Starting phenix.real_space_refine on Tue Mar 3 18:55:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u6e_26364/03_2026/7u6e_26364.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u6e_26364/03_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_26364/03_2026/7u6e_26364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u6e_26364/03_2026/7u6e_26364.map" model { file = "/net/cci-nas-00/data/ceres_data/7u6e_26364/03_2026/7u6e_26364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u6e_26364/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.80, per 1000 atoms: 0.22 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: 0.76 Conformation dependent library (CDL) restraints added in 276.6 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: 0.32 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: 1.49 Time building geometry restraints manager: 0.99 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: 4557 17.44 - 34.89: 373 34.89 - 52.33: 89 52.33 - 69.77: 21 69.77 - 87.22: 12 Dihedral angle restraints: 5052 sinusoidal: 2216 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 5049 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: 2.120 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.310 Find NCS groups from input model: 0.050 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:7.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 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 : 14.187 87.215 3150 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 covalent geometry : bond 0.00830 ( 8187) covalent geometry : angle 0.91358 (11079) SS BOND : bond 0.00951 ( 24) SS BOND : angle 1.65478 ( 48) hydrogen bonds : bond 0.19280 ( 207) hydrogen bonds : angle 9.47748 ( 552) Misc. bond : bond 0.10637 ( 2) link_BETA1-4 : bond 0.01320 ( 1) link_BETA1-4 : angle 7.55203 ( 3) link_NAG-ASN : bond 0.00284 ( 7) link_NAG-ASN : angle 5.24460 ( 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 : 0.315 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: 0.6106 time to fit residues: 127.3171 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 : 0.322 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.159745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.142706 restraints weight = 12928.521| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 2.06 r_work: 0.4089 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3958 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 8221 Z= 0.225 Angle : 0.827 12.730 11151 Z= 0.426 Chirality : 0.051 0.352 1221 Planarity : 0.005 0.044 1416 Dihedral : 8.141 55.237 1237 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.86 % Allowed : 16.12 % 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 0.020 0.002 TYR E 60 PHE 0.031 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 covalent geometry : bond 0.00512 ( 8187) covalent geometry : angle 0.79417 (11079) SS BOND : bond 0.00661 ( 24) SS BOND : angle 2.49814 ( 48) hydrogen bonds : bond 0.05262 ( 207) hydrogen bonds : angle 6.77058 ( 552) Misc. bond : bond 0.00068 ( 2) link_BETA1-4 : bond 0.00584 ( 1) link_BETA1-4 : angle 4.73954 ( 3) link_NAG-ASN : bond 0.00342 ( 7) link_NAG-ASN : angle 3.58882 ( 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 142 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7627 (mp0) cc_final: 0.7118 (mp0) REVERT: E 16 ASN cc_start: 0.5669 (OUTLIER) cc_final: 0.5460 (p0) REVERT: E 110 MET cc_start: 0.8095 (mmp) cc_final: 0.7316 (mmt) REVERT: E 426 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7684 (mt) REVERT: E 483 ASP cc_start: 0.7106 (p0) cc_final: 0.6847 (p0) REVERT: E 553 MET cc_start: 0.7151 (mpp) cc_final: 0.6714 (mpp) REVERT: F 318 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6958 (tp30) REVERT: F 504 MET cc_start: 0.8383 (ptp) cc_final: 0.8093 (mtp) REVERT: F 521 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6997 (tm-30) REVERT: F 579 TYR cc_start: 0.7776 (m-80) cc_final: 0.7396 (m-80) REVERT: G 8 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8064 (pp30) outliers start: 34 outliers final: 7 residues processed: 133 average time/residue: 0.4924 time to fit residues: 70.1372 Evaluate side-chains 96 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 5 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 0.0060 chunk 57 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 ASN E 348 ASN F 405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.160019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.143453 restraints weight = 12953.017| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 