Starting phenix.real_space_refine on Fri Jul 25 23:14:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u6e_26364/07_2025/7u6e_26364.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u6e_26364/07_2025/7u6e_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_2025/7u6e_26364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u6e_26364/07_2025/7u6e_26364.map" model { file = "/net/cci-nas-00/data/ceres_data/7u6e_26364/07_2025/7u6e_26364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u6e_26364/07_2025/7u6e_26364.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.41, per 1000 atoms: 0.68 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: 2.87 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.11 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: 2.76 Time building geometry restraints manager: 2.83 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: 1.610 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.720 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:15.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.440 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (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 TRP 0.035 0.003 TRP F 414 HIS 0.012 0.002 HIS E 144 PHE 0.042 0.004 PHE E 89 TYR 0.025 0.004 TYR F 507 ARG 0.021 0.002 ARG F 717 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 7) link_NAG-ASN : angle 5.24460 ( 21) link_BETA1-4 : bond 0.01320 ( 1) link_BETA1-4 : angle 7.55203 ( 3) hydrogen bonds : bond 0.19280 ( 207) hydrogen bonds : angle 9.47748 ( 552) SS BOND : bond 0.00951 ( 24) SS BOND : angle 1.65478 ( 48) covalent geometry : bond 0.00830 ( 8187) covalent geometry : angle 0.91358 (11079) Misc. bond : bond 0.10637 ( 2) *********************** 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 : 1.037 Fit side-chains revert: symmetry clash REVERT: E 299 LEU cc_start: 0.7723 (tp) cc_final: 0.7523 (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: 0.6915 (mm-30) cc_final: 0.6641 (tp30) REVERT: F 423 GLN cc_start: 0.8025 (tp40) cc_final: 0.7755 (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: 1.2016 time to fit residues: 251.7459 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 : 0.864 ------------------------------------------------------------------------------- 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 79 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.0060 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 F 405 ASN F 548 HIS F 561 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.161195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.144256 restraints weight = 12842.907| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 2.05 r_work: 0.4115 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3982 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2690 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= 0.193 Angle : 0.804 12.251 11151 Z= 0.414 Chirality : 0.050 0.335 1221 Planarity : 0.005 0.046 1416 Dihedral : 8.027 53.472 1237 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.09 % Allowed : 15.10 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.25), residues: 954 helix: -0.57 (0.39), residues: 173 sheet: -1.08 (0.40), residues: 169 loop : -1.43 (0.22), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 559 HIS 0.008 0.002 HIS E 275 PHE 0.032 0.003 PHE E 482 TYR 0.017 0.002 TYR E 60 ARG 0.006 0.001 ARG B 22 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 7) link_NAG-ASN : angle 3.43529 ( 21) link_BETA1-4 : bond 0.00431 ( 1) link_BETA1-4 : angle 4.32365 ( 3) hydrogen bonds : bond 0.04944 ( 207) hydrogen bonds : angle 6.63399 ( 552) SS BOND : bond 0.00577 ( 24) SS BOND : angle 2.40505 ( 48) covalent geometry : bond 0.00439 ( 8187) covalent geometry : angle 0.77357 (11079) Misc. bond : bond 0.00325 ( 2) *********************** 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 152 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7652 (mp0) cc_final: 0.7149 (mp0) REVERT: E 44 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7775 (mm-30) REVERT: E 73 LYS cc_start: 0.8151 (pttp) cc_final: 0.7861 (pptt) REVERT: E 110 MET cc_start: 0.8051 (mmp) cc_final: 0.7299 (mmt) REVERT: E 299 LEU cc_start: 0.8165 (tp) cc_final: 0.7686 (tp) REVERT: E 483 ASP cc_start: 0.7053 (p0) cc_final: 0.6799 (p0) REVERT: E 553 MET cc_start: 0.7122 (mpp) cc_final: 0.6784 (mpp) REVERT: F 318 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7062 (tp30) REVERT: F 350 LEU cc_start: 0.3924 (OUTLIER) cc_final: 0.3586 (tt) REVERT: F 