B 252 ILE cc_start: 0.8339 (mt) cc_final: 0.8105 (mm) REVERT: C 105 TYR cc_start: 0.8811 (t80) cc_final: 0.8551 (t80) REVERT: C 111 TYR cc_start: 0.8660 (m-80) cc_final: 0.8268 (m-80) REVERT: C 153 ASP cc_start: 0.7533 (t70) cc_final: 0.7202 (t0) REVERT: C 154 ASP cc_start: 0.7832 (m-30) cc_final: 0.7589 (m-30) REVERT: C 189 SER cc_start: 0.8526 (t) cc_final: 0.8317 (p) REVERT: C 212 ASP cc_start: 0.7599 (t0) cc_final: 0.7152 (t70) REVERT: C 303 ASP cc_start: 0.7382 (t0) cc_final: 0.6904 (m-30) REVERT: C 335 PHE cc_start: 0.7729 (m-10) cc_final: 0.7495 (m-80) outliers start: 13 outliers final: 8 residues processed: 174 average time/residue: 0.5609 time to fit residues: 103.1991 Evaluate side-chains 171 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 163 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 336 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 58 optimal weight: 0.0980 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 ASN B 246 ASN B 259 ASN B 359 ASN C 230 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.137426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.118191 restraints weight = 9603.534| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.05 r_work: 0.3378 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7367 Z= 0.166 Angle : 0.586 6.254 10023 Z= 0.315 Chirality : 0.044 0.167 1152 Planarity : 0.005 0.042 1276 Dihedral : 5.486 38.658 1004 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.15 % Allowed : 14.92 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.28), residues: 914 helix: 1.74 (0.26), residues: 407 sheet: 0.17 (0.38), residues: 167 loop : 0.18 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 202 TYR 0.021 0.002 TYR A 75 PHE 0.013 0.002 PHE A 173 TRP 0.023 0.002 TRP C 169 HIS 0.006 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 7366) covalent geometry : angle 0.58543 (10021) SS BOND : bond 0.00526 ( 1) SS BOND : angle 1.61257 ( 2) hydrogen bonds : bond 0.04255 ( 404) hydrogen bonds : angle 4.99093 ( 1170) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8161 (mt) cc_final: 0.7875 (mm) REVERT: A 111 ARG cc_start: 0.8043 (mtt-85) cc_final: 0.7640 (mtt90) REVERT: A 150 ARG cc_start: 0.8001 (mtp-110) cc_final: 0.7784 (mtm180) REVERT: A 232 ARG cc_start: 0.7399 (ttt-90) cc_final: 0.7042 (ttt180) REVERT: B 188 LYS cc_start: 0.8709 (mtmm) cc_final: 0.8484 (mttm) REVERT: B 297 GLU cc_start: 0.8215 (pt0) cc_final: 0.7823 (pm20) REVERT: C 105 TYR cc_start: 0.8795 (t80) cc_final: 0.8519 (t80) REVERT: C 111 TYR cc_start: 0.8638 (m-80) cc_final: 0.8193 (m-80) REVERT: C 137 ARG cc_start: 0.7853 (ttm110) cc_final: 0.7620 (tpp-160) REVERT: C 153 ASP cc_start: 0.7552 (t70) cc_final: 0.7257 (t70) REVERT: C 191 SER cc_start: 0.8472 (p) cc_final: 0.8263 (t) REVERT: C 212 ASP cc_start: 0.7631 (t0) cc_final: 0.7183 (t70) REVERT: C 303 ASP cc_start: 0.7466 (t0) cc_final: 0.7050 (m-30) outliers start: 16 outliers final: 11 residues processed: 165 average time/residue: 0.6051 time to fit residues: 104.9889 Evaluate side-chains 159 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 53 optimal weight: 20.0000 chunk 18 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 52 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN B 216 ASN B 246 ASN B 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.138092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118756 restraints weight = 9800.332| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.14 