Starting phenix.real_space_refine on Sun May 3 06:13:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nzr_49957/05_2026/9nzr_49957.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nzr_49957/05_2026/9nzr_49957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nzr_49957/05_2026/9nzr_49957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nzr_49957/05_2026/9nzr_49957.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nzr_49957/05_2026/9nzr_49957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nzr_49957/05_2026/9nzr_49957.map" } resolution = 3.26 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= -0.000 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: 5 Type Number sf(0) Gaussians P 184 5.49 5 S 24 5.16 5 C 6288 2.51 5 N 2038 2.21 5 O 2526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11060 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 668 Classifications: {'DNA': 33} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 32} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 471 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "A" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3611 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 13, 'TRANS': 434} Chain breaks: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 3543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3543 Classifications: {'peptide': 441} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 28} Link IDs: {'PTRANS': 12, 'TRANS': 428} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 95 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 4, 'ARG:plan': 2, 'ASP:plan': 4, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "C" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 2767 Classifications: {'RNA': 129} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 4, 'rna3p_pur': 63, 'rna3p_pyr': 50} Link IDs: {'rna2p': 16, 'rna3p': 112} Chain breaks: 2 Time building chain proxies: 2.87, per 1000 atoms: 0.26 Number of scatterers: 11060 At special positions: 0 Unit cell: (121.29, 127.821, 110.094, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 184 15.00 O 2526 8.00 N 2038 7.00 C 6288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.96 Conformation dependent library (CDL) restraints added in 367.3 milliseconds 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1672 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 50.6% alpha, 16.0% beta 73 base pairs and 119 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 24 through 41 Processing helix chain 'A' and resid 42 through 68 removed outlier: 3.699A pdb=" N GLU A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 80 removed outlier: 3.755A pdb=" N GLN A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 73 " --> pdb=" O PRO A 69 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.588A pdb=" N ASN A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 114 Processing helix chain 'A' and resid 125 through 137 removed outlier: 3.638A pdb=" N TYR A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 158 removed outlier: 3.963A pdb=" N ASN A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'A' and resid 300 through 306 Processing helix chain 'A' and resid 308 through 314 removed outlier: 3.862A pdb=" N ARG A 314 " --> pdb=" O ARG A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 4.047A pdb=" N THR A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 331 through 335 removed outlier: 3.571A pdb=" N ARG A 335 " --> pdb=" O ALA A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 337 No H-bonds generated for 'chain 'A' and resid 336 through 337' Processing helix chain 'A' and resid 338 through 362 removed outlier: 3.855A pdb=" N ASN A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 468 through 478 Processing helix chain 'B' and resid 24 through 68 removed outlier: 4.942A pdb=" N TYR B 44 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LYS B 45 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLU B 61 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N TYR B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 80 removed outlier: 3.672A pdb=" N TYR B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 114 removed outlier: 4.274A pdb=" N ARG B 114 " --> pdb=" O HIS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 137 removed outlier: 3.839A pdb=" N VAL B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU B 135 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 137 " --> pdb=" O SER B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 166 removed outlier: 3.685A pdb=" N ASN B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ASP B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 220 through 229 removed outlier: 4.207A pdb=" N ARG B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 318 removed outlier: 3.589A pdb=" N PHE B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 362 removed outlier: 3.532A pdb=" N ASN B 362 " --> pdb=" O TYR B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 410 removed outlier: 4.116A pdb=" N LEU B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 478 Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 181 removed outlier: 3.818A pdb=" N SER A 237 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 238 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG A 247 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 251 " --> pdb=" O ARG A 10 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU A 13 " --> pdb=" O SER A 212 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE A 199 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 181 removed outlier: 3.818A pdb=" N SER A 237 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 238 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 185 Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 291 removed outlier: 6.176A pdb=" N ALA A 366 " --> pdb=" O PRO A 264 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG A 266 " --> pdb=" O ALA A 366 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLN A 368 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 268 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N GLU A 370 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N VAL A 270 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY A 365 " --> pdb=" O GLU A 413 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ARG A 415 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ILE A 367 " --> pdb=" O ARG A 415 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL A 417 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N MET A 369 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 442 through 443 Processing sheet with id=AA6, first strand: chain 'B' and resid 179 through 180 removed outlier: 5.000A pdb=" N ARG B 247 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE B 199 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 179 through 180 Processing sheet with id=AA8, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.622A pdb=" N LEU B 278 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B 279 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLY B 365 " --> pdb=" O PRO B 264 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ARG B 266 " --> pdb=" O GLY B 365 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE B 367 " --> pdb=" O ARG B 266 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL B 268 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N MET B 369 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL B 270 " --> pdb=" O MET B 369 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY B 365 " --> pdb=" O GLU B 413 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ARG B 415 " --> pdb=" O GLY B 365 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE B 367 " --> pdb=" O ARG B 415 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 442 through 443 384 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 181 hydrogen bonds 338 hydrogen bond angles 0 basepair planarities 73 basepair parallelities 119 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2524 1.33 - 1.46: 3616 1.46 - 1.58: 5124 1.58 - 1.70: 364 1.70 - 1.82: 36 Bond restraints: 11664 Sorted by residual: bond pdb=" C3' DT D 1 " pdb=" O3' DT D 1 " ideal model delta sigma weight residual 1.422 1.487 -0.065 3.00e-02 1.11e+03 4.66e+00 bond pdb=" C3' DC D 16 " pdb=" O3' DC D 16 " ideal model delta sigma weight residual 1.422 1.485 -0.063 3.00e-02 1.11e+03 4.38e+00 bond pdb=" CB ASP A 104 " pdb=" CG ASP A 104 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.63e+00 bond pdb=" CB ASP A 418 " pdb=" CG ASP A 418 " ideal model delta sigma weight residual 1.516 1.561 -0.045 2.50e-02 1.60e+03 3.18e+00 bond pdb=" CB ASP B 284 " pdb=" CG ASP B 284 " ideal model delta sigma weight residual 1.516 1.560 -0.044 2.50e-02 1.60e+03 3.06e+00 ... (remaining 11659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 16351 2.83 - 5.67: 213 5.67 - 8.50: 40 8.50 - 11.33: 3 11.33 - 14.17: 1 Bond angle restraints: 16608 Sorted by residual: angle pdb=" C3' U C 39 " pdb=" O3' U C 39 " pdb=" P U C 40 " ideal model delta sigma weight residual 120.20 127.47 -7.27 1.50e+00 4.44e-01 2.35e+01 angle pdb=" CB MET B 301 " pdb=" CG MET B 301 " pdb=" SD MET B 301 " ideal model delta sigma weight residual 112.70 98.53 14.17 3.00e+00 1.11e-01 2.23e+01 angle pdb=" O4' A C 60 " pdb=" C1' A C 60 " pdb=" N9 A C 60 " ideal model delta sigma weight residual 108.20 114.20 -6.00 1.50e+00 4.44e-01 1.60e+01 angle pdb=" O3' G C 136 " pdb=" C3' G C 136 " pdb=" C2' G C 136 " ideal model delta sigma weight residual 113.70 119.69 -5.99 1.50e+00 4.44e-01 1.59e+01 angle pdb=" CA MET B 305 " pdb=" CB MET B 305 " pdb=" CG MET B 305 " ideal model delta sigma weight residual 114.10 122.04 -7.94 2.00e+00 2.50e-01 1.58e+01 ... (remaining 16603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 6371 34.93 - 69.87: 572 69.87 - 104.80: 45 104.80 - 139.74: 3 139.74 - 174.67: 3 Dihedral angle restraints: 6994 sinusoidal: 4400 harmonic: 2594 Sorted by residual: dihedral pdb=" CA THR A 320 " pdb=" C THR A 320 " pdb=" N ASN A 321 " pdb=" CA ASN A 321 " ideal model delta harmonic sigma weight residual 180.00 154.41 25.59 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA ILE B 276 " pdb=" C ILE