417 HIS cc_start: 0.7615 (OUTLIER) cc_final: 0.7105 (t70) REVERT: F 504 MET cc_start: 0.8342 (ptp) cc_final: 0.8084 (mtp) REVERT: F 579 TYR cc_start: 0.7786 (m-80) cc_final: 0.7331 (m-80) REVERT: G 8 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8072 (pp30) outliers start: 36 outliers final: 6 residues processed: 140 average time/residue: 1.0382 time to fit residues: 155.6615 Evaluate side-chains 96 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 65 optimal weight: 0.8980 chunk 25 optimal weight: 0.0020 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 0.0060 overall best weight: 0.3404 ------------------------------------------------------------------------------- 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 E 513 GLN E 561 GLN F 405 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.161878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.145335 restraints weight = 12971.017| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 2.04 r_work: 0.4130 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3998 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8221 Z= 0.148 Angle : 0.696 11.362 11151 Z= 0.354 Chirality : 0.047 0.289 1221 Planarity : 0.004 0.037 1416 Dihedral : 7.317 52.327 1235 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.75 % Allowed : 17.71 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.25), residues: 954 helix: -0.60 (0.38), residues: 173 sheet: -1.23 (0.39), residues: 171 loop : -1.25 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 559 HIS 0.005 0.001 HIS E 185 PHE 0.020 0.002 PHE F 705 TYR 0.014 0.001 TYR E 60 ARG 0.009 0.001 ARG E 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 7) link_NAG-ASN : angle 2.90987 ( 21) link_BETA1-4 : bond 0.00362 ( 1) link_BETA1-4 : angle 4.03738 ( 3) hydrogen bonds : bond 0.04255 ( 207) hydrogen bonds : angle 6.17566 ( 552) SS BOND : bond 0.00649 ( 24) SS BOND : angle 1.71908 ( 48) covalent geometry : bond 0.00329 ( 8187) covalent geometry : angle 0.67423 (11079) Misc. bond : bond 0.00019 ( 2) *********************** 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 127 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7499 (mp0) cc_final: 0.6971 (mp0) REVERT: E 110 MET cc_start: 0.7999 (mmp) cc_final: 0.7289 (mmt) REVERT: E 299 LEU cc_start: 0.8163 (tp) cc_final: 0.7626 (tp) REVERT: E 406 GLN cc_start: 0.7575 (mm-40) cc_final: 0.7240 (mm-40) REVERT: E 426 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7760 (mt) REVERT: E 483 ASP cc_start: 0.6885 (p0) cc_final: 0.6640 (p0) REVERT: E 553 MET cc_start: 0.6661 (mpp) cc_final: 0.6324 (mpp) REVERT: F 350 LEU cc_start: 0.4182 (OUTLIER) cc_final: 0.3710 (tt) REVERT: F 417 HIS cc_start: 0.7646 (OUTLIER) cc_final: 0.6816 (t70) REVERT: F 579 TYR cc_start: 0.7747 (m-80) cc_final: 0.7341 (m-80) REVERT: F 706 GLU cc_start: 0.7790 (tt0) cc_final: 0.7289 (pt0) REVERT: G 8 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8194 (pp30) REVERT: H 2 LEU cc_start: 0.7664 (mp) cc_final: 0.7422 (mp) outliers start: 33 outliers final: 9 residues processed: 115 average time/residue: 1.1618 time to fit residues: 143.1940 Evaluate side-chains 88 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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 571 THR Chi-restraints excluded: chain F residue 578 THR 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 1 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 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 = 0.4393 r_free = 0.4393 target = 0.158375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.141556 restraints weight = 12896.080| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 2.03 r_work: 0.4082 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3949 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8221 Z= 0.223 Angle : 0.740 9.430 11151 Z= 0.374 Chirality : 0.049 0.319 1221 Planarity : 0.004 0.043 1416 Dihedral : 7.365 53.460 1235 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.29 % Allowed : 19.07 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.25), residues: 954 helix: -0.61 (0.39), residues: 173 sheet: -1.32 (0.40), residues: 165 loop : -1.37 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 551 HIS 0.006 0.002 HIS E 144 PHE 0.025 0.003 PHE E 89 TYR 0.022 0.002 TYR E 60 ARG 0.005 0.001 ARG E 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 7) link_NAG-ASN : angle 3.02244 ( 21) link_BETA1-4 : bond 0.00514 ( 1) link_BETA1-4 : angle 4.47865 ( 3) hydrogen bonds : bond 0.04363 ( 207) hydrogen bonds : angle 6.08321 ( 552) SS BOND : bond 0.00476 ( 24) SS BOND : angle 1.93669 ( 48) covalent geometry : bond 0.00514 ( 8187) covalent geometry : angle 0.71532 (11079) Misc. bond : bond 0.00026 ( 2) *********************** 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 113 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7559 (mp0) cc_final: 0.7005 (mp0) REVERT: E 299 LEU cc_start: 0.8219 (tp) cc_final: 0.7773 (tp) REVERT: E 406 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7229 (mm-40) REVERT: E 426 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7641 (mp) REVERT: F 382 PHE cc_start: 0.8151 (m-80) cc_final: 0.7910 (m-80) REVERT: F 460 LYS cc_start: 0.7789 (mmmm) cc_final: 0.7578 (mtpt) REVERT: F 579 TYR cc_start: 0.7730 (m-80) cc_final: 0.7309 (m-80) REVERT: F 698 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7514 (tm-30) REVERT: F 706 GLU cc_start: 0.7710 (tt0) cc_final: 0.7185 (pt0) REVERT: G 8 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8239 (pp30) REVERT: H 2 LEU cc_start: 0.7635 (mp) cc_final: 0.7431 (mp) outliers start: 29 outliers final: 12 residues processed: 102 average time/residue: 1.0764 time to fit residues: 118.2438 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 : 0.853 ------------------------------------------------------------------------------- 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 233 LEU 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 377 VAL Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 559 TRP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 36 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.158239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.141496 restraints weight = 12861.519| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.02 r_work: 0.4071 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3938 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8221 Z= 0.193 Angle : 0.687 8.801 11151 Z= 0.350 Chirality : 0.048 0.307 1221 Planarity : 0.004 0.053 1416 Dihedral : 7.235 53.794 1235 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.86 % Allowed : 19.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.25), residues: 954 helix: -0.52 (0.40), residues: 173 sheet: -1.27 (0.41), residues: 159 loop : -1.41 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 551 HIS 0.007 0.001 HIS E 199 PHE 0.020 0.002 PHE E 89 TYR 0.017 0.002 TYR E 60 ARG 0.011 0.001 ARG E 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 7) link_NAG-ASN : angle 2.89790 ( 21) link_BETA1-4 : bond 0.00629 ( 1) link_BETA1-4 : angle 4.28673 ( 3) hydrogen bonds : bond 0.04024 ( 207) hydrogen bonds : angle 5.90765 ( 552) SS BOND : bond 0.00681 ( 24) SS BOND : angle 1.54294 ( 48) covalent geometry : bond 0.00442 ( 8187) covalent geometry : angle 0.66601 (11079) Misc. bond : bond 0.00040 ( 2) *********************** 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 122 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: E 38 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7697 (mtt) REVERT: E 406 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7277 (mm-40) REVERT: E 426 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7794 (mt) REVERT: F 350 LEU cc_start: 0.4269 (OUTLIER) cc_final: 0.3821 (tt) REVERT: F 382 PHE cc_start: 0.8142 (m-80) cc_final: 0.7919 (m-80) REVERT: F 579 TYR cc_start: 0.7758 (m-80) cc_final: 0.7369 (m-80) REVERT: F 698 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7454 (tm-30) REVERT: F 706 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7130 (pt0) REVERT: G 8 GLN cc_start: 0.8544 (tm-30) cc_final: 0.7880 (pp30) REVERT: H 14 TYR cc_start: 0.6581 (m-10) cc_final: 0.6344 (m-10) outliers start: 34 outliers final: 12 residues processed: 108 average time/residue: 1.4415 time to fit residues: 166.9754 Evaluate side-chains 93 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 56 MET 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 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 480 THR Chi-restraints excluded: chain F residue 559 TRP Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 706 GLU 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 74 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4384 r_free = 0.4384 target = 0.157658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.140917 restraints weight = 12903.334| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.03 r_work: 0.4070 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3936 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8221 