2.03 r_work: 0.4110 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3977 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8221 Z= 0.176 Angle : 0.721 9.314 11151 Z= 0.368 Chirality : 0.048 0.310 1221 Planarity : 0.004 0.039 1416 Dihedral : 7.527 53.515 1235 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.86 % Allowed : 18.05 % Favored : 78.09 % 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: -1.74 (0.25), residues: 954 helix: -0.55 (0.39), residues: 173 sheet: -1.26 (0.39), residues: 170 loop : -1.32 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 498 TYR 0.015 0.002 TYR E 60 PHE 0.021 0.002 PHE E 482 TRP 0.023 0.002 TRP F 559 HIS 0.009 0.002 HIS E 263 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 8187) covalent geometry : angle 0.69833 (11079) SS BOND : bond 0.00554 ( 24) SS BOND : angle 1.73478 ( 48) hydrogen bonds : bond 0.04434 ( 207) hydrogen bonds : angle 6.24514 ( 552) Misc. bond : bond 0.00048 ( 2) link_BETA1-4 : bond 0.00338 ( 1) link_BETA1-4 : angle 4.32196 ( 3) link_NAG-ASN : bond 0.00386 ( 7) link_NAG-ASN : angle 3.04762 ( 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 128 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7502 (mp0) cc_final: 0.6987 (mp0) REVERT: E 110 MET cc_start: 0.8086 (mmp) cc_final: 0.7309 (mmt) REVERT: E 355 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7398 (tp30) REVERT: E 406 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7267 (mm-40) REVERT: F 318 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6993 (tp30) REVERT: F 417 HIS cc_start: 0.7350 (OUTLIER) cc_final: 0.6827 (t70) REVERT: F 579 TYR cc_start: 0.7740 (m-80) cc_final: 0.7355 (m-80) REVERT: F 698 GLU cc_start: 0.8135 (tp30) cc_final: 0.7917 (tm-30) REVERT: F 706 GLU cc_start: 0.7800 (tt0) cc_final: 0.7283 (pt0) REVERT: G 8 GLN cc_start: 0.8515 (tm-30) cc_final: 0.7911 (pp30) outliers start: 34 outliers final: 13 residues processed: 116 average time/residue: 0.4631 time to fit residues: 57.5527 Evaluate side-chains 92 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain E residue 264 HIS Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 355 GLU 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 472 LEU 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: 0.8980 chunk 35 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 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 = 0.4394 r_free = 0.4394 target = 0.158422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.141615 restraints weight = 13145.568| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 2.06 r_work: 0.4085 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3949 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8221 Z= 0.202 Angle : 0.716 8.137 11151 Z= 0.364 Chirality : 0.049 0.322 1221 Planarity : 0.004 0.042 1416 Dihedral : 7.417 53.711 1235 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.52 % Allowed : 18.96 % 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: -1.78 (0.25), residues: 954 helix: -0.50 (0.39), residues: 173 sheet: -1.33 (0.40), residues: 165 loop : -1.37 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 498 TYR 0.018 0.002 TYR E 60 PHE 0.021 0.002 PHE E 89 TRP 0.023 0.002 TRP F 559 HIS 0.005 0.002 HIS E 144 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 8187) covalent geometry : angle 0.69362 (11079) SS BOND : bond 0.00519 ( 24) SS BOND : angle 1.67559 ( 48) hydrogen bonds : bond 0.04369 ( 207) hydrogen bonds : angle 6.11121 ( 552) Misc. bond : bond 0.00016 ( 2) link_BETA1-4 : bond 0.00492 ( 1) link_BETA1-4 : angle 4.32832 ( 3) link_NAG-ASN : bond 0.00305 ( 7) link_NAG-ASN : angle 3.03068 ( 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 117 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7541 (mp0) cc_final: 0.6995 (mp0) REVERT: E 44 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7829 (mm-30) REVERT: E 355 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7277 (tp30) REVERT: E 406 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7217 (mm-40) REVERT: E 426 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7620 (mp) REVERT: F 350 LEU cc_start: 0.4277 (OUTLIER) cc_final: 0.3835 (tt) REVERT: F 460 LYS cc_start: 0.8184 (mmmm) cc_final: 0.7889 (mtpt) REVERT: F 579 TYR cc_start: 0.7748 (m-80) cc_final: 0.7389 (m-80) REVERT: F 706 GLU cc_start: 0.7717 (tt0) cc_final: 0.7179 (pt0) REVERT: G 8 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8145 (pp30) outliers start: 31 outliers final: 9 residues processed: 107 average time/residue: 0.5470 time to