Starting phenix.real_space_refine on Wed Aug 5 02:59:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s6q_54628/08_2026/9s6q_54628.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s6q_54628/08_2026/9s6q_54628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9s6q_54628/08_2026/9s6q_54628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s6q_54628/08_2026/9s6q_54628.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9s6q_54628/08_2026/9s6q_54628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s6q_54628/08_2026/9s6q_54628.map" } resolution = 3.57 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= 0.001 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 5106 2.51 5 N 1320 2.21 5 O 1568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8023 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1653 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "B" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1752 Classifications: {'peptide': 230} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 214} Chain: "C" Number of atoms: 4478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4478 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 38, 'TRANS': 523} Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 1.29, per 1000 atoms: 0.16 Number of scatterers: 8023 At special positions: 0 Unit cell: (88.56, 100.44, 168.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 1568 8.00 N 1320 7.00 C 5106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 97 " distance=2.04 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 213 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 324 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 420 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 512 " distance=2.03 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 525 " - pdb=" SG CYS C 577 " 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=0, symmetry=0 Links applied NAG-ASN " NAG C1301 " - " ASN C 31 " " NAG C1302 " - " ASN C 66 " " NAG C1303 " - " ASN C 120 " " NAG C1304 " - " ASN C 145 " " NAG C1305 " - " ASN C 228 " " NAG C1306 " - " ASN C 319 " " NAG C1307 " - " ASN C 331 " " NAG C1308 " - " ASN C 358 " " NAG C1309 " - " ASN C 110 " " NAG C1310 " - " ASN C 159 " Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 356.6 milliseconds 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1880 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 19 sheets defined 6.8% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.557A pdb=" N HIS A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 66 removed outlier: 3.661A pdb=" N LYS B 66 " --> pdb=" O PRO B 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 63 through 66' Processing helix chain 'B' and resid 173 through 175 No H-bonds generated for 'chain 'B' and resid 173 through 175' Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'C' and resid 282 through 292 Processing helix chain 'C' and resid 326 through 331 removed outlier: 3.518A pdb=" N PHE C 330 " --> pdb=" O PHE C 326 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN C 331 " --> pdb=" O GLY C 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 326 through 331' Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.846A pdb=" N TRP C 341 " --> pdb=" O VAL C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 377 removed outlier: 3.692A pdb=" N ASN C 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.986A pdb=" N TYR C 409 " --> pdb=" O VAL C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 431 removed outlier: 3.782A pdb=" N ALA C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 493 removed outlier: 3.514A pdb=" N TYR C 492 " --> pdb=" O GLY C 489 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN C 493 " --> pdb=" O ILE C 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 489 through 493' Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.696A pdb=" N GLU A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.463A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 139 removed outlier: 5.650A pdb=" N TYR A 173 " --> pdb=" O ASN A 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 150 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'B' and resid 59 through 61 removed outlier: 6.620A pdb=" N TRP B 38 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N SER B 52 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP B 36 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N CYS B 97 " --> pdb=" O TRP B 120 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N TRP B 120 " --> pdb=" O CYS B 97 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG B 99 " --> pdb=" O GLN B 118 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 59 through 61 removed outlier: 6.620A pdb=" N TRP B 38 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N SER B 52 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP B 36 " --> pdb=" O SER B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.719A pdb=" N TYR B 104 " --> pdb=" O GLN B 112 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 137 through 141 removed outlier: 3.948A pdb=" N GLY B 156 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N TYR B 193 " --> pdb=" O ASP B 161 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL B 198 " --> pdb=" O HIS B 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 137 through 141 removed outlier: 3.948A pdb=" N GLY B 156 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N TYR B 193 " --> pdb=" O ASP B 161 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 168 through 171 removed outlier: 4.270A