r_work: 0.3383 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7367 Z= 0.142 Angle : 0.551 5.973 10023 Z= 0.296 Chirality : 0.043 0.220 1152 Planarity : 0.005 0.062 1276 Dihedral : 5.065 26.793 1004 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.49 % Allowed : 15.32 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.29), residues: 914 helix: 1.97 (0.26), residues: 406 sheet: 0.06 (0.38), residues: 174 loop : 0.20 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 320 TYR 0.019 0.002 TYR A 75 PHE 0.014 0.001 PHE B 189 TRP 0.020 0.002 TRP C 169 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 7366) covalent geometry : angle 0.55111 (10021) SS BOND : bond 0.00278 ( 1) SS BOND : angle 1.35356 ( 2) hydrogen bonds : bond 0.03953 ( 404) hydrogen bonds : angle 4.82247 ( 1170) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8138 (mt) cc_final: 0.7870 (mm) REVERT: A 150 ARG cc_start: 0.7957 (mtp-110) cc_final: 0.7725 (mtm180) REVERT: A 176 ARG cc_start: 0.8498 (tpp-160) cc_final: 0.8139 (ttt90) REVERT: A 232 ARG cc_start: 0.7379 (ttt-90) cc_final: 0.6955 (ttt180) REVERT: B 188 LYS cc_start: 0.8688 (mtmm) cc_final: 0.8362 (mttm) REVERT: B 233 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7334 (tp) REVERT: B 297 GLU cc_start: 0.8247 (pt0) cc_final: 0.7854 (pm20) REVERT: B 348 ASP cc_start: 0.8282 (t0) cc_final: 0.7987 (t70) REVERT: C 105 TYR cc_start: 0.8780 (t80) cc_final: 0.8490 (t80) REVERT: C 111 TYR cc_start: 0.8629 (m-80) cc_final: 0.8201 (m-80) REVERT: C 137 ARG cc_start: 0.7797 (ttm110) cc_final: 0.7574 (tpp-160) REVERT: C 153 ASP cc_start: 0.7622 (t70) cc_final: 0.7344 (t70) REVERT: C 160 SER cc_start: 0.8498 (p) cc_final: 0.8193 (t) REVERT: C 188 MET cc_start: 0.8086 (mmm) cc_final: 0.7835 (mmp) REVERT: C 303 ASP cc_start: 0.7568 (t0) cc_final: 0.7140 (m-30) REVERT: C 327 VAL cc_start: 0.8819 (OUTLIER) cc_final: 0.8471 (t) REVERT: C 334 SER cc_start: 0.8068 (OUTLIER) cc_final: 0.7853 (m) outliers start: 26 outliers final: 11 residues processed: 173 average time/residue: 0.5714 time to fit residues: 104.5349 Evaluate side-chains 165 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 55 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 71 optimal weight: 0.0770 chunk 24 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 89 optimal weight: 0.0010 chunk 78 optimal weight: 2.9990 overall best weight: 0.5346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 298 ASN A 329 GLN B 246 ASN B 259 ASN C 91 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.139578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.120355 restraints weight = 9703.448| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.11 r_work: 0.3384 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7367 Z= 0.134 Angle : 0.541 7.384 10023 Z= 0.290 Chirality : 0.042 0.161 1152 Planarity : 0.005 0.051 1276 Dihedral : 4.782 27.377 1000 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.49 % Allowed : 17.47 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.29), residues: 914 helix: 2.06 (0.26), residues: 406 sheet: -0.19 (0.38), residues: 169 loop : 0.13 (0.36), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 320 TYR 0.018 0.001 TYR A 75 PHE 0.025 0.001 PHE A 43 TRP 0.021 0.002 TRP C 82 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 7366) covalent geometry : angle 0.54109 (10021) SS BOND : bond 0.00267 ( 1) SS BOND : angle 1.19246 ( 2) hydrogen bonds : bond 0.03853 ( 404) hydrogen bonds : angle 4.70887 ( 1170) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.277 Fit side-chains REVERT: A 52 LEU cc_start: 0.7807 (mm) cc_final: 0.7559 (mt) REVERT: A 56 LEU cc_start: 0.8109 (mt) cc_final: 0.7859 (mm) REVERT: A 232 ARG cc_start: 0.7421 (ttt-90) cc_final: 0.6967 (ttt180) REVERT: B 188 LYS cc_start: 0.8600 (mtmm) cc_final: 0.8370 (mttm) REVERT: B 233 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7326 (tp) REVERT: B 297 GLU cc_start: 0.8191 (pt0) cc_final: 0.7801 (pm20) REVERT: C 105 TYR cc_start: 0.8767 (t80) cc_final: 0.8542 (t80) REVERT: C 111 TYR cc_start: 0.8631 (m-80) cc_final: 0.8236 (m-80) REVERT: C 137 ARG cc_start: 0.7778 (ttm110) cc_final: 0.7574 (tpp-160) REVERT: C 153 ASP cc_start: 0.7640 (t70) cc_final: 0.7348 (t70) REVERT: C 160 SER cc_start: 0.8470 (p) cc_final: 0.8208 (t) REVERT: C 188 MET cc_start: 0.8091 (mmm) cc_final: 0.7823 (mmp) REVERT: C 327 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8482 (t) REVERT: C 334 SER cc_start: 0.8066 (OUTLIER) cc_final: 0.7857 (m) outliers start: 26 outliers final: 16 residues processed: 177 average time/residue: 0.5779 time to fit residues: 107.9173 Evaluate side-chains 167 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.4156 > 50: distance: 86 - 165: 17.560 distance: 89 - 162: 20.296 distance: 99 - 152: 24.443 distance: 102 - 149: 7.251 distance: 113 - 117: 12.647 distance: 117 - 118: 8.934 distance: 118 - 119: 8.267 distance: 119 - 120: 14.627 distance: 119 - 121: 19.453 distance: 121 - 122: 9.015 distance: 122 - 123: 36.627 distance: 122 - 125: 48.151 distance: 123 - 124: 40.460 distance: 123 - 129: 40.840 distance: 125 - 126: 27.390 distance: 126 - 127: 16.995 distance: 126 - 128: 22.435 distance: 129 - 130: 22.067 distance: 130 - 131: 3.634 distance: 130 - 133: 30.775 distance: 131 - 132: 31.033 distance: 131 - 136: 8.212 distance: 133 - 134: 28.551 distance: 133 - 135: 28.825 distance: 136 - 137: 22.621 distance: 137 - 138: 15.556 distance: 137 - 140: 15.628 distance: 138 - 139: 13.932 distance: 138 - 143: 23.663 distance: 140 - 141: 49.551 distance: 140 - 142: 24.047 distance: 143 - 144: 9.904 distance: 143 - 239: 20.154 distance: 144 - 145: 3.589 distance: 144 - 147: 7.686 distance: 145 - 146: 35.001 distance: 145 - 149: 16.085 distance: 146 - 236: 26.259 distance: 147 - 148: 21.346 distance: 149 - 150: 23.059 distance: 150 - 151: 10.972 distance: 150 - 153: 16.672 distance: 151 - 152: 11.410 distance: 154 - 155: 5.088 distance: 154 - 226: 19.550 distance: 155 - 156: 3.720 distance: 155 - 158: 8.258 distance: 156 - 157: 12.641 distance: 156 - 162: 17.028 distance: 157 - 223: 9.576 distance: 158 - 159: 10.659 distance: 159 - 160: 29.265 distance: 159 - 161: 21.083 distance: 162 - 163: 3.263 distance: 163 - 164: 13.235 distance: 163 - 166: 18.043 distance: 164 - 165: 8.682 distance: 164 - 176: 24.095 distance: 166 - 167: 7.578 distance: 167 - 168: 9.894 distance: 167 - 169: 9.253 distance: 168 - 170: 4.115 distance: 169 - 171: 19.037 distance: 169 - 172: 6.951 distance: 170 - 171: 12.353 distance: 171 - 173: 10.086 distance: 172 - 174: 3.975 distance: 174 - 175: 3.426 distance: 176 - 177: 5.393 distance: 177 - 178: 12.638 distance: 177 - 180: 28.806 distance: 178 - 179: 14.887 distance: 178 - 181: 7.213 distance: 181 - 182: 26.755 distance: 182 - 183: 3.582 distance: 182 - 185: 11.549 distance: 183 - 184: 6.134 distance: 183 - 189: 30.193 distance: 185 - 186: 20.073 distance: 185 - 187: 24.644 distance: 186 - 188: 31.051