fit residues: 62.2672 Evaluate side-chains 86 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain E residue 355 GLU 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 474 LYS Chi-restraints excluded: chain F residue 578 THR 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: 0.6980 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 69 optimal weight: 0.0770 chunk 17 optimal weight: 0.0980 chunk 49 optimal weight: 0.0770 chunk 93 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4436 r_free = 0.4436 target = 0.161639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.144919 restraints weight = 12993.928| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 2.05 r_work: 0.4115 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3982 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8221 Z= 0.131 Angle : 0.638 7.138 11151 Z= 0.326 Chirality : 0.046 0.282 1221 Planarity : 0.004 0.037 1416 Dihedral : 6.966 51.167 1235 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.75 % Allowed : 19.64 % Favored : 76.62 % 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: -1.68 (0.25), residues: 954 helix: -0.46 (0.39), residues: 173 sheet: -1.24 (0.41), residues: 159 loop : -1.30 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 409 TYR 0.012 0.001 TYR E 60 PHE 0.019 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 covalent geometry : bond 0.00298 ( 8187) covalent geometry : angle 0.62078 (11079) SS BOND : bond 0.00574 ( 24) SS BOND : angle 1.28187 ( 48) hydrogen bonds : bond 0.03762 ( 207) hydrogen bonds : angle 5.85910 ( 552) Misc. bond : bond 0.00023 ( 2) link_BETA1-4 : bond 0.00266 ( 1) link_BETA1-4 : angle 3.63324 ( 3) link_NAG-ASN : bond 0.00369 ( 7) link_NAG-ASN : angle 2.70480 ( 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 123 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7534 (mp0) cc_final: 0.6990 (mp0) REVERT: E 110 MET cc_start: 0.8057 (mmp) cc_final: 0.7375 (mmt) REVERT: E 355 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7345 (tp30) REVERT: E 406 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7243 (mm-40) REVERT: E 426 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7788 (mt) REVERT: E 483 ASP cc_start: 0.6723 (p0) cc_final: 0.6500 (p0) REVERT: F 579 TYR cc_start: 0.7678 (m-80) cc_final: 0.7304 (m-80) REVERT: F 706 GLU cc_start: 0.7607 (tt0) cc_final: 0.7047 (pt0) REVERT: G 8 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8241 (pp30) outliers start: 33 outliers final: 11 residues processed: 109 average time/residue: 0.4565 time to fit residues: 53.5705 Evaluate side-chains 87 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 355 GLU 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 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 ************** Weight determination summary: number of chunks: 94 random chunks: chunk 22 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 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 = 0.4413 r_free = 0.4413 target = 0.159633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.143120 restraints weight = 12881.323| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 2.01 r_work: 0.4110 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3978 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8221 Z= 0.166 Angle : 0.671 10.355 11151 Z= 0.342 Chirality : 0.047 0.289 1221 Planarity : 0.004 0.060 1416 Dihedral : 7.002 51.377 1234 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.09 % Allowed : 20.09 % Favored : 75.82 % 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: -1.69 (0.26), residues: 954 helix: -0.37 (0.40), residues: 173 sheet: -1.22 (0.41), residues: 159 loop : -1.35 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 498 TYR 0.015 0.001 TYR E 60 PHE 0.019 0.002 PHE E 89 TRP 0.032 0.002 TRP F 559 HIS 0.005 0.001 HIS E 185 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8187) covalent geometry : angle 0.64553 (11079) SS BOND : bond 0.00467 ( 24) SS BOND : angle 2.05547 ( 48) hydrogen bonds : bond 0.03895 ( 207) hydrogen bonds : angle 5.84209 ( 552) Misc. bond : bond 0.00024 ( 2) link_BETA1-4 : bond 0.00274 ( 1) link_BETA1-4 : angle 3.98324 ( 3) link_NAG-ASN : bond 0.00300 ( 7) link_NAG-ASN : angle 2.71208 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 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 114 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 78 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7579 (mp0) cc_final: 0.7355 (mp0) REVERT: E 355 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7361 (tp30) REVERT: E 406 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7299 (mm-40) REVERT: E 426 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7806 (mt) REVERT: F 350 LEU cc_start: 0.4278 (OUTLIER) cc_final: 0.3889 (tt) REVERT: F 417 HIS cc_start: 0.7800 (OUTLIER) cc_final: 0.6504 (t70) REVERT: F 579 TYR cc_start: 0.7648 (m-80) cc_final: 0.7218 (m-80) REVERT: G 8 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8250 (pp30) outliers start: 36 outliers final: 12 residues processed: 104 average time/residue: 0.4698 time to fit residues: 52.3869 Evaluate side-chains 91 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 538 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 480 THR Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain G residue 1 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 79 optimal weight: 0.2980 chunk 18 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 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 = 0.4406 r_free = 0.4406 target = 0.158926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.142281 restraints weight = 13065.194| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 2.03 r_work: 0.4086 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3952 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8221 Z= 0.181 Angle : 0.686 10.475 11151 Z= 0.349 Chirality : 0.047 0.302 1221 Planarity : 0.004 0.053 1416 Dihedral : 7.022 52.023 1234 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.75 % Allowed : 21.57 % Favored : 74.69 % 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: -1.75 (0.26), residues: 954 helix: -0.34 (0.40), residues: 173 sheet: -1.32 (0.41), residues: 157 loop : -1.40 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 409 TYR 0.038 0.002 TYR F 367 PHE 0.019 0.002 PHE E 89 TRP 0.024 0.002 TRP F 559 HIS 0.004 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 8187) covalent geometry : angle 0.66351 (11079) SS BOND : bond 0.00414 ( 24) SS BOND : angle 1.86980 ( 48) hydrogen bonds : bond 0.03879 ( 207) hydrogen bonds : angle 5.87027 ( 552) Misc. bond : bond 0.00015 ( 2) link_BETA1-4 : bond 0.00586 ( 1) link_BETA1-4 : angle 4.13562 ( 3) link_NAG-ASN : bond 0.00254 ( 7) link_NAG-ASN : angle 2.66196 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 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 114 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 81 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: E 188 CYS cc_start: 0.5330 (OUTLIER) cc_final: 0.4717 (p) REVERT: E 355 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7083 (tp30) REVERT: E 383 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7463 (mmt180) REVERT: E 406 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7289 (mm-40) REVERT: E 426 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7853 (mt) REVERT: F 350 LEU cc_start: 0.4279 (OUTLIER) cc_final: 0.3907 (tt) REVERT: F 417 HIS cc_start: 0.7882 (OUTLIER) cc_final: 0.6514 (t70) REVERT: F 579 TYR cc_start: 0.7592 (m-80) cc_final: 0.7150 (m-80) REVERT: G 8 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8268 (pp30) outliers start: 33 outliers final: 14 residues processed: 106 average time/residue: 0.4802 time to fit residues: 54.6023 Evaluate side-chains 95 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 188 CYS Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 383 ARG Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 474 LYS 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 480 THR Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain H residue 2 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 73 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 52 optimal weight: 0.0980 chunk 89 optimal weight: 0.7980 chunk 21 optimal weight: 0.2980 chunk 76 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 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 = 0.4416 r_free = 0.4416 target = 0.159671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.142986 restraints weight = 12932.507| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 2.03 r_work: 0.4089 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3957 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8221 Z= 0.157 Angle : 0.675 8.774 11151 Z= 0.344 Chirality : 0.046 0.297 1221 Planarity : 0.005 0.082 1416 Dihedral : 6.904 51.461 1234 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.20 % Allowed : 21.34 % Favored : 74.46 % 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: -1.76 (0.26), residues: 954 helix: -0.39 (0.40), residues: 173 