Starting phenix.real_space_refine on Thu Jul 2 09:35:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u6e_26364/07_2026/7u6e_26364.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u6e_26364/07_2026/7u6e_26364.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7u6e_26364/07_2026/7u6e_26364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u6e_26364/07_2026/7u6e_26364.map" model { file = "/net/cci-nas-00/data/ceres_data/7u6e_26364/07_2026/7u6e_26364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u6e_26364/07_2026/7u6e_26364.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7u6e_26364/07_2026/7u6e_26364.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u6e_26364/07_2026/7u6e_26364.cif" } 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= 0.000 sd= 0.002 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 60 5.16 5 C 5077 2.51 5 N 1357 2.21 5 O 1510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8004 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "B" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "E" Number of atoms: 4708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4708 Classifications: {'peptide': 584} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 555} Chain breaks: 2 Chain: "F" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2507 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 12, 'TRANS': 295} Chain breaks: 2 Chain: "G" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Unusual residues: {'HY1': 1} Classifications: {'peptide': 18, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 16, None: 1} Not linked: pdbres="HY1 G 0 " pdbres="SER G 1 " Chain: "H" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Unusual residues: {'HY1': 1} Classifications: {'peptide': 18, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 16, None: 1} Not linked: pdbres="HY1 H 0 " pdbres="SER H 1 " Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.39, per 1000 atoms: 0.17 Number of scatterers: 8004 At special positions: 0 Unit cell: (117.307, 86.2133, 83.3866, 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 60 16.00 O 1510 8.00 N 1357 7.00 C 5077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 11 " distance=2.02 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS B 7 " distance=2.03 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS B 19 " distance=2.01 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS E 26 " distance=2.02 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 182 " distance=2.03 Simple disulfide: pdb=" SG CYS E 169 " - pdb=" SG CYS E 188 " distance=2.04 Simple disulfide: pdb=" SG CYS E 192 " - pdb=" SG CYS E 201 " distance=2.04 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS E 207 " distance=2.02 Simple disulfide: pdb=" SG CYS E 208 " - pdb=" SG CYS E 216 " distance=2.02 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 225 " distance=2.01 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 237 " distance=2.03 Simple disulfide: pdb=" SG CYS E 241 " - pdb=" SG CYS E 253 " distance=2.02 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 284 " distance=2.03 Simple disulfide: pdb=" SG CYS E 266 " - pdb=" SG CYS E 274 " distance=2.02 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 308 " distance=2.04 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 333 " distance=2.02 Simple disulfide: pdb=" SG CYS E 435 " - pdb=" SG CYS E 468 " distance=2.03 Simple disulfide: pdb=" SG CYS E 524 " - pdb=" SG CYS F 524 " distance=2.04 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 333 " distance=2.02 Simple disulfide: pdb=" SG CYS F 435 " - pdb=" SG CYS F 468 " distance=2.02 Simple disulfide: pdb=" SG CYS G 11 " - pdb=" SG CYS G 17 " distance=2.03 Simple disulfide: pdb=" SG CYS H 11 " - pdb=" SG CYS H 17 " 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=2, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN E 111 " " NAG E1001 " - " ASN E 25 " " NAG E1002 " - " ASN E 255 " " NAG E1003 " - " ASN E 418 " " NAG F1001 " - " ASN F 337 " " NAG F1002 " - " ASN F 397 " " NAG F1003 " - " ASN F 514 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 300.5 milliseconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 16 sheets defined 19.9% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 Processing helix chain 'A' and resid 12 through 18 Processing helix chain 'B' and resid 7 through 19 removed outlier: 3.775A pdb=" N VAL B 12 " --> pdb=" O GLY B 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 24 removed outlier: 3.664A pdb=" N ARG E 19 " --> pdb=" O ASN E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 47 removed outlier: 3.571A pdb=" N PHE E 46 " --> pdb=" O ARG E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 76 removed outlier: 4.427A pdb=" N LEU E 75 " --> pdb=" O SER E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 137 removed outlier: 3.642A pdb=" N ILE E 136 " --> pdb=" O ASP E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 152 Processing helix chain 'E' and resid 255 through 269 Processing helix chain 'E' and resid 323 through 329 Processing helix chain 'E' and resid 350 through 359 Processing helix chain 'E' and resid 435 through 446 removed outlier: 3.787A pdb=" N MET E 442 " --> pdb=" O GLU E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 498 No H-bonds generated for 'chain 'E' and resid 496 through 498' Processing helix chain 'F' and resid 323 through 328 Processing helix chain 'F' and resid 329 through 331 No H-bonds generated for 'chain 'F' and resid 329 through 331' Processing helix chain 'F' and resid 352 through 360 removed outlier: 3.599A pdb=" N ASN F 357 " --> pdb=" O GLU F 353 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU F 360 " --> pdb=" O ALA F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'F' and resid 496 through 498 No H-bonds generated for 'chain 'F' and resid 496 through 498' Processing helix chain 'F' and resid 542 through 546 Processing helix chain 'F' and resid 691 through 714 Processing helix chain 'G' and resid 1 through 13 Processing helix chain 'H' and resid 1 through 13 Processing sheet with id=AA1, first strand: chain 'E' and resid 7 through 14 removed outlier: 6.709A pdb=" N CYS E 8 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N HIS E 32 " --> pdb=" O CYS E 8 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLY E 10 " --> pdb=" O HIS E 32 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLN E 34 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP E 12 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU E 36 " --> pdb=" O ASP E 12 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG E 14 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET E 38 " --> pdb=" O ARG E 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 7 through 14 removed outlier: 6.709A pdb=" N CYS E 8 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N HIS E 32 " --> pdb=" O CYS E 8 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLY E 10 " --> pdb=" O HIS E 32 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLN E 34 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP E 12 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU E 36 " --> pdb=" O ASP E 12 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG E 14 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET E 38 " --> pdb=" O ARG E 14 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL E 66 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ARG E 118 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL E 94 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLU E 120 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE E 96 " --> pdb=" O GLU E 120 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL E 117 " --> pdb=" O HIS E 144 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL E 146 " --> pdb=" O VAL E 117 