pdb=" N TYR B 211 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 31 through 35 removed outlier: 5.495A pdb=" N THR C 32 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ARG C 69 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL C 67 " --> pdb=" O PHE C 34 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS C 181 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 189 " --> pdb=" O HIS C 196 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 223 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL C 197 " --> pdb=" O PHE C 221 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE C 221 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N SER C 199 " --> pdb=" O PRO C 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 52 through 60 removed outlier: 3.747A pdb=" N LYS C 266 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP C 275 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.529A pdb=" N ILE C 82 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE C 139 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL C 140 " --> pdb=" O ILE C 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.529A pdb=" N ILE C 82 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN C 231 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY C 101 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR C 237 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE C 99 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG C 100 " --> pdb=" O ASN C 119 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN C 119 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE C 162 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 313 through 316 removed outlier: 5.900A pdb=" N ASP C 561 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY C 553 " --> pdb=" O ASP C 561 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 342 through 346 removed outlier: 3.756A pdb=" N GLU C 342 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER C 387 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 511 " --> pdb=" O PHE C 380 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N CYS C 349 " --> pdb=" O CYS C 512 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 342 through 346 removed outlier: 3.756A pdb=" N GLU C 342 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER C 387 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ASN C 382 " --> pdb=" O GLU C 503 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU C 503 " --> pdb=" O ASN C 382 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 501 " --> pdb=" O TYR C 384 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP C 386 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL C 499 " --> pdb=" O ASP C 386 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE C 388 " --> pdb=" O VAL C 497 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 390 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR C 364 " --> pdb=" O ALA C 423 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 440 through 442 263 hydrogen bonds defined for protein. 696 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2521 1.34 - 1.46: 2007 1.46 - 1.58: 3675 1.58 - 1.70: 0 1.70 - 1.82: 33 Bond restraints: 8236 Sorted by residual: bond pdb=" C LYS C 412 " pdb=" N LEU C 413 " ideal model delta sigma weight residual 1.339 1.415 -0.076 5.57e-02 3.22e+02 1.86e+00 bond pdb=" N SER B 144 " pdb=" CA SER B 144 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 1.01e+00 bond pdb=" CG PRO C 336 " pdb=" CD PRO C 336 " ideal model delta sigma weight residual 1.503 1.478 0.025 3.40e-02 8.65e+02 5.39e-01 bond pdb=" CB PRO C 400 " pdb=" CG PRO C 400 " ideal model delta sigma weight residual 1.492 1.455 0.037 5.00e-02 4.00e+02 5.34e-01 bond pdb=" CA TYR B 35 " pdb=" CB TYR B 35 " ideal model delta sigma weight residual 1.532 1.521 0.011 1.62e-02 3.81e+03 4.78e-01 ... (remaining 8231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 10693 1.05 - 2.11: 403 2.11 - 3.16: 95 3.16 - 4.21: 23 4.21 - 5.26: 5 Bond angle restraints: 11219 Sorted by residual: angle pdb=" C SER B 144 " pdb=" CA SER B 144 " pdb=" CB SER B 144 " ideal model delta sigma weight residual 110.42 115.68 -5.26 1.99e+00 2.53e-01 7.00e+00 angle pdb=" C ILE B 50 " pdb=" N GLY B 51 " pdb=" CA GLY B 51 " ideal model delta sigma weight residual 121.22 116.00 5.22 2.07e+00 2.33e-01 6.35e+00 angle pdb=" N PRO C 470 " pdb=" CA PRO C 470 " pdb=" C PRO C 470 " ideal model delta sigma weight residual 110.70 113.49 -2.79 1.22e+00 6.72e-01 5.22e+00 angle pdb=" CA TYR A 91 " pdb=" CB TYR A 91 " pdb=" CG TYR A 91 " ideal model delta sigma weight residual 113.90 117.99 -4.09 1.80e+00 3.09e-01 5.17e+00 angle pdb=" CA TYR C 357 " pdb=" CB TYR C 357 " pdb=" CG TYR C 357 " ideal model delta sigma weight residual 113.90 117.53 -3.63 1.80e+00 3.09e-01 4.07e+00 ... (remaining 11214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.04: 4616 12.04 - 24.08: 302 24.08 - 36.13: 64 36.13 - 48.17: 30 48.17 - 60.21: 16 Dihedral angle restraints: 5028 sinusoidal: 2093 harmonic: 2935 Sorted by residual: dihedral pdb=" CB CYS C 468 " pdb=" SG CYS C 468 " pdb=" SG CYS C 475 " pdb=" CB CYS C 475 " ideal model delta sinusoidal sigma weight residual 93.00 127.90 -34.90 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CA LEU C 449 " pdb=" C LEU C 449 " pdb=" N ARG C 450 " pdb=" CA ARG C 450 " ideal model delta harmonic sigma weight residual 180.00 164.15 15.85 0 5.00e+00 4.00e-02 1.00e+01 dihedral pdb=" CA GLN B 79 " pdb=" C GLN B 79 " pdb=" N PHE B 80 " pdb=" CA PHE B 80 " ideal model delta