sheet: -1.37 (0.40), residues: 162 loop : -1.38 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 498 TYR 0.030 0.002 TYR F 367 PHE 0.017 0.002 PHE E 482 TRP 0.025 0.002 TRP E 551 HIS 0.004 0.001 HIS E 185 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8187) covalent geometry : angle 0.65580 (11079) SS BOND : bond 0.00363 ( 24) SS BOND : angle 1.63454 ( 48) hydrogen bonds : bond 0.03770 ( 207) hydrogen bonds : angle 5.76334 ( 552) Misc. bond : bond 0.00038 ( 2) link_BETA1-4 : bond 0.00449 ( 1) link_BETA1-4 : angle 3.86519 ( 3) link_NAG-ASN : bond 0.00281 ( 7) link_NAG-ASN : angle 2.54232 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 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 122 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: E 188 CYS cc_start: 0.5299 (OUTLIER) cc_final: 0.4867 (p) REVERT: E 355 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7144 (tp30) REVERT: E 383 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7429 (mmt180) REVERT: E 406 GLN cc_start: 0.7640 (mm-40) cc_final: 0.7266 (mm-40) REVERT: E 426 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7793 (mt) REVERT: F 350 LEU cc_start: 0.4449 (OUTLIER) cc_final: 0.4121 (tt) REVERT: F 417 HIS cc_start: 0.7950 (OUTLIER) cc_final: 0.6737 (t70) REVERT: F 579 TYR cc_start: 0.7602 (m-80) cc_final: 0.7198 (m-80) REVERT: G 8 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8208 (pp30) outliers start: 37 outliers final: 14 residues processed: 109 average time/residue: 0.4598 time to fit residues: 53.8392 Evaluate side-chains 97 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 188 CYS Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 383 ARG Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain E residue 553 MET 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 480 THR Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain H residue 2 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 55 optimal weight: 0.4980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 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 = 0.4411 r_free = 0.4411 target = 0.159173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.142552 restraints weight = 12904.758| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 2.03 r_work: 0.4094 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3961 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8221 Z= 0.167 Angle : 0.705 10.384 11151 Z= 0.357 Chirality : 0.047 0.298 1221 Planarity : 0.004 0.061 1416 Dihedral : 6.899 51.453 1234 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.50 % Allowed : 23.27 % Favored : 74.23 % 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: -1.77 (0.26), residues: 954 helix: -0.37 (0.39), residues: 173 sheet: -1.38 (0.40), residues: 162 loop : -1.39 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 409 TYR 0.028 0.002 TYR F 367 PHE 0.018 0.002 PHE E 89 TRP 0.036 0.002 TRP F 559 HIS 0.004 0.001 HIS E 185 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8187) covalent geometry : angle 0.68459 (11079) SS BOND : bond 0.00422 ( 24) SS BOND : angle 1.86833 ( 48) hydrogen bonds : bond 0.03967 ( 207) hydrogen bonds : angle 5.77590 ( 552) Misc. bond : bond 0.00018 ( 2) link_BETA1-4 : bond 0.00478 ( 1) link_BETA1-4 : angle 3.93723 ( 3) link_NAG-ASN : bond 0.00251 ( 7) link_NAG-ASN : angle 2.50265 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 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 102 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: E 188 CYS cc_start: 0.5293 (OUTLIER) cc_final: 0.4814 (p) REVERT: E 355 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7115 (tp30) REVERT: E 383 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7466 (mmt180) REVERT: E 406 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7283 (mm-40) REVERT: E 426 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7778 (mt) REVERT: F 350 LEU cc_start: 0.4315 (OUTLIER) cc_final: 0.4003 (tt) REVERT: F 417 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.6716 (t70) REVERT: F 501 LEU cc_start: 0.8361 (mp) cc_final: 0.8024 (mp) REVERT: F 579 TYR cc_start: 0.7603 (m-80) cc_final: 0.7302 (m-80) REVERT: G 8 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8222 (pp30) outliers start: 22 outliers final: 10 residues processed: 97 average time/residue: 0.5259 time to fit residues: 54.5245 Evaluate side-chains 92 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 188 CYS Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 383 ARG Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 