Starting phenix.real_space_refine on Thu Jul 2 04:58:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fhb_50444/07_2026/9fhb_50444.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fhb_50444/07_2026/9fhb_50444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fhb_50444/07_2026/9fhb_50444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fhb_50444/07_2026/9fhb_50444.map" model { file = "/net/cci-nas-00/data/ceres_data/9fhb_50444/07_2026/9fhb_50444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fhb_50444/07_2026/9fhb_50444.cif" } resolution = 3.87 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= 0.050 sd= 0.131 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 2 7.16 5 S 42 5.16 5 C 4268 2.51 5 N 1171 2.21 5 O 1266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6751 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1069 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "B" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1123 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "C" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1982 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 12, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2447 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 3, 'TRANS': 317} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 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: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.50, per 1000 atoms: 0.22 Number of scatterers: 6751 At special positions: 0 Unit cell: (86.92, 98.58, 108.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 Ca 2 19.99 S 42 16.00 O 1266 8.00 N 1171 7.00 C 4268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG CYS C 266 " distance=2.05 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 351 " - pdb=" SG CYS C 381 " distance=2.03 Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 202 " distance=2.02 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 197 " - pdb=" SG CYS D 258 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 238 " distance=2.03 Simple disulfide: pdb=" SG CYS D 275 " - pdb=" SG CYS D 309 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 355 " distance=2.04 Simple disulfide: pdb=" SG CYS D 304 " - pdb=" SG CYS D 365 " distance=2.03 Simple disulfide: pdb=" SG CYS D 335 " - pdb=" SG CYS D 345 " distance=2.03 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 416 " distance=2.02 Simple disulfide: pdb=" SG CYS D 398 " - pdb=" SG CYS D 462 " distance=2.03 Simple disulfide: pdb=" SG CYS D 411 " - pdb=" SG CYS D 472 " distance=2.04 Simple disulfide: pdb=" SG CYS D 442 " - pdb=" SG CYS D 452 " distance=2.03 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=3, symmetry=0 Links applied NAG-ASN " NAG C1001 " - " ASN C 184 " " NAG C1002 " - " ASN C 241 " " NAG D2003 " - " ASN D 320 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 428.5 milliseconds 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 8 sheets defined 39.8% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 37 through 43 removed outlier: 3.573A pdb=" N THR A 41 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 95 through 113 removed outlier: 3.738A pdb=" N LYS A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 137 Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 36 through 46 removed outlier: 4.134A pdb=" N GLU B 43 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N SER B 44 " --> pdb=" O PHE B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 57 Processing helix chain 'B' and resid 57 through 76 Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.508A pdb=" N THR B 84 " --> pdb=" O ASN B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 95 removed outlier: 3.562A pdb=" N LYS B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 119 removed outlier: 3.857A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 123 through 142 Processing helix chain 'C' and resid 200 through 205 Processing helix chain 'C' and resid 213 through 218 Processing helix chain 'C' and resid 305 through 314 Processing helix chain 'C' and resid 318 through 322 Processing helix chain 'C' and resid 395 through 405 Processing helix chain 'D' and resid 189 through 200 Processing helix chain 'D' and resid 234 through 238 Processing helix chain 'D' and resid 249 through 253 Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 296 through 308 Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 403 through 414 Processing helix chain 'D' and resid 448 through 452 Processing sheet with id=AA1, first strand: chain 'C' and resid 229 through 