Z= 0.195 Angle : 0.697 9.458 11151 Z= 0.354 Chirality : 0.048 0.329 1221 Planarity : 0.004 0.051 1416 Dihedral : 7.202 53.729 1234 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.97 % Allowed : 21.00 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.25), residues: 954 helix: -0.48 (0.40), residues: 173 sheet: -1.32 (0.41), residues: 157 loop : -1.46 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 551 HIS 0.005 0.001 HIS E 144 PHE 0.021 0.002 PHE E 89 TYR 0.017 0.002 TYR E 60 ARG 0.008 0.001 ARG E 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 7) link_NAG-ASN : angle 2.81379 ( 21) link_BETA1-4 : bond 0.00501 ( 1) link_BETA1-4 : angle 4.24944 ( 3) hydrogen bonds : bond 0.04080 ( 207) hydrogen bonds : angle 5.95662 ( 552) SS BOND : bond 0.00446 ( 24) SS BOND : angle 2.10061 ( 48) covalent geometry : bond 0.00451 ( 8187) covalent geometry : angle 0.67121 (11079) Misc. bond : bond 0.00024 ( 2) *********************** 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 115 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 80 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: E 406 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7268 (mm-40) REVERT: E 426 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7722 (mt) REVERT: F 382 PHE cc_start: 0.8246 (m-80) cc_final: 0.8021 (m-80) REVERT: F 579 TYR cc_start: 0.7722 (m-80) cc_final: 0.7429 (m-80) REVERT: F 698 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7215 (tm-30) REVERT: F 706 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7129 (pt0) REVERT: H 10 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.6268 (tt0) outliers start: 35 outliers final: 15 residues processed: 104 average time/residue: 0.9751 time to fit residues: 109.2755 Evaluate side-chains 94 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain E residue 538 LEU Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 559 TRP Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 706 GLU Chi-restraints excluded: chain H residue 10 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 15 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 77 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.156432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.139913 restraints weight = 12954.850| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.01 r_work: 0.4063 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3932 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8221 Z= 0.208 Angle : 0.711 11.281 11151 Z= 0.358 Chirality : 0.048 0.337 1221 Planarity : 0.005 0.069 1416 Dihedral : 7.236 54.814 1234 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.09 % Allowed : 21.91 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.26), residues: 954 helix: -0.56 (0.39), residues: 173 sheet: -1.41 (0.40), residues: 164 loop : -1.48 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 551 HIS 0.004 0.001 HIS E 144 PHE 0.022 0.002 PHE E 89 TYR 0.016 0.002 TYR E 60 ARG 0.018 0.001 ARG E 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 7) link_NAG-ASN : angle 2.80618 ( 21) link_BETA1-4 : bond 0.00613 ( 1) link_BETA1-4 : angle 4.27961 ( 3) hydrogen bonds : bond 0.04043 ( 207) hydrogen bonds : angle 5.96199 ( 552) SS BOND : bond 0.00426 ( 24) SS BOND : angle 1.73612 ( 48) covalent geometry : bond 0.00486 ( 8187) covalent geometry : angle 0.68970 (11079) Misc. bond : bond 0.00042 ( 2) *********************** 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 117 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 81 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 406 GLN cc_start: 0.7634 (mm-40) cc_final: 0.7221 (mm-40) REVERT: E 426 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7733 (mt) REVERT: F 350 LEU cc_start: 0.4518 (OUTLIER) cc_final: 0.4129 (tt) REVERT: F 382 PHE cc_start: 0.8192 (m-80) cc_final: 0.7988 (m-80) REVERT: F 501 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8307 (mt) REVERT: F 579 TYR cc_start: 0.7702 (m-80) cc_final: 0.7388 (m-80) REVERT: F 698 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7202 (tm-30) REVERT: F 706 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7116 (pt0) outliers start: 36 outliers final: 19 residues processed: 102 average time/residue: 1.0422 time to fit residues: 113.9577 Evaluate side-chains 102 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 44 GLU 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 339 SER Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 467 SER 