474 LYS 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 480 THR Chi-restraints excluded: chain F residue 578 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.0670 chunk 82 optimal weight: 0.0870 chunk 18 optimal weight: 0.0670 chunk 40 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.160544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.144046 restraints weight = 12885.221| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.02 r_work: 0.4111 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3980 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8221 Z= 0.140 Angle : 0.678 10.222 11151 Z= 0.344 Chirality : 0.046 0.285 1221 Planarity : 0.004 0.060 1416 Dihedral : 6.741 51.406 1234 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.04 % Allowed : 23.95 % Favored : 74.01 % 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: -1.77 (0.26), residues: 954 helix: -0.39 (0.39), residues: 173 sheet: -1.47 (0.40), residues: 157 loop : -1.35 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 409 TYR 0.023 0.001 TYR F 367 PHE 0.021 0.002 PHE F 572 TRP 0.033 0.002 TRP F 559 HIS 0.004 0.001 HIS E 185 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8187) covalent geometry : angle 0.66107 (11079) SS BOND : bond 0.00360 ( 24) SS BOND : angle 1.63705 ( 48) hydrogen bonds : bond 0.03746 ( 207) hydrogen bonds : angle 5.69794 ( 552) Misc. bond : bond 0.00021 ( 2) link_BETA1-4 : bond 0.00307 ( 1) link_BETA1-4 : angle 3.46038 ( 3) link_NAG-ASN : bond 0.00308 ( 7) link_NAG-ASN : angle 2.35478 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 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 102 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: E 188 CYS cc_start: 0.5210 (OUTLIER) cc_final: 0.4701 (p) REVERT: E 250 ASP cc_start: 0.6444 (t0) cc_final: 0.6110 (t0) REVERT: E 355 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6964 (tp30) REVERT: E 383 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7522 (mmt180) REVERT: E 406 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7300 (mm-40) REVERT: F 350 LEU cc_start: 0.4378 (OUTLIER) cc_final: 0.4118 (tt) REVERT: F 417 HIS cc_start: 0.8150 (OUTLIER) cc_final: 0.6953 (t70) REVERT: F 501 LEU cc_start: 0.8367 (mp) cc_final: 0.8021 (mp) REVERT: F 579 TYR cc_start: 0.7534 (m-80) cc_final: 0.7271 (m-80) REVERT: G 3 GLU cc_start: 0.5944 (mp0) cc_final: 0.5705 (tp30) REVERT: G 8 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8262 (pp30) outliers start: 18 outliers final: 9 residues processed: 101 average time/residue: 0.4892 time to fit residues: 52.8944 Evaluate side-chains 92 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 188 CYS Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 383 ARG Chi-restraints excluded: chain E residue 474 LYS 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 480 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.0170 chunk 64 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 55 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 56 optimal weight: 0.1980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 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 = 0.4420 r_free = 0.4420 target = 0.160023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.143514 restraints weight = 12814.813| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 2.02 r_work: 0.4111 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3979 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8221 Z= 0.153 Angle : 0.683 10.017 11151 Z= 0.348 Chirality : 0.046 0.284 1221 Planarity : 0.004 0.062 1416 Dihedral : 6.730 51.246 1234 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.16 % Allowed : 24.52 % Favored : 73.33 % 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: -1.78 (0.26), residues: 954 helix: -0.36 (0.39), residues: 173 sheet: -1.50 (0.40), residues: 157 loop : -1.37 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 409 TYR 0.023 0.001 TYR F 367 PHE 0.016 0.002 PHE E 89 TRP 0.031 0.002 TRP F 559 HIS 0.004 0.001 HIS E 185 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8187) covalent geometry : angle 0.66466 (11079) SS BOND : bond 0.00428 ( 24) SS BOND : angle 1.75902 ( 48) hydrogen bonds : bond 0.03782 ( 207) hydrogen bonds : angle 5.75404 ( 552) Misc. bond : bond 0.00017 ( 2) link_BETA1-4 : bond 0.00383 ( 1) link_BETA1-4 : angle 3.61771 ( 3) link_NAG-ASN : bond 0.00261 ( 7) link_NAG-ASN : angle 2.32358 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2642.30 seconds wall clock time: 45 minutes 43.76 seconds (2743.76 seconds total)