230 Processing sheet with id=AA2, first strand: chain 'C' and resid 278 through 283 removed outlier: 4.742A pdb=" N CYS C 340 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C 388 " --> pdb=" O SER C 376 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N TRP C 369 " --> pdb=" O ASP C 363 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASP C 363 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ALA C 371 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 361 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C 373 " --> pdb=" O PHE C 359 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ALA C 358 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N SER C 282 " --> pdb=" O ALA C 358 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N HIS C 362 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N VAL C 278 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 158 through 166 removed outlier: 3.633A pdb=" N GLU D 158 " --> pdb=" O LYS D 175 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER D 169 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER D 207 " --> pdb=" O ILE D 257 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 158 through 166 removed outlier: 3.633A pdb=" N GLU D 158 " --> pdb=" O LYS D 175 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER D 169 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE D 172 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL D 183 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N TRP D 222 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR D 182 " --> pdb=" O TRP D 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 264 through 269 Processing sheet with id=AA6, first strand: chain 'D' and resid 264 through 269 removed outlier: 7.038A pdb=" N LEU D 279 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE D 290 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N TRP D 329 " --> pdb=" O TRP D 287 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N THR D 289 " --> pdb=" O TRP D 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 372 through 380 removed outlier: 4.934A pdb=" N ALA D 383 " --> pdb=" O GLY D 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 372 through 380 removed outlier: 4.934A pdb=" N ALA D 383 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL D 386 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL D 397 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N LEU D 437 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS D 396 " --> pdb=" O LEU D 437 " (cutoff:3.500A) 324 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 2796 1.39 - 1.55: 4066 1.55 - 1.72: 1 1.72 - 1.89: 51 1.89 - 2.05: 8 Bond restraints: 6922 Sorted by residual: bond pdb=" CB CYS C 149 " pdb=" SG CYS C 149 " ideal model delta sigma weight residual 1.808 1.874 -0.066 3.30e-02 9.18e+02 3.96e+00 bond pdb=" CB CYS C 266 " pdb=" SG CYS C 266 " ideal model delta sigma weight residual 1.808 1.748 0.060 3.30e-02 9.18e+02 3.25e+00 bond pdb=" CA ASP A 75 " pdb=" C ASP A 75 " ideal model delta sigma weight residual 1.522 1.547 -0.026 1.52e-02 4.33e+03 2.81e+00 bond pdb=" CB VAL B 54 " pdb=" CG2 VAL B 54 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.49e+00 bond pdb=" CG ASP A 75 " pdb=" OD1 ASP A 75 " ideal model delta sigma weight residual 1.249 1.220 0.029 1.90e-02 2.77e+03 2.31e+00 ... (remaining 6917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 9034 2.19 - 4.38: 319 4.38 - 6.57: 50 6.57 - 8.76: 14 8.76 - 10.95: 2 Bond angle restraints: 9419 Sorted by residual: angle pdb=" N ASP A 75 " pdb=" CA ASP A 75 " pdb=" C ASP A 75 " ideal model delta sigma weight residual 110.61 103.76 6.85 1.25e+00 6.40e-01 3.00e+01 angle pdb=" CA ASP A 75 " pdb=" C ASP A 75 " pdb=" O ASP A 75 " ideal model delta sigma weight residual 121.20 126.75 -5.55 1.04e+00 9.25e-01 2.85e+01 angle pdb=" N LYS C 379 " pdb=" CA LYS C 379 " pdb=" C LYS C 379 " ideal model delta sigma weight residual 113.61 106.28 7.33 1.50e+00 4.44e-01 2.39e+01 angle pdb=" CA CYS C 266 " pdb=" CB CYS C 266 " pdb=" SG CYS C 266 " ideal model delta sigma weight residual 114.40 125.35 -10.95 2.30e+00 1.89e-01 2.27e+01 angle pdb=" C CYS C 266 " pdb=" CA CYS C 266 " pdb=" CB CYS C 266 " ideal model delta sigma weight residual 109.46 117.17 -7.71 1.84e+00 2.95e-01 1.75e+01 ... (remaining 9414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.84: 3773 22.84 - 45.67: 241 45.67 - 68.51: 46 68.51 - 91.35: 17 91.35 - 114.18: 1 Dihedral angle restraints: 4078 sinusoidal: 1633 harmonic: 2445 Sorted by residual: dihedral pdb=" CB