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE E 119 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 171 through 172 removed outlier: 3.587A pdb=" N THR E 172 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL E 179 " --> pdb=" O THR E 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 231 through 233 Processing sheet with id=AA5, first strand: chain 'E' and resid 252 through 254 removed outlier: 6.543A pdb=" N HIS E 247 " --> pdb=" O CYS E 284 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 292 through 294 Processing sheet with id=AA7, first strand: chain 'E' and resid 311 through 321 removed outlier: 10.749A pdb=" N VAL E 335 " --> pdb=" O HIS E 313 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N LEU E 315 " --> pdb=" O VAL E 335 " (cutoff:3.500A) removed outlier: 10.359A pdb=" N ASN E 337 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLY E 317 " --> pdb=" O ASN E 337 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 311 through 321 removed outlier: 10.749A pdb=" N VAL E 335 " --> pdb=" O HIS E 313 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N LEU E 315 " --> pdb=" O VAL E 335 " (cutoff:3.500A) removed outlier: 10.359A pdb=" N ASN E 337 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLY E 317 " --> pdb=" O ASN E 337 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N PHE E 427 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TYR E 401 " --> pdb=" O PHE E 427 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N HIS E 429 " --> pdb=" O TYR E 401 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU E 403 " --> pdb=" O HIS E 429 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU E 426 " --> pdb=" O ASP E 456 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 471 through 472 removed outlier: 6.359A pdb=" N GLU E 471 " --> pdb=" O LYS E 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 477 through 480 removed outlier: 3.517A pdb=" N MET E 553 " --> pdb=" O ILE E 485 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 530 through 534 Processing sheet with id=AB3, first strand: chain 'F' and resid 311 through 321 removed outlier: 6.918A pdb=" N CYS F 312 " --> pdb=" O ASN F 337 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N SER F 339 " --> pdb=" O CYS F 312 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU F 314 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 11.385A pdb=" N ILE F 341 " --> pdb=" O LEU F 314 " (cutoff:3.500A) removed outlier: 12.281A pdb=" N GLU F 316 " --> pdb=" O ILE F 341 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLY F 338 " --> pdb=" O SER F 365 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY F 366 " --> pdb=" O ARG F 389 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLU F 391 " --> pdb=" O GLY F 366 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 311 through 321 removed outlier: 6.918A pdb=" N CYS F 312 " --> pdb=" O ASN F 337 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N SER F 339 " --> pdb=" O CYS F 312 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU F 314 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 11.385A pdb=" N ILE F 341 " --> pdb=" O LEU F 314 " (cutoff:3.500A) removed outlier: 12.281A pdb=" N GLU F 316 " --> pdb=" O ILE F 341 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N LYS F 369 " --> pdb=" O GLY F 338 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU F 340 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ARG F 371 " --> pdb=" O LEU F 340 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE F 342 " --> pdb=" O ARG F 371 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N PHE F 427 " --> pdb=" O SER F 399 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR F 401 " --> pdb=" O PHE F 427 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N HIS F 429 " --> pdb=" O TYR F 401 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU F 403 " --> pdb=" O HIS F 429 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 471 through 473 removed outlier: 5.995A pdb=" N GLU F 471 " --> pdb=" O LYS F 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 475 through 480 Processing sheet with id=AB7, first strand: chain 'F' and resid 532 through 534 211 hydrogen bonds defined for protein. 