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 480 THR Chi-restraints excluded: chain F residue 501 LEU Chi-restraints excluded: chain F residue 559 TRP 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 F residue 706 GLU Chi-restraints excluded: chain H residue 10 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 89 optimal weight: 0.0370 chunk 52 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 48 optimal weight: 0.0980 chunk 51 optimal weight: 0.1980 overall best weight: 0.2858 ------------------------------------------------------------------------------- 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 = 0.4426 r_free = 0.4426 target = 0.160701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.143911 restraints weight = 13057.534| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 2.06 r_work: 0.4112 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3981 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8221 Z= 0.128 Angle : 0.632 8.874 11151 Z= 0.323 Chirality : 0.045 0.306 1221 Planarity : 0.004 0.044 1416 Dihedral : 6.816 51.211 1234 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.72 % Allowed : 23.50 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.26), residues: 954 helix: -0.50 (0.39), residues: 173 sheet: -1.35 (0.40), residues: 162 loop : -1.36 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 551 HIS 0.003 0.001 HIS B 10 PHE 0.015 0.002 PHE F 705 TYR 0.011 0.001 TYR E 507 ARG 0.012 0.001 ARG E 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 7) link_NAG-ASN : angle 2.48659 ( 21) link_BETA1-4 : bond 0.00286 ( 1) link_BETA1-4 : angle 3.49484 ( 3) hydrogen bonds : bond 0.03585 ( 207) hydrogen bonds : angle 5.71794 ( 552) SS BOND : bond 0.00305 ( 24) SS BOND : angle 1.32930 ( 48) covalent geometry : bond 0.00295 ( 8187) covalent geometry : angle 0.61597 (11079) Misc. bond : bond 0.00047 ( 2) *********************** 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 111 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 110 MET cc_start: 0.8055 (mmp) cc_final: 0.7290 (mmt) REVERT: E 250 ASP cc_start: 0.6373 (t0) cc_final: 0.6048 (t0) REVERT: E 406 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7307 (mm-40) REVERT: E 426 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7892 (mt) REVERT: F 579 TYR cc_start: 0.7659 (m-80) cc_final: 0.7380 (m-80) REVERT: F 698 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7176 (tm-30) REVERT: F 706 GLU cc_start: 0.7574 (tt0) cc_final: 0.7110 (pt0) outliers start: 24 outliers final: 10 residues processed: 102 average time/residue: 1.0970 time to fit residues: 120.3747 Evaluate side-chains 90 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 300 LEU 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 480 THR Chi-restraints excluded: chain F residue 559 TRP Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 696 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.156944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.140108 restraints weight = 13130.970| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.05 r_work: 0.4063 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3930 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8221 Z= 0.218 Angle : 0.706 8.919 11151 Z= 0.359 Chirality : 0.049 0.323 1221 Planarity : 0.005 0.089 1416 Dihedral : 7.079 53.881 1234 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.84 % Allowed : 23.61 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.25), residues: 954 helix: -0.56 (0.39), residues: 173 sheet: -1.37 (0.40), residues: 159 loop : -1.47 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 551 HIS 0.004 0.001 HIS E 199 PHE 0.023 0.002 PHE E 89 TYR 0.015 0.002 TYR E 60 ARG 0.020 0.001 ARG E 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 7) link_NAG-ASN : angle 2.65436 ( 21) link_BETA1-4 : bond 0.00594 ( 1) link_BETA1-4 : angle 4.39599 ( 3) hydrogen bonds : bond 0.03984 ( 207) hydrogen bonds : angle 5.93013 ( 552) SS BOND : bond 0.00439 ( 24) SS BOND : angle 1.52156 ( 48) covalent geometry : bond 0.00511 ( 8187) covalent geometry : angle 0.68765 (11079) Misc. bond : bond 0.00047 ( 2) *********************** 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 108 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: E 250 ASP cc_start: 0.6658 (t0) cc_final: 0.6369 (t0) REVERT: E 406 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7324 (mm-40) REVERT: E 426 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7820 (mt) REVERT: F 579 TYR cc_start: 0.7703 (m-80) cc_final: 