CYS D 411 " pdb=" SG CYS D 411 " pdb=" SG CYS D 472 " pdb=" CB CYS D 472 " ideal model delta sinusoidal sigma weight residual 93.00 163.09 -70.09 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" CB CYS C 149 " pdb=" SG CYS C 149 " pdb=" SG CYS C 266 " pdb=" CB CYS C 266 " ideal model delta sinusoidal sigma weight residual -86.00 -15.96 -70.04 1 1.00e+01 1.00e-02 6.32e+01 dihedral pdb=" CB CYS D 291 " pdb=" SG CYS D 291 " pdb=" SG CYS D 355 " pdb=" CB CYS D 355 " ideal model delta sinusoidal sigma weight residual 93.00 28.74 64.26 1 1.00e+01 1.00e-02 5.43e+01 ... (remaining 4075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 664 0.043 - 0.085: 240 0.085 - 0.128: 89 0.128 - 0.170: 19 0.170 - 0.213: 11 Chirality restraints: 1023 Sorted by residual: chirality pdb=" CA CYS D 382 " pdb=" N CYS D 382 " pdb=" C CYS D 382 " pdb=" CB CYS D 382 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA PRO B 5 " pdb=" N PRO B 5 " pdb=" C PRO B 5 " pdb=" CB PRO B 5 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CG LEU D 264 " pdb=" CB LEU D 264 " pdb=" CD1 LEU D 264 " pdb=" CD2 LEU D 264 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1020 not shown) Planarity restraints: 1203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 35 " 0.030 2.00e-02 2.50e+03 3.72e-02 2.77e+01 pdb=" CG TYR B 35 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 TYR B 35 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 35 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR B 35 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR B 35 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 35 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 35 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 47 " -0.016 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" C ASP B 47 " 0.055 2.00e-02 2.50e+03 pdb=" O ASP B 47 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU B 48 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 198 " 0.186 9.50e-02 1.11e+02 8.41e-02 5.71e+00 pdb=" NE ARG D 198 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG D 198 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG D 198 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG D 198 " -0.000 2.00e-02 2.50e+03 ... (remaining 1200 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 213 2.69 - 3.24: 6717 3.24 - 3.80: 10782 3.80 - 4.35: 13593 4.35 - 4.90: 22418 Nonbonded interactions: 53723 Sorted by model distance: nonbonded pdb=" OD1 ASP D 249 " pdb=" N HIS D 250 " model vdw 2.140 3.120 nonbonded pdb=" O GLY D 164 " pdb=" OG SER D 169 " model vdw 2.147 3.040 nonbonded pdb=" ND2 ASN D 247 " pdb="CA CA D2001 " model vdw 2.154 3.330 nonbonded pdb=" OD1 ASP C 349 " pdb=" N THR C 350 " model vdw 2.203 3.120 nonbonded pdb=" N ASP B 99 " pdb=" OD1 ASP B 99 " model vdw 2.225 3.120 ... (remaining 53718 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.080 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.050 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 6943 Z= 0.208 Angle : 0.987 12.948 9458 Z= 0.537 Chirality : 0.054 0.213 1023 Planarity : 0.006 0.084 1200 Dihedral : 15.857 114.181 2467 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.82 % Allowed : 4.11 % Favored : 95.07 % Rotamer: Outliers : 3.25 % Allowed : 17.51 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.26), residues: 852 helix: 0.50 (0.27), residues: 289 sheet: -1.05 (0.48), residues: 92 loop : -0.54 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG D 198 TYR 0.092 0.003 TYR B 35 PHE 0.016 0.002 PHE D 438 TRP 0.039 0.003 TRP D 455 HIS 0.009 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 ( 6922) covalent geometry : angle 0.95551 / 0.53 ( 9419) SS BOND : bond 0.00719 / 0.44 ( 15) SS BOND : angle 2.80485 / 1.72 ( 30) hydrogen bonds : bond 0.13156 / 8.96 ( 305) hydrogen bonds : angle 8.17348 / 6.55 ( 879) Misc. bond : bond 0.08377 / 3.62 ( 3) link_NAG-ASN : bond 0.05610 / 2.69 ( 3) link_NAG-ASN : angle 6.50852 / 3.65 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 GLU cc_start: 0.8062 (tp30) cc_final: 0.7458 (tp30) REVERT: B 94 ASP cc_start: 0.6962 (t70) cc_final: 0.6365 (m-30) REVERT: B 122 PHE cc_start: 0.8255 (t80) cc_final: 0.7999 (t80) REVERT: C 242 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6411 (m-80) REVERT: C 314 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: C 354 ASP cc_start: 0.7376 (m-30) cc_final: 0.6806 (m-30) REVERT: D 161 LEU cc_start: 0.8743 (mt) cc_final: 0.8331 (mt) REVERT: D 436 TRP cc_start: 0.8404 (m-90) cc_final: 0.8137 (m-10) outliers start: 23 outliers final: 16 residues processed: 146 average time/residue: 0.0669 time to fit residues: 13.6645 Evaluate side-chains 128 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 242 TYR Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 434 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 97 HIS C 195 GLN C 208 HIS C 289 ASN ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.138689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.118265 restraints weight = 14362.