B 276 " pdb=" N PRO B 277 " pdb=" CA PRO B 277 " ideal model delta harmonic sigma weight residual -180.00 -159.20 -20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" C4' U C 39 " pdb=" C3' U C 39 " pdb=" O3' U C 39 " pdb=" P U C 40 " ideal model delta sinusoidal sigma weight residual -110.00 64.67 -174.67 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 6991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1744 0.077 - 0.153: 154 0.153 - 0.230: 9 0.230 - 0.306: 5 0.306 - 0.383: 1 Chirality restraints: 1913 Sorted by residual: chirality pdb=" C1' A C 60 " pdb=" O4' A C 60 " pdb=" C2' A C 60 " pdb=" N9 A C 60 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C3' G C 136 " pdb=" C4' G C 136 " pdb=" O3' G C 136 " pdb=" C2' G C 136 " both_signs ideal model delta sigma weight residual False -2.48 -2.19 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CB ILE B 356 " pdb=" CA ILE B 356 " pdb=" CG1 ILE B 356 " pdb=" CG2 ILE B 356 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1910 not shown) Planarity restraints: 1471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 418 " 0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO A 419 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 419 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 419 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 470 " -0.024 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP A 470 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP A 470 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 470 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 470 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 470 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 470 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 470 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 470 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 470 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 335 " 0.231 9.50e-02 1.11e+02 1.04e-01 7.77e+00 pdb=" NE ARG A 335 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 335 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG A 335 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 335 " 0.002 2.00e-02 2.50e+03 ... (remaining 1468 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2213 2.78 - 3.31: 9554 3.31 - 3.84: 20814 3.84 - 4.37: 23477 4.37 - 4.90: 35592 Nonbonded interactions: 91650 Sorted by model distance: nonbonded pdb=" O ASN A 315 " pdb=" OG SER A 319 " model vdw 2.254 3.040 nonbonded pdb=" OE2 GLU A 404 " pdb=" OH TYR A 416 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR B 129 " pdb=" OG SER B 142 " model vdw 2.300 3.040 nonbonded pdb=" OH TYR A 279 " pdb=" CD1 TRP A 470 " model vdw 2.326 3.260 nonbonded pdb=" NH2 ARG A 317 " pdb=" OE2 GLU B 357 " model vdw 2.332 3.120 ... (remaining 91645 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 33 or (resid 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 60 or (resid 61 and (n \ ame N or name CA or name C or name O or name CB )) or resid 62 through 78 or (re \ sid 79 and (name N or name CA or name C or name O or name CB )) or resid 80 thro \ ugh 88 or (resid 89 through 90 and (name N or name CA or name C or name O or nam \ e CB )) or resid 91 through 114 or (resid 125 and (name N or name CA or name C o \ r name O or name CB )) or resid 126 through 137 or (resid 138 and (name N or nam \ e CA or name C or name O or name CB )) or resid 139 through 191 or (resid 192 an \ d (name N or name CA or name C or name O or name CB )) or resid 193 through 195 \ or (resid 196 and (name N or name CA or name C or name O or name CB )) or resid \ 197 through 221 or (resid 222 and (name N or name CA or name C or name O or name \ CB )) or resid 223 through 230 or (resid 231 and (name N or name CA or name C o \ r name O or name CB )) or resid 232 through 235 or (resid 236 and (name N or nam \ e CA or name C or name O or name CB )) or resid 237 through 287 or (resid 288 an \ d (name N or name CA or name C )) or resid 289 through 295 or (resid 296 and (na \ me N or name CA or name C or name O or name CB )) or resid 297 through 305 or (r \ esid 306 through 307 and (name N or name CA or name C or name O or name CB )) or \ resid 308 through 317 or (resid 318 and (name N or name CA or name C or name O \ or name CB )) or resid 327 through 368 or (resid 369 through 370 and (name N or \ name CA or name C or name O or name CB )) or resid 371 through 436 or (resid 437 \ and (name N or name CA or name C or name O or name CB )) or resid 438 through 4 \ 48 or (resid 449 and (name N or name CA or name C or name O or name CB )) or res \ id 450 through 478)) selection = (chain 'B' and (resid 6 through 81 or (resid 82 and (name N or name CA or name C \ or name O or name CB )) or resid 83 through 89 or (resid 90 and (name N or name \ CA or name C or name O or name CB )) or resid 91 through 242 or (resid 243 and \ (name N or name CA or name C or name O or name CB )) or resid 244 through 300 or \ (resid 301 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 2 through 308 or (resid 309 and (name N or name CA or name C or name O or name C \ B )) or