552 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: 0.92 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1333 1.32 - 1.44: 2277 1.44 - 1.57: 4505 1.57 - 1.70: 0 1.70 - 1.83: 72 Bond restraints: 8187 Sorted by residual: bond pdb=" C1 NAG F1002 " pdb=" O5 NAG F1002 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C1 NAG E1001 " pdb=" O5 NAG E1001 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.33e+00 bond pdb=" C1 NAG F1001 " pdb=" O5 NAG F1001 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" C1 NAG C 1 " pdb=" C2 NAG C 1 " ideal model delta sigma weight residual 1.532 1.499 0.033 2.00e-02 2.50e+03 2.77e+00 bond pdb=" CB ASN E 122 " pdb=" CG ASN E 122 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.14e+00 ... (remaining 8182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 10426 1.84 - 3.67: 571 3.67 - 5.51: 75 5.51 - 7.35: 4 7.35 - 9.18: 3 Bond angle restraints: 11079 Sorted by residual: angle pdb=" CA TRP E 559 " pdb=" CB TRP E 559 " pdb=" CG TRP E 559 " ideal model delta sigma weight residual 113.60 119.95 -6.35 1.90e+00 2.77e-01 1.12e+01 angle pdb=" N MET E 56 " pdb=" CA MET E 56 " pdb=" C MET E 56 " ideal model delta sigma weight residual 108.32 113.08 -4.76 1.64e+00 3.72e-01 8.42e+00 angle pdb=" N ILE F 388 " pdb=" CA ILE F 388 " pdb=" C ILE F 388 " ideal model delta sigma weight residual 108.17 104.16 4.01 1.40e+00 5.10e-01 8.20e+00 angle pdb=" C5 NAG C 1 " pdb=" C4 NAG C 1 " pdb=" O4 NAG C 1 " ideal model delta sigma weight residual 111.70 103.34 8.36 3.00e+00 1.11e-01 7.76e+00 angle pdb=" N PHE E 382 " pdb=" CA PHE E 382 " pdb=" C PHE E 382 " ideal model delta sigma weight residual 109.96 105.83 4.13 1.49e+00 4.50e-01 7.69e+00 ... (remaining 11074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 4411 17.44 - 34.89: 361 34.89 - 52.33: 81 52.33 - 69.77: 19 69.77 - 87.22: 12 Dihedral angle restraints: 4884 sinusoidal: 2048 harmonic: 2836 Sorted by residual: dihedral pdb=" CB CYS E 192 " pdb=" SG CYS E 192 " pdb=" SG CYS E 201 " pdb=" CB CYS E 201 " ideal model delta sinusoidal sigma weight residual -86.00 -167.88 81.88 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS E 288 " pdb=" SG CYS E 288 " pdb=" SG CYS E 301 " pdb=" CB CYS E 301 " ideal model delta sinusoidal sigma weight residual -86.00 -164.61 78.61 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CB CYS H 11 " pdb=" SG CYS H 11 " pdb=" SG CYS H 17 " pdb=" CB CYS H 17 " ideal model delta sinusoidal sigma weight residual 93.00 166.66 -73.66 1 1.00e+01 1.00e-02 6.90e+01 ... (remaining 4881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 994 0.079 - 0.157: 208 0.157 - 0.236: 16 0.236 - 0.315: 2 0.315 - 0.394: 1 Chirality restraints: 1221 Sorted by residual: chirality pdb=" C1 NAG E1002 " pdb=" ND2 ASN E 255 " pdb=" C2 NAG E1002 " pdb=" O5 NAG E1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CB THR F 421 " pdb=" CA THR F 421 " pdb=" OG1 THR F 421 " pdb=" CG2 THR F 421 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C1 NAG E1001 " pdb=" ND2 ASN E 25 " pdb=" C2 NAG E1001 " pdb=" O5 NAG E1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1218 not shown) Planarity restraints: 1423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 255 " 0.029 2.00e-02 2.50e+03 2.94e-02 1.08e+01 pdb=" CG ASN E 255 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN E 255 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN E 255 " -0.043 2.00e-02 2.50e+03 pdb=" C1 NAG E1002 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 717 " 0.216 9.50e-02 1.11e+02 9.76e-02 7.29e+00 pdb=" NE ARG F 717 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG F 717 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG F 717 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG F 717 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 345 " -0.212 9.50e-02 1.11e+02 9.56e-02 6.59e+00 pdb=" NE ARG F 345 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG F 345 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG F 345 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG F 345 " -0.002 2.00e-02 2.50e+03 ... (remaining 1420 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 418 2.72 - 3.26: 8223 3.26 - 3.81: 13796 3.81 - 4.35: 18306 4.35 - 4.90: 29626 Nonbonded interactions: 70369 Sorted by model distance: nonbonded pdb=" OE2 GLU E 211 " pdb=" ND2 ASN E 230 " model vdw 2.171 3.120 nonbonded pdb=" O3 NAG E1002 " pdb=" O7 NAG E1002 " model vdw 2.288 3.040 nonbonded pdb=" OE2 GLU E 120 " pdb=" NZ LYS E 121 " model vdw 2.310 3.120 nonbonded pdb=" OH TYR F 398 " pdb=" OD2 ASP F 456 " model vdw 2.328 3.040 nonbonded pdb=" OE2 GLU E 471 " pdb=" OH TYR E 492 " model vdw 2.357 3.040 ... (remaining 70364 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 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.540 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:5.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 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 : 0.008 0.108 8221 Z= 0.397 Angle : 0.953 12.321 11151 Z= 0.505 Chirality : 0.061 0.394 1221 Planarity : 0.008 0.098 1416 Dihedral : 14.136 87.215 2982 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.61 % Favored : 95.28 % Rotamer: Outliers : 1.82 % Allowed : 8.29 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -2.19 (0.24), residues: 954 helix: -1.27 (0.37), residues: 182 sheet: -1.55 (0.42), residues: 148 loop : -1.53 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG F 717 TYR 0.025 0.004 TYR F 507 PHE 0.042 0.004 PHE E 89 TRP 0.035 0.003 TRP F 414 HIS 0.012 0.002 HIS E 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00830 / 0.36 ( 8187) covalent geometry : angle 0.91358 / 0.50 (11079) SS BOND : bond 0.00951 / 0.56 ( 24) SS BOND : angle 1.65478 / 1.26 ( 48) hydrogen bonds : bond 0.19280 / 12.86 ( 207) hydrogen bonds : angle 9.47748 / 6.59 ( 552) Misc. bond : bond 0.10637 / 6.30 ( 2) link_BETA1-4 : bond 0.01320 / 0.83 ( 1) link_BETA1-4 : angle 7.55203 / 3.23 ( 3) link_NAG-ASN : bond 0.00284 / 0.21 ( 7) link_NAG-ASN : angle 5.24460 / 3.07 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: E 299 LEU cc_start: 0.7723 (tp) cc_final: 0.7522 (tp) REVERT: E 483 ASP cc_start: 0.6432 (p0) cc_final: 0.6142 (p0) REVERT: E 505 LEU cc_start: 0.7781 (tt) cc_final: 0.7518 (tp) REVERT: E 553 MET cc_start: 0.7061 (mpp) cc_final: 0.6748 (mpp) REVERT: F 318 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6641 (tp30) REVERT: F 423 GLN cc_start: 0.8025 (tp40) cc_final: 0.7756 (tp-100) REVERT: F 579 TYR cc_start: 0.7289 (m-80) cc_final: 0.6999 (m-80) outliers start: 16 outliers final: 3 residues processed: 198 average time/residue: 0.5628 time to fit residues: 117.9022 Evaluate side-chains 99 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain F residue 412 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 HIS E 343 ASN E 348 ASN E 417 HIS ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 ASN F 548 HIS F 561 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.159752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.142702 restraints weight = 12922.591| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 2.06 r_work: 0.4089 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3959 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8221 Z= 0.228 Angle : 0.831 12.479 11151 Z= 0.428 Chirality : 0.051 0.352 1221 Planarity : 0.005 0.042 1416 Dihedral : 7.000 48.462 1069 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.09 % Allowed : 15.89 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.83 (0.25), residues: 954 helix: -0.55 (0.39), residues: 173 sheet: -1.07 (0.42), residues: 159 loop : -1.50 (0.22), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 454 TYR 0.019 0.002 TYR E 60 PHE 0.032 0.003 PHE E 482 TRP 0.018 0.002 TRP E 559 HIS 0.007 0.002 HIS E 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.23 ( 8187) covalent geometry : angle 0.79877 / 0.42 (11079) SS BOND : bond 0.00593 / 0.39 ( 24) SS BOND : angle 2.57352 / 1.95 ( 48) hydrogen bonds : bond 0.05299 / 3.54 ( 207) hydrogen bonds : angle 6.75371 / 4.80 ( 552) Misc. bond : bond 0.00239 / 0.14 ( 2) link_BETA1-4 : bond 0.00124 / 0.08 ( 1) link_BETA1-4 : angle 4.04832 / 1.98 ( 3) link_NAG-ASN : bond 0.00344 / 0.23 ( 7) link_NAG-ASN : angle 3.52758 / 2.13 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7623 (mp0) cc_final: 0.7117 (mp0) REVERT: E 16 ASN cc_start: 0.5665 (OUTLIER) cc_final: 0.5449 (p0) REVERT: E 110 MET cc_start: 0.8092 (mmp) cc_final: 0.7313 (mmt) REVERT: E 426 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7686 (mt) REVERT: E 483 ASP cc_start: 0.7105 (p0) cc_final: 0.6849 (p0) REVERT: E 553 MET cc_start: 0.7154 (mpp) cc_final: 0.6724 (mpp) REVERT: F 318 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6966 (tp30) REVERT: F 417 HIS cc_start: 0.7722 (OUTLIER) cc_final: 0.7091 (t70) REVERT: F 504 MET cc_start: 0.8380 (ptp) cc_final: 0.8098 (mtp) REVERT: F 521 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6956 (tm-30) REVERT: F 579 TYR cc_start: 0.7803 (m-80) cc_final: 0.7382 (m-80) REVERT: G 8 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8077 (pp30) outliers start: 36 outliers final: 7 residues processed: 133 average time/residue: 0.4509 time to fit residues: 64.1638 Evaluate side-chains 97 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 521 GLN Chi-restraints excluded: chain F residue 693 LEU Chi-restraints excluded: chain F residue 696 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 57 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 93 optimal weight: 0.3980 chunk 42 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 ASN E 348 ASN E 513 GLN E 521 GLN E 561 GLN F 405 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.161061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.144523 restraints weight = 12924.532| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 2.03 r_work: 0.4122 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3989 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8221 Z= 0.159 Angle : 0.713 11.017 11151 Z= 0.362 Chirality : 0.047 0.293 1221 Planarity : 0.004 0.036 1416 Dihedral : 6.417 45.981 1067 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.63 % Allowed : 17.71 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -1.68 (0.25), residues: 954 helix: -0.49 (0.39), residues: 173 sheet: -1.27 (0.39), residues: 171 loop : -1.27 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 498 TYR 0.013 0.001 TYR E 60 PHE 0.021 0.002 PHE E 482 TRP 0.023 0.002 TRP F 559 HIS 0.008 0.001 HIS E 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 8187) covalent geometry : angle 0.69353 / 0.36 (11079) SS BOND : bond 0.00669 / 0.50 ( 24) SS BOND : angle 1.66463 / 1.23 ( 48) hydrogen bonds : bond 0.04341 / 2.89 ( 207) hydrogen bonds : angle 6.21044 / 4.46 ( 552) Misc. bond : bond 0.00108 / 0.06 ( 2) link_BETA1-4 : bond 0.00087 / 0.05 ( 1) link_BETA1-4 : angle 3.40836 / 1.69 ( 3) link_NAG-ASN : bond 0.00387 / 0.26 ( 7) link_NAG-ASN : angle 2.88293 / 1.74 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7479 (mp0) cc_final: 0.7026 (mp0) REVERT: E 110 MET cc_start: 0.8034 (mmp) cc_final: 0.7281 (mmt) REVERT: E 406 GLN cc_start: 0.7582 (mm-40) cc_final: 0.7252 (mm-40) REVERT: E 553 MET cc_start: 0.6679 (mpp) cc_final: 0.6311 (mpp) REVERT: F 318 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6965 (tp30) REVERT: F 417 HIS cc_start: 0.7780 (OUTLIER) cc_final: 0.6879 (t70) REVERT: F 579 TYR cc_start: 0.7716 (m-80) cc_final: 0.7325 (m-80) REVERT: F 706 GLU cc_start: 0.7775 (tt0) cc_final: 0.7247 (pt0) REVERT: G 8 GLN cc_start: 0.8514 (tm-30) cc_final: 0.7893 (pp30) outliers start: 32 outliers final: 11 residues processed: 114 average time/residue: 0.4660 time to fit residues: 57.2347 Evaluate side-chains 90 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 433 LYS Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 696 LEU Chi-restraints excluded: chain G residue 1 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 2 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 48 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.160023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.143173 restraints weight = 13027.754| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 2.05 r_work: 0.4107 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3973 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8221 Z= 0.172 Angle : 0.693 7.562 11151 Z= 0.351 Chirality : 0.048 0.299 1221 Planarity : 0.004 0.038 1416 Dihedral : 6.235 46.262 1067 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.41 % Allowed : 19.07 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.67 (0.25), residues: 954 helix: -0.46 (0.39), residues: 173 sheet: -1.24 (0.41), residues: 159 loop : -1.29 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 498 TYR 0.016 0.001 TYR E 60 PHE 0.019 0.002 PHE E 89 TRP 0.024 0.002 TRP F 559 HIS 0.007 0.001 HIS E 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 8187) covalent geometry : angle 0.67135 / 0.35 (11079) SS BOND : bond 0.00380 / 0.22 ( 24) SS BOND : angle 1.80180 / 1.39 ( 48) hydrogen bonds : bond 0.04173 / 2.79 ( 207) hydrogen bonds : angle 5.98835 / 4.30 ( 552) Misc. bond : bond 0.00023 / 0.01 ( 2) link_BETA1-4 : bond 0.00232 / 0.15 ( 1) link_BETA1-4 : angle 3.61798 / 1.78 ( 3) link_NAG-ASN : bond 0.00323 / 0.21 ( 7) link_NAG-ASN : angle 2.77649 / 1.69 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7492 (mp0) cc_final: 0.7105 (mp0) REVERT: E 110 MET cc_start: 0.8110 (mmp) cc_final: 0.7282 (mmt) REVERT: E 406 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7169 (mm-40) REVERT: E 426 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7753 (mt) REVERT: F 350 LEU cc_start: 0.4266 (OUTLIER) cc_final: 0.3825 (tt) REVERT: F 417 HIS cc_start: 0.7826 (OUTLIER) cc_final: 0.6654 (t70) REVERT: F 579 TYR cc_start: 0.7719 (m-80) cc_final: 0.7351 (m-80) REVERT: F 698 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7395 (tm-30) REVERT: F 706 GLU cc_start: 0.7673 (tt0) cc_final: 0.7117 (pt0) REVERT: G 8 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8149 (pp30) REVERT: H 2 LEU cc_start: 0.7432 (mp) cc_final: 0.7207 (mp) outliers start: 30 outliers final: 10 residues processed: 105 average time/residue: 0.4476 time to fit residues: 50.3398 Evaluate side-chains 91 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 696 LEU Chi-restraints excluded: chain G residue 1 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 1 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 17 optimal weight: 0.0970 chunk 49 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 50 optimal weight: 0.0770 chunk 55 optimal weight: 3.9990 chunk 82 optimal weight: 0.0980 chunk 7 optimal weight: 0.9980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 513 GLN E 561 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.162119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.145276 restraints weight = 12987.022| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 2.05 r_work: 0.4121 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3987 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8221 Z= 0.135 Angle : 0.637 7.400 11151 Z= 0.325 Chirality : 0.046 0.275 1221 Planarity : 0.004 0.056 1416 Dihedral : 5.917 47.359 1067 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.52 % Allowed : 19.75 