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.121641 restraints weight = 8126.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.123797 restraints weight = 5447.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.125239 restraints weight = 4134.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.126241 restraints weight = 3390.786| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 6943 Z= 0.158 Angle : 0.687 8.398 9458 Z= 0.346 Chirality : 0.045 0.158 1023 Planarity : 0.004 0.040 1200 Dihedral : 10.434 112.071 1013 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.40 % Favored : 96.48 % Rotamer: Outliers : 4.66 % Allowed : 15.96 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.28), residues: 852 helix: 2.21 (0.31), residues: 281 sheet: -0.37 (0.51), residues: 92 loop : -0.19 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 40 TYR 0.026 0.002 TYR B 35 PHE 0.011 0.001 PHE C 359 TRP 0.016 0.001 TRP D 455 HIS 0.005 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 6922) covalent geometry : angle 0.66980 / 0.34 ( 9419) SS BOND : bond 0.00408 / 0.22 ( 15) SS BOND : angle 1.02876 / 0.67 ( 30) hydrogen bonds : bond 0.03721 / 2.60 ( 305) hydrogen bonds : angle 5.41589 / 4.24 ( 879) Misc. bond : bond 0.09273 / 4.16 ( 3) link_NAG-ASN : bond 0.00581 / 0.28 ( 3) link_NAG-ASN : angle 4.72206 / 2.70 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 SER cc_start: 0.8964 (m) cc_final: 0.8420 (p) REVERT: B 35 TYR cc_start: 0.8193 (m-80) cc_final: 0.7436 (m-10) REVERT: C 242 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.6769 (m-80) REVERT: C 354 ASP cc_start: 0.7696 (m-30) cc_final: 0.7447 (m-30) REVERT: D 348 HIS cc_start: 0.6238 (t-90) cc_final: 0.5750 (t70) REVERT: D 396 LYS cc_start: 0.8364 (pttt) cc_final: 0.7928 (pttt) REVERT: D 436 TRP cc_start: 0.8576 (m-90) cc_final: 0.8281 (m-10) outliers start: 33 outliers final: 19 residues processed: 136 average time/residue: 0.0689 time to fit residues: 13.1274 Evaluate side-chains 121 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 HIS Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 242 TYR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 71 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 117 HIS C 203 ASN C 208 HIS ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.138168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.117940 restraints weight = 14183.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.121290 restraints weight = 8101.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.123459 restraints weight = 5479.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.124867 restraints weight = 4168.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.125766 restraints weight = 3427.118| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 6943 Z= 0.126 Angle : 0.611 8.086 9458 Z= 0.307 Chirality : 0.043 0.153 1023 Planarity : 0.004 0.046 1200 Dihedral : 9.630 108.306 997 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.17 % Favored : 96.71 % Rotamer: Outliers : 4.80 % Allowed : 17.80 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.28), residues: 852 helix: 2.19 (0.31), residues: 284 sheet: -0.19 (0.54), residues: 73 loop : 0.01 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 40 TYR 0.016 0.001 TYR B 35 PHE 0.013 0.002 PHE C 377 TRP 0.011 0.001 TRP D 455 HIS 0.003 0.001 HIS D 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 6922) covalent geometry : angle 0.60060 / 0.30 ( 9419) SS BOND : bond 0.00178 / 0.11 ( 15) SS BOND : angle 0.94328 / 0.56 ( 30) hydrogen bonds : bond 0.03368 / 2.32 ( 305) hydrogen bonds : angle 4.97862 / 3.89 ( 879) Misc. bond : bond 0.06354 / 2.96 ( 3) link_NAG-ASN : bond 0.00522 / 0.25 ( 3) link_NAG-ASN : angle 3.51864 / 2.04 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 TYR cc_start: 0.8370 (m-80) cc_final: 0.7705 (m-10) REVERT: C 242 TYR cc_start: 0.7148 (OUTLIER) cc_final: 0.6830 (m-80) REVERT: C 354 ASP cc_start: 0.7979 (m-30) cc_final: 0.7525 (m-30) REVERT: D 396 LYS cc_start: 0.8321 (pttt) cc_final: 0.7973 (pttt) REVERT: D 436 TRP cc_start: 0.8568 (m-90) cc_final: 0.8351 (m-10) outliers start: 34 outliers final: 20 residues processed: 137 average time/residue: 0.0626 time to fit residues: 12.4580 Evaluate side-chains 120 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 242 TYR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain D residue 199 GLN Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 37 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 208 HIS C 331 GLN ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.137245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116909 restraints weight = 14428.