resid 310 or (resid 311 and (name N or name CA or name C or name O or na \ me CB )) or resid 312 through 336 or (resid 337 and (name N or name CA or name C \ or name O or name CB )) or resid 338 through 371 or (resid 392 and (name N or n \ ame CA or name C or name O or name CB )) or resid 393 through 435 or (resid 436 \ through 437 and (name N or name CA or name C or name O or name CB )) or resid 43 \ 8 through 455 or (resid 456 and (name N or name CA or name C or name O or name C \ B )) or resid 465 through 478)) } 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: 2.540 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.820 Find NCS groups from input model: 0.130 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11664 Z= 0.198 Angle : 0.844 14.168 16608 Z= 0.448 Chirality : 0.046 0.383 1913 Planarity : 0.007 0.104 1471 Dihedral : 21.625 174.672 5322 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.13 % Allowed : 12.05 % Favored : 87.82 % 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 are not related in a simple way. whole: -0.63 (0.27), residues: 875 helix: -0.04 (0.23), residues: 427 sheet: -0.04 (0.49), residues: 127 loop : -0.92 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 314 TYR 0.020 0.002 TYR A 129 PHE 0.020 0.002 PHE B 71 TRP 0.056 0.003 TRP A 470 HIS 0.011 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00442 (11664) covalent geometry : angle 0.84399 (16608) hydrogen bonds : bond 0.12645 ( 553) hydrogen bonds : angle 5.24774 ( 1439) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.344 Fit side-chains REVERT: A 174 LYS cc_start: 0.8259 (mtmt) cc_final: 0.7997 (mmtm) REVERT: A 362 ASN cc_start: 0.8372 (m-40) cc_final: 0.8146 (m-40) REVERT: B 11 LYS cc_start: 0.8406 (tttt) cc_final: 0.8072 (ttmt) REVERT: B 392 ARG cc_start: 0.6600 (ttp-110) cc_final: 0.6016 (tpm170) outliers start: 1 outliers final: 1 residues processed: 114 average time/residue: 0.1253 time to fit residues: 19.7260 Evaluate side-chains 85 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 30.0000 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 GLN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN B 363 ASN B 368 GLN B 471 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.190378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.139902 restraints weight = 15414.976| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.98 r_work: 0.3426 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11664 Z= 0.189 Angle : 0.633 7.107 16608 Z= 0.344 Chirality : 0.040 0.306 1913 Planarity : 0.005 0.052 1471 Dihedral : 22.852 168.743 3574 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.41 % Allowed : 11.91 % Favored : 85.68 % 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 are not related in a simple way. whole: 0.29 (0.28), residues: 875 helix: 1.14 (0.25), residues: 434 sheet: -0.32 (0.45), residues: 137 loop : -0.85 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 314 TYR 0.020 0.002 TYR A 405 PHE 0.013 0.002 PHE A 56 TRP 0.030 0.002 TRP A 470 HIS 0.005 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00424 (11664) covalent geometry : angle 0.63274 (16608) hydrogen bonds : bond 0.04935 ( 553) hydrogen bonds : angle 3.84171 ( 1439) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.311 Fit side-chains REVERT: A 157 LYS cc_start: 0.7873 (tttt) cc_final: 0.7556 (ttmt) REVERT: A 174 LYS cc_start: 0.8516 (mtmt) cc_final: 0.8300 (mmtm) REVERT: B 11 LYS cc_start: 0.8570 (tttt) cc_final: 0.8317 (ttmt) REVERT: B 66 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8359 (mm) REVERT: B 211 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8540 (mt) REVERT: B 315 ASN cc_start: 0.6735 (p0) cc_final: 0.6274 (p0) REVERT: B 337 GLU cc_start: 0.8495 (mt-10) cc_final: 0.7859 (pt0) REVERT: B 405 TYR cc_start: 0.8650 (t80) cc_final: 0.8336 (t80) outliers start: 18 outliers final: 11 residues processed: 115 average time/residue: 0.1153 time to fit residues: 18.4889 Evaluate side-chains 96 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 267 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 58 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.188766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.138542 restraints weight = 15213.843| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.05 r_work: 0.3358 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11664 Z= 0.133 Angle : 0.558 6.478 16608 Z= 0.303 Chirality : 0.037 0.253 1913 Planarity : 0.004 0.045 1471 Dihedral : 22.782 171.072 3573 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.34 % Allowed : 14.73 % Favored : 83.94 % 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 are not related in a simple way. whole: 0.86 (0.29), residues: 875 helix: 1.81 (0.25), residues: 428 sheet: -0.34 (0.45), residues: 135 loop : -0.72 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 314 TYR 0.023 0.001 TYR A 405 PHE 0.011 0.001 PHE A 56 TRP 0.031 0.002 TRP A 470 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00288 (11664) covalent geometry : angle 0.55783 (16608) hydrogen bonds : bond 0.04410 ( 553) hydrogen bonds : angle 3.62297 ( 