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.61 (0.26), residues: 954 helix: -0.35 (0.40), residues: 173 sheet: -1.24 (0.41), residues: 159 loop : -1.26 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 498 TYR 0.014 0.001 TYR E 60 PHE 0.018 0.002 PHE F 705 TRP 0.030 0.001 TRP F 559 HIS 0.004 0.001 HIS E 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 8187) covalent geometry : angle 0.62060 / 0.32 (11079) SS BOND : bond 0.00512 / 0.40 ( 24) SS BOND : angle 1.38843 / 1.02 ( 48) hydrogen bonds : bond 0.03743 / 2.51 ( 207) hydrogen bonds : angle 5.75873 / 4.15 ( 552) Misc. bond : bond 0.00014 / 0.01 ( 2) link_BETA1-4 : bond 0.00004 / 0.00 ( 1) link_BETA1-4 : angle 3.09282 / 1.58 ( 3) link_NAG-ASN : bond 0.00374 / 0.24 ( 7) link_NAG-ASN : angle 2.53201 / 1.55 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7506 (mp0) cc_final: 0.7106 (mp0) REVERT: E 110 MET cc_start: 0.8094 (mmp) cc_final: 0.7340 (mmt) REVERT: E 406 GLN cc_start: 0.7605 (mm-40) cc_final: 0.7222 (mm-40) REVERT: E 426 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7796 (mt) REVERT: E 483 ASP cc_start: 0.6684 (p0) cc_final: 0.6458 (p0) REVERT: F 417 HIS cc_start: 0.7823 (OUTLIER) cc_final: 0.6612 (t70) REVERT: F 579 TYR cc_start: 0.7671 (m-80) cc_final: 0.7310 (m-80) REVERT: F 698 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7355 (tm-30) REVERT: G 8 GLN cc_start: 0.8545 (tm-30) cc_final: 0.7876 (pp30) outliers start: 31 outliers final: 11 residues processed: 111 average time/residue: 0.4717 time to fit residues: 56.1139 Evaluate side-chains 84 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 696 LEU Chi-restraints excluded: chain G residue 1 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.7554 > 50: distance: 19 - 140: 11.711 distance: 22 - 137: 19.339 distance: 34 - 118: 18.495 distance: 37 - 115: 22.842 distance: 100 - 104: 23.093 distance: 104 - 105: 25.523 distance: 104 - 110: 20.965 distance: 105 - 106: 10.681 distance: 105 - 108: 32.364 distance: 106 - 107: 14.809 distance: 106 - 111: 11.479 distance: 108 - 109: 24.936 distance: 109 - 110: 15.545 distance: 111 - 112: 26.100 distance: 112 - 113: 42.145 distance: 113 - 114: 27.578 distance: 113 - 115: 54.755 distance: 115 - 116: 4.693 distance: 116 - 117: 29.907 distance: 116 - 119: 29.394 distance: 117 - 118: 15.202 distance: 117 - 129: 17.651 distance: 119 - 120: 14.855 distance: 120 - 121: 8.716 distance: 120 - 122: 4.522 distance: 125 - 127: 3.051 distance: 127 - 128: 3.359 distance: 129 - 130: 23.221 distance: 130 - 131: 24.221 distance: 130 - 133: 17.595 distance: 131 - 132: 20.600 distance: 131 - 137: 29.169 distance: 133 - 134: 15.892 distance: 134 - 135: 16.359 distance: 134 - 136: 16.155 distance: 137 - 138: 10.292 distance: 138 - 139: 26.401 distance: 138 - 141: 28.046 distance: 139 - 140: 11.470 distance: 139 - 145: 17.615 distance: 141 - 142: 24.879 distance: 142 - 143: 7.143 distance: 143 - 144: 6.582 distance: 145 - 146: 6.949 distance: 146 - 147: 11.020 distance: 146 - 149: 7.644 distance: 147 - 148: 11.450 distance: 147 - 156: 13.188 distance: 149 - 150: 8.063 distance: 150 - 151: 3.317 distance: 151 - 152: 4.081 distance: 156 - 157: 14.675 distance: 157 - 158: 9.160 distance: 158 - 159: 8.805 distance: 158 - 160: 12.245 distance: 160 - 161: 15.748 distance: 161 - 162: 18.815 distance: 161 - 164: 26.601 distance: 162 - 163: 14.370 distance: 162 - 168: 29.600 distance: 164 - 165: 18.487 distance: 165 - 166: 15.471 distance: 165 - 167: 12.508 distance: 169 - 170: 31.773 distance: 169 - 172: 23.474 distance: 170 - 171: 20.091 distance: 170 - 177: 26.919 distance: 172 - 173: 18.383 distance: 173 - 174: 14.358 distance: 174 - 175: 14.138 distance: 175 - 176: 18.428 distance: 177 - 178: 20.632 distance: 177 - 183: 16.949 distance: 178 - 179: 17.652 distance: 178 - 181: 15.064 distance: 179 - 180: 4.756 distance: 179 - 184: 6.463 distance: 181 - 182: 4.990 distance: 182 - 183: 5.352