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.120234 restraints weight = 8322.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.122423 restraints weight = 5684.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.123887 restraints weight = 4326.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.124896 restraints weight = 3552.918| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 6943 Z= 0.127 Angle : 0.598 8.338 9458 Z= 0.298 Chirality : 0.043 0.170 1023 Planarity : 0.004 0.046 1200 Dihedral : 9.386 106.085 991 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.40 % Favored : 96.48 % Rotamer: Outliers : 3.81 % Allowed : 19.49 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.29), residues: 852 helix: 2.08 (0.32), residues: 286 sheet: -0.45 (0.50), residues: 83 loop : 0.15 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 40 TYR 0.013 0.001 TYR B 35 PHE 0.019 0.001 PHE A 36 TRP 0.009 0.001 TRP B 37 HIS 0.003 0.001 HIS D 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 6922) covalent geometry : angle 0.59058 / 0.30 ( 9419) SS BOND : bond 0.00202 / 0.14 ( 15) SS BOND : angle 0.77585 / 0.46 ( 30) hydrogen bonds : bond 0.03127 / 2.17 ( 305) hydrogen bonds : angle 4.81920 / 3.75 ( 879) Misc. bond : bond 0.06018 / 2.85 ( 3) link_NAG-ASN : bond 0.00442 / 0.21 ( 3) link_NAG-ASN : angle 2.91540 / 1.69 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 THR cc_start: 0.8708 (p) cc_final: 0.8496 (p) REVERT: B 35 TYR cc_start: 0.8403 (m-80) cc_final: 0.7788 (m-10) REVERT: D 223 PHE cc_start: 0.7915 (m-80) cc_final: 0.7627 (m-10) REVERT: D 396 LYS cc_start: 0.8365 (pttt) cc_final: 0.8065 (pttt) outliers start: 27 outliers final: 21 residues processed: 126 average time/residue: 0.0740 time to fit residues: 12.8429 Evaluate side-chains 120 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 373 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 68 optimal weight: 0.0670 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 8 optimal weight: 0.0980 chunk 45 optimal weight: 0.3980 chunk 56 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 9 optimal weight: 0.0040 chunk 76 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.2730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** 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 = 0.3866 r_free = 0.3866 target = 0.140792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.120757 restraints weight = 14684.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.124166 restraints weight = 8426.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.126380 restraints weight = 5707.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.127893 restraints weight = 4308.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.128858 restraints weight = 3505.672| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6943 Z= 0.105 Angle : 0.585 7.546 9458 Z= 0.292 Chirality : 0.042 0.147 1023 Planarity : 0.004 0.047 1200 Dihedral : 9.056 103.904 989 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.64 % Favored : 96.24 % Rotamer: Outliers : 2.82 % Allowed : 20.20 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.29), residues: 852 helix: 2.10 (0.32), residues: 285 sheet: -0.87 (0.51), residues: 79 loop : 0.20 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 163 TYR 0.011 0.001 TYR B 35 PHE 0.020 0.001 PHE A 36 TRP 0.007 0.001 TRP C 284 HIS 0.003 0.000 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.10 ( 6922) covalent geometry : angle 0.57670 / 0.29 ( 9419) SS BOND : bond 0.00349 / 0.20 ( 15) SS BOND : angle 1.28587 / 0.75 ( 30) hydrogen bonds : bond 0.02840 / 1.95 ( 305) hydrogen bonds : angle 4.61532 / 3.62 ( 879) Misc. bond : bond 0.04243 / 2.02 ( 3) link_NAG-ASN : bond 0.00422 / 0.20 ( 3) link_NAG-ASN : angle 2.48776 / 1.44 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8631 (tmm) cc_final: 0.8416 (tmm) REVERT: A 137 THR cc_start: 0.8699 (p) cc_final: 0.8465 (p) REVERT: B 90 GLU cc_start: 0.8170 (tp30) cc_final: 0.7252 (tp30) REVERT: B 94 ASP cc_start: 0.7227 (t70) cc_final: 0.6701 (m-30) REVERT: D 176 PHE cc_start: 0.7155 (t80) cc_final: 0.6506 (m-80) REVERT: D 213 ASN cc_start: 0.7175 (m-40) cc_final: 0.6724 (t0) REVERT: D 223 PHE cc_start: 0.7849 (m-80) cc_final: 0.7610 (m-10) REVERT: D 436 TRP cc_start: 0.8499 (m-10) cc_final: 0.7705 (m-90) outliers start: 20 outliers final: 17 residues processed: 124 average time/residue: 0.0591 time to fit residues: 10.7329 Evaluate side-chains 114 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 HIS A 112 HIS ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.132911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.112585 restraints weight = 14591.