1439) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 111 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8490 (m) REVERT: A 157 LYS cc_start: 0.7827 (tttt) cc_final: 0.7549 (ttmt) REVERT: A 174 LYS cc_start: 0.8490 (mtmt) cc_final: 0.8254 (mmtm) REVERT: B 11 LYS cc_start: 0.8496 (tttt) cc_final: 0.8234 (ttmt) REVERT: B 337 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7894 (pt0) REVERT: B 405 TYR cc_start: 0.8636 (t80) cc_final: 0.8317 (t80) outliers start: 10 outliers final: 5 residues processed: 101 average time/residue: 0.1170 time to fit residues: 16.5371 Evaluate side-chains 85 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 267 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 99 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 45 optimal weight: 20.0000 chunk 44 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.185954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.135800 restraints weight = 15205.136| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.10 r_work: 0.3298 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11664 Z= 0.163 Angle : 0.575 10.360 16608 Z= 0.310 Chirality : 0.038 0.232 1913 Planarity : 0.004 0.044 1471 Dihedral : 22.723 170.008 3573 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.68 % Allowed : 14.86 % Favored : 82.46 % 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 are not related in a simple way. whole: 0.96 (0.29), residues: 875 helix: 1.95 (0.25), residues: 430 sheet: -0.51 (0.45), residues: 132 loop : -0.65 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 341 TYR 0.017 0.001 TYR A 405 PHE 0.014 0.001 PHE B 336 TRP 0.030 0.002 TRP A 470 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00367 (11664) covalent geometry : angle 0.57458 (16608) hydrogen bonds : bond 0.04489 ( 553) hydrogen bonds : angle 3.65147 ( 1439) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 157 LYS cc_start: 0.7758 (tttt) cc_final: 0.7393 (ttmt) REVERT: A 174 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8353 (mmtm) REVERT: A 290 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.6906 (tmm) REVERT: B 66 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8347 (mm) REVERT: B 143 GLU cc_start: 0.7380 (pp20) cc_final: 0.6910 (tm-30) REVERT: B 172 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.8592 (p0) REVERT: B 315 ASN cc_start: 0.6262 (p0) cc_final: 0.5983 (p0) REVERT: B 337 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8066 (pt0) REVERT: B 405 TYR cc_start: 0.8737 (t80) cc_final: 0.8310 (t80) outliers start: 20 outliers final: 11 residues processed: 100 average time/residue: 0.1130 time to fit residues: 15.9143 Evaluate side-chains 92 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 390 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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-2.1rc2-6044/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.9184 > 50: distance: 74 - 78: 7.846 distance: 78 - 79: 7.180 distance: 79 - 80: 22.031 distance: 79 - 82: 21.625 distance: 80 - 81: 14.899 distance: 80 - 89: 9.880 distance: 82 - 83: 18.182 distance: 83 - 84: 13.508 distance: 84 - 85: 18.426 distance: 85 - 86: 20.021 distance: 86 - 87: 26.592 distance: 86 - 88: 29.226 distance: 89 - 90: 5.827 distance: 90 - 91: 13.629 distance: 91 - 92: 32.432 distance: 91 - 93: 12.712 distance: 93 - 94: 11.415 distance: 94 - 95: 25.084 distance: 94 - 97: 10.702 distance: 95 - 101: 30.893 distance: 97 - 99: 14.350 distance: 98 - 100: 10.928 distance: 101 - 102: 16.140 distance: 101 - 107: 8.098 distance: 102 - 103: 25.939 distance: 102 - 105: 24.802 distance: 103 - 104: 27.097 distance: 103 - 108: 14.825 distance: 105 - 106: 28.198 distance: 108 - 109: 32.353 distance: 108 - 221: 27.135 distance: 109 - 110: 30.518 distance: 109 - 112: 11.118 distance: 110 - 111: 42.123 distance: 110 - 115: 20.808 distance: 111 - 218: 28.689 distance: 112 - 113: 23.777 distance: 112 - 114: 15.572 distance: 115 - 116: 14.705 distance: 115 - 121: 3.940 distance: 116 - 117: 13.143 distance: 116 - 119: 12.634 distance: 117 - 118: 17.741 distance: 117 - 122: 13.993 distance: 119 - 120: 8.093 distance: 120 - 121: 10.659 distance: 122 - 123: 10.087 distance: 123 - 124: 7.986 distance: 123 - 126: 12.461 distance: 124 - 125: 6.451 distance: 124 - 133: 6.412 distance: 126 - 127: 6.215 distance: 127 - 128: 15.723 distance: 127 - 129: 19.319 distance: 128 - 130: 20.538 distance: 129 - 131: 13.450 distance: 130 - 132: 22.746 distance: 131 - 132: 20.325 distance: 133 - 134: 12.021 distance: 134 - 135: 9.835 distance: 134 - 137: 17.008 distance: 135 - 136: 6.129 distance: 135 - 139: 8.723 distance: 137 - 138: 13.191 distance: 139 - 140: 23.614 distance: 140 - 141: 27.347 distance: 140 - 143: 18.715 distance: 141 - 142: 17.578 distance: 141 - 147: 41.014 distance: 143 - 144: 6.492 distance: 143 - 145: 13.707 distance: 144 - 146: 35.265 distance: 147 - 148: 16.958 distance: 148 - 149: 14.581 distance: 148 - 151: 16.145 distance: 149 - 150: 9.301 distance: 149 - 156: 23.718 distance: 151 - 152: 21.390 distance: 152 - 153: 23.400 distance: 153 - 154: 30.218 distance: 154 - 155: 23.993