0.7430 (m-80) REVERT: F 698 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7231 (tm-30) REVERT: F 706 GLU cc_start: 0.7655 (tt0) cc_final: 0.7122 (pt0) outliers start: 25 outliers final: 15 residues processed: 98 average time/residue: 0.9853 time to fit residues: 104.1256 Evaluate side-chains 95 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 377 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 538 LEU Chi-restraints excluded: chain E residue 553 MET Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 559 TRP Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 696 LEU Chi-restraints excluded: chain H residue 10 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 80 optimal weight: 0.0980 chunk 90 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.158689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.142121 restraints weight = 12931.974| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.02 r_work: 0.4095 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3963 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8221 Z= 0.157 Angle : 0.675 9.998 11151 Z= 0.342 Chirality : 0.047 0.308 1221 Planarity : 0.004 0.063 1416 Dihedral : 6.920 52.287 1234 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.58 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 : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.25), residues: 954 helix: -0.63 (0.38), residues: 173 sheet: -1.39 (0.40), residues: 157 loop : -1.45 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 551 HIS 0.004 0.001 HIS E 185 PHE 0.018 0.002 PHE F 565 TYR 0.011 0.001 TYR E 60 ARG 0.013 0.001 ARG E 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 7) link_NAG-ASN : angle 2.51803 ( 21) link_BETA1-4 : bond 0.00496 ( 1) link_BETA1-4 : angle 3.87509 ( 3) hydrogen bonds : bond 0.03743 ( 207) hydrogen bonds : angle 5.86111 ( 552) SS BOND : bond 0.00318 ( 24) SS BOND : angle 1.36902 ( 48) covalent geometry : bond 0.00366 ( 8187) covalent geometry : angle 0.65887 (11079) Misc. bond : bond 0.00026 ( 2) ********************** 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 101 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: E 250 ASP cc_start: 0.6524 (t0) cc_final: 0.6266 (t0) REVERT: E 406 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7282 (mm-40) REVERT: E 426 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7873 (mt) REVERT: F 579 TYR cc_start: 0.7680 (m-80) cc_final: 0.7402 (m-80) REVERT: F 698 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7461 (tm-30) REVERT: F 706 GLU cc_start: 0.7568 (tt0) cc_final: 0.7051 (pt0) outliers start: 19 outliers final: 16 residues processed: 95 average time/residue: 1.2174 time to fit residues: 124.6915 Evaluate side-chains 96 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 300 LEU Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 559 TRP Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 696 LEU Chi-restraints excluded: chain H residue 10 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 55 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.0570 chunk 42 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.157979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.141378 restraints weight = 12992.007| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 2.02 r_work: 0.4076 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3945 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4439 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= 0.181 Angle : 0.704 11.418 11151 Z= 0.353 Chirality : 0.047 0.311 1221 Planarity : 0.005 0.092 1416 Dihedral : 6.978 52.879 1234 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.61 % Allowed : 24.18 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.25), residues: 954 helix: -0.64 (0.38), residues: 173 sheet: -1.50 (0.40), residues: 157 loop : -1.48 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 551 HIS 0.005 0.001 HIS E 144 PHE 0.019 0.002 PHE E 89 TYR 0.012 0.002 TYR E 60 ARG 0.020 0.001 ARG E 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 7) link_NAG-ASN : angle 2.55282 ( 21) link_BETA1-4 : bond 0.00579 ( 1) link_BETA1-4 : angle 4.22525 ( 3) hydrogen bonds : bond 0.03859 ( 207) hydrogen bonds : angle 5.90229 ( 552) SS BOND : bond 0.00359 ( 24) SS BOND : angle 1.39281 ( 48) covalent geometry : bond 0.00426 ( 8187) covalent geometry : angle 0.68751 (11079) Misc. bond : bond 0.00024 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5896.79 seconds wall clock time: 105 minutes 7.37 seconds (6307.37 seconds total)