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.115842 restraints weight = 8445.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.117933 restraints weight = 5793.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.119410 restraints weight = 4441.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.120321 restraints weight = 3653.434| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 6943 Z= 0.176 Angle : 0.640 7.731 9458 Z= 0.322 Chirality : 0.044 0.152 1023 Planarity : 0.004 0.050 1200 Dihedral : 9.382 103.212 989 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.76 % Favored : 96.13 % Rotamer: Outliers : 4.52 % Allowed : 20.20 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.29), residues: 852 helix: 1.82 (0.32), residues: 291 sheet: -0.46 (0.52), residues: 81 loop : 0.08 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 267 TYR 0.014 0.002 TYR C 224 PHE 0.017 0.002 PHE A 36 TRP 0.012 0.001 TRP B 37 HIS 0.004 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.18 ( 6922) covalent geometry : angle 0.63166 / 0.32 ( 9419) SS BOND : bond 0.00351 / 0.20 ( 15) SS BOND : angle 1.41623 / 0.85 ( 30) hydrogen bonds : bond 0.03440 / 2.45 ( 305) hydrogen bonds : angle 4.90001 / 3.81 ( 879) Misc. bond : bond 0.07835 / 3.54 ( 3) link_NAG-ASN : bond 0.00370 / 0.18 ( 3) link_NAG-ASN : angle 2.57805 / 1.48 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 THR cc_start: 0.8818 (p) cc_final: 0.8598 (p) REVERT: B 35 TYR cc_start: 0.8497 (m-80) cc_final: 0.8048 (m-10) REVERT: B 80 ASN cc_start: 0.6964 (t0) cc_final: 0.6590 (t0) REVERT: B 90 GLU cc_start: 0.8218 (tp30) cc_final: 0.7241 (tp30) REVERT: B 94 ASP cc_start: 0.7152 (t70) cc_final: 0.6786 (m-30) REVERT: B 121 GLU cc_start: 0.8323 (tp30) cc_final: 0.8093 (tp30) REVERT: C 242 TYR cc_start: 0.7319 (OUTLIER) cc_final: 0.6870 (m-80) REVERT: D 360 ASP cc_start: 0.8223 (m-30) cc_final: 0.7835 (m-30) REVERT: D 436 TRP cc_start: 0.8596 (m-10) cc_final: 0.8275 (m-10) outliers start: 32 outliers final: 21 residues processed: 122 average time/residue: 0.0604 time to fit residues: 11.1540 Evaluate side-chains 120 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 182 HIS Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 242 TYR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 373 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 7 optimal weight: 0.0060 chunk 64 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 46 optimal weight: 0.0030 chunk 67 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.5006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 HIS ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.136258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.116218 restraints weight = 14370.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.119513 restraints weight = 8398.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.121672 restraints weight = 5738.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.123036 restraints weight = 4376.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.124129 restraints weight = 3623.227| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 6943 Z= 0.113 Angle : 0.584 7.662 9458 Z= 0.292 Chirality : 0.042 0.145 1023 Planarity : 0.004 0.051 1200 Dihedral : 9.079 103.200 988 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.76 % Favored : 96.13 % Rotamer: Outliers : 2.97 % Allowed : 22.18 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.29), residues: 852 helix: 1.91 (0.32), residues: 291 sheet: -0.71 (0.53), residues: 83 loop : 0.12 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 31 TYR 0.010 0.001 TYR B 35 PHE 0.018 0.001 PHE A 36 TRP 0.011 0.001 TRP C 398 HIS 0.004 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.11 ( 6922) covalent geometry : angle 0.57723 / 0.29 ( 9419) SS BOND : bond 0.00189 / 0.13 ( 15) SS BOND : angle 1.16811 / 0.69 ( 30) hydrogen bonds : bond 0.02958 / 2.07 ( 305) hydrogen bonds : angle 4.65308 / 3.64 ( 879) Misc. bond : bond 0.05641 / 2.57 ( 3) link_NAG-ASN : bond 0.00346 / 0.17 ( 3) link_NAG-ASN : angle 2.32731 / 1.33 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 THR cc_start: 0.8747 (p) cc_final: 0.8477 (p) REVERT: B 80 ASN cc_start: 0.6893 (t0) cc_final: 0.6574 (t0) REVERT: B 90 GLU cc_start: 0.8189 (tp30) cc_final: 0.7285 (tp30) REVERT: B 94 ASP cc_start: 0.7325 (t70) cc_final: 0.6833 (m-30) REVERT: B 121 GLU cc_start: 0.8342 (tp30) cc_final: 0.8111 (tp30) REVERT: D 436 TRP cc_start: 0.8564 (m-10) cc_final: 0.8213 (m-10) outliers start: 21 outliers final: 16 residues processed: 120 average time/residue: 0.0483 time to fit residues: 8.8043 Evaluate side-chains 116 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 373 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 HIS C 244 GLN ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.135180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115061 restraints weight = 14553.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118391 restraints weight = 8378.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.120527 restraints weight = 5694.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.122011 restraints weight = 4343.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.122966 restraints weight = 3552.915| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 6943 Z= 0.130 Angle : 0.607 9.591 9458 Z= 0.302 Chirality : 0.042 0.150 1023 Planarity : 0.004 0.051 1200 Dihedral : 9.048 101.369 987 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.11 % Favored : 95.77 % Rotamer: Outliers : 2.54 % Allowed : 23.59 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.29), residues: 852 helix: 1.89 (0.32), residues: 291 sheet: -0.62 (0.53), residues: 81 loop : 0.14 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 31 TYR 0.010 0.001 TYR B 35 PHE 0.014 0.001 PHE A 36 TRP 0.012 0.001 TRP C 398 HIS 0.004 0.001 HIS D 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.13 ( 6922) covalent geometry : angle 0.60145 / 0.30 ( 9419) SS BOND : bond 0.00448 / 0.28 ( 15) SS BOND : angle 0.92800 / 0.56 ( 30) hydrogen bonds : bond 0.03120 / 2.21 ( 305) hydrogen bonds : angle 4.73023 / 3.69 ( 879) Misc. bond : bond 0.06337 / 2.83 ( 3) link_NAG-ASN : bond 0.00329 / 0.16 ( 3) link_NAG-ASN : angle 2.27964 / 1.30 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.263 Fit side-chains REVERT: A 137 THR cc_start: 0.8774 (p) cc_final: 0.8501 (p) REVERT: B 40 ARG cc_start: 0.8379 (ttm110) cc_final: 0.8067 (ttm110) REVERT: B 80 ASN cc_start: 0.6885 (t0) cc_final: 0.6559 (t0) REVERT: B 94 ASP cc_start: 0.7197 (t70) cc_final: 0.6866 (t0) REVERT: D 436 TRP cc_start: 0.8575 (m-10) cc_final: 0.8206 (m-10) outliers start: 18 outliers final: 18 residues processed: 114 average time/residue: 0.0679 time to fit residues: 11.0478 Evaluate side-chains 118 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 78 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 0.0070 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 HIS ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.135822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.115931 restraints weight = 14440.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.119158 restraints weight = 8337.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.121277 restraints weight = 5705.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.122753 restraints weight = 4348.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.123740 restraints weight = 3553.245| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 6943 Z= 0.118 Angle : 0.597 7.840 9458 Z= 0.296 Chirality : 0.042 0.149 1023 Planarity : 0.004 0.051 1200 Dihedral : 8.946 101.196 987 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.40 % Favored : 96.48 % Rotamer: Outliers : 3.25 % Allowed : 23.45 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.29), residues: 852 helix: 1.92 (0.32), residues: 291 sheet: -0.70 (0.53), residues: 81 loop : 0.16 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 31 TYR 0.009 0.001 TYR B 35 PHE 0.015 0.001 PHE A 36 TRP 0.013 0.001 TRP C 398 HIS 0.004 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 ( 6922) covalent geometry : angle 0.59271 / 0.30 ( 9419) SS BOND : bond 0.00175 / 0.12 ( 15) SS BOND : angle 0.80939 / 0.50 ( 30) hydrogen bonds : bond 0.03003 / 2.12 ( 305) hydrogen bonds : angle 4.64935 / 3.63 ( 879) Misc. bond : bond 0.05806 / 2.59 ( 3) link_NAG-ASN : bond 0.00332 / 0.16 ( 3) link_NAG-ASN : angle 2.24285 / 1.27 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 137 THR cc_start: 0.8807 (p) cc_final: 0.8555 (p) REVERT: B 40 ARG cc_start: 0.8351 (ttm110) cc_final: 0.8024 (ttm110) REVERT: B 80 ASN cc_start: 0.6854 (t0) cc_final: 0.6460 (t0) REVERT: B 94 ASP cc_start: 0.7176 (t70) cc_final: 0.6945 (t0) REVERT: D 436 TRP cc_start: 0.8558 (m-10) cc_final: 0.8195 (m-10) outliers start: 23 outliers final: 19 residues processed: 113 average time/residue: 0.0550 time to fit residues: 9.2941 Evaluate side-chains 115 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 365 CYS Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 HIS ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.131053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.110788 restraints weight = 14559.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.113989 restraints weight = 8561.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.115964 restraints weight = 5903.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.117509 restraints weight = 4580.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.118399 restraints weight = 3742.636| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 6943 Z= 0.186 Angle : 0.664 8.584 9458 Z= 0.334 Chirality : 0.044 0.172 1023 Planarity : 0.004 0.051 1200 Dihedral : 9.431 103.562 987 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.58 % Favored : 95.31 % Rotamer: Outliers : 3.25 % Allowed : 23.73 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.30), residues: 852 helix: 1.63 (0.32), residues: 298 sheet: -0.57 (0.53), residues: 78 loop : -0.01 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 31 TYR 0.014 0.002 TYR C 224 PHE 0.017 0.002 PHE C 173 TRP 0.013 0.001 TRP C 398 HIS 0.005 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.19 ( 6922) covalent geometry : angle 0.65927 / 0.33 ( 9419) SS BOND : bond 0.00344 / 0.19 ( 15) SS BOND : angle 0.95910 / 0.61 ( 30) hydrogen bonds : bond 0.03583 / 2.56 ( 305) hydrogen bonds : angle 4.97003 / 3.86 ( 879) Misc. bond : bond 0.09009 / 3.90 ( 3) link_NAG-ASN : bond 0.00289 / 0.14 ( 3) link_NAG-ASN : angle 2.37135 / 1.34 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 THR cc_start: 0.8760 (p) cc_final: 0.8556 (p) REVERT: B 35 TYR cc_start: 0.8536 (m-80) cc_final: 0.8192 (m-10) REVERT: B 40 ARG cc_start: 0.8393 (ttm110) cc_final: 0.8068 (ttm110) REVERT: B 80 ASN cc_start: 0.6934 (t0) cc_final: 0.6587 (t0) REVERT: B 92 HIS cc_start: 0.8665 (OUTLIER) cc_final: 0.8134 (m90) REVERT: D 436 TRP cc_start: 0.8605 (m-10) cc_final: 0.8241 (m-10) outliers start: 23 outliers final: 19 residues processed: 114 average time/residue: 0.0552 time to fit residues: 9.2304 Evaluate side-chains 119 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 365 CYS Chi-restraints excluded: chain D residue 373 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 59 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 199 GLN ** 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 = 0.3766 r_free = 0.3766 target = 0.133399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.113333 restraints weight = 14570.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.116605 restraints weight = 8474.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.118762 restraints weight = 5778.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.120208 restraints weight = 4399.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.121164 restraints weight = 3606.134| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 6943 Z= 0.138 Angle : 0.626 8.213 9458 Z= 0.314 Chirality : 0.044 0.202 1023 Planarity : 0.004 0.060 1200 Dihedral : 9.301 103.644 987 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.23 % Favored : 95.66 % Rotamer: Outliers : 2.68 % Allowed : 24.58 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.30), residues: 852 helix: 1.86 (0.32), residues: 289 sheet: -0.92 (0.52), residues: 81 loop : 0.07 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 31 TYR 0.011 0.001 TYR C 224 PHE 0.014 0.001 PHE A 36 TRP 0.013 0.001 TRP C 398 HIS 0.005 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.14 ( 6922) covalent geometry : angle 0.62144 / 0.31 ( 9419) SS BOND : bond 0.00246 / 0.15 ( 15) SS BOND : angle 0.87089 / 0.54 ( 30) hydrogen bonds : bond 0.03245 / 2.30 ( 305) hydrogen bonds : angle 4.80623 / 3.75 ( 879) Misc. bond : bond 0.07316 / 3.18 ( 3) link_NAG-ASN : bond 0.00309 / 0.15 ( 3) link_NAG-ASN : angle 2.33687 / 1.32 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1142.92 seconds wall clock time: 20 minutes 35.70 seconds (1235.70 seconds total)