harmonic sigma weight residual 180.00 164.26 15.74 0 5.00e+00 4.00e-02 9.91e+00 ... (remaining 5025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1121 0.074 - 0.148: 133 0.148 - 0.221: 3 0.221 - 0.295: 0 0.295 - 0.369: 2 Chirality restraints: 1259 Sorted by residual: chirality pdb=" C1 NAG C1310 " pdb=" ND2 ASN C 159 " pdb=" C2 NAG C1310 " pdb=" O5 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 145 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 319 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 1256 not shown) Planarity restraints: 1453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 165 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO B 166 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 166 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 166 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 459 " 0.027 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO C 460 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 460 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 460 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 507 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO C 508 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 508 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 508 " -0.022 5.00e-02 4.00e+02 ... (remaining 1450 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.05: 4858 3.05 - 3.51: 6973 3.51 - 3.97: 11578 3.97 - 4.44: 13050 4.44 - 4.90: 22594 Nonbonded interactions: 59053 Sorted by model distance: nonbonded pdb=" N ALA C 507 " pdb=" O ALA C 507 " model vdw 2.583 2.496 nonbonded pdb=" O ASN C 319 " pdb=" OD1 ASN C 319 " model vdw 2.622 3.040 nonbonded pdb=" N ASP C 58 " pdb=" O ASP C 58 " model vdw 2.636 2.496 nonbonded pdb=" O ILE B 50 " pdb=" CA GLY B 51 " model vdw 2.637 2.752 nonbonded pdb=" N SER B 129 " pdb=" O SER B 129 " model vdw 2.638 2.496 ... (remaining 59048 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=1.00 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.200 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 : 0.003 0.076 8257 Z= 0.130 Angle : 0.541 9.758 11271 Z= 0.275 Chirality : 0.047 0.369 1259 Planarity : 0.004 0.050 1443 Dihedral : 9.648 60.211 3115 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.69 % Allowed : 4.50 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: -0.66 (0.27), residues: 1000 helix: -0.95 (0.85), residues: 38 sheet: 0.77 (0.30), residues: 362 loop : -1.23 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 496 TYR 0.019 0.001 TYR A 91 PHE 0.017 0.001 PHE B 80 TRP 0.011 0.001 TRP C 424 HIS 0.002 0.001 HIS C 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 8236) covalent geometry : angle 0.51280 / 0.27 (11219) SS BOND : bond 0.00379 / 0.20 ( 11) SS BOND : angle 0.71861 / 0.40 ( 22) hydrogen bonds : bond 0.14230 / 9.32 ( 233) hydrogen bonds : angle 6.92493 / 4.68 ( 696) link_NAG-ASN : bond 0.00720 / 0.45 ( 10) link_NAG-ASN : angle 3.36722 / 2.56 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8230 (mp) REVERT: B 31 ARG cc_start: 0.7977 (mtt180) cc_final: 0.7549 (tpt170) REVERT: C 85 LYS cc_start: 0.7873 (mttt) cc_final: 0.7483 (mtpt) REVERT: C 202 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7199 (tt0) REVERT: C 521 ILE cc_start: 0.8294 (mt) cc_final: 0.8030 (mp) REVERT: C 559 PHE cc_start: 0.4505 (t80) cc_final: 0.4078 (t80) outliers start: 15 outliers final: 10 residues processed: 124 average time/residue: 0.0832 time to fit residues: 14.3838 Evaluate side-chains 80 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 357 TYR Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 506 ASN Chi-restraints excluded: chain C residue 571 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN B 181 HIS ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.240960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.226545 restraints weight = 8878.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.224020 restraints weight = 15154.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.221504 restraints weight = 19964.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.220408 restraints weight = 17053.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.188093 restraints weight = 17134.736| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 8257 Z= 0.215 Angle : 0.646 9.522 11271 Z= 0.328 Chirality : 0.050 0.375 1259 Planarity : 0.005 0.047 1443 Dihedral : 6.752 59.301 1322 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.92 % Allowed : 9.45 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: -0.77 (0.27), residues: 1000 helix: -1.50 (0.75), residues: 44 sheet: 0.78 (0.30), residues: 364 loop : -1.34 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 99 TYR 0.022 0.002 TYR A 91 PHE 0.021 0.002 PHE B 80 TRP 0.014 0.002 TRP B 49 HIS 0.005 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.21 ( 8236) covalent geometry : angle 0.62151 / 0.32 (11219) SS BOND : bond 0.00599 / 0.31 ( 11) SS BOND : angle 1.11877 / 0.65 ( 22) hydrogen bonds : bond 0.04317 / 2.89 ( 233) hydrogen bonds : angle 5.59820 / 3.89 ( 696) link_NAG-ASN : bond 0.00700 / 0.43 ( 10) link_NAG-ASN : angle 3.38639 / 2.57 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 LEU cc_start: 0.8447 (tp) cc_final: 0.7943 (tp) REVERT: A 104 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8242 (mp) REVERT: B 31 ARG cc_start: 0.7864 (mtt180) cc_final: 0.7492 (tpt170) REVERT: C 85 LYS cc_start: 0.7808 (mttt) cc_final: 0.7308 (mtpt) outliers start: 26 outliers final: 18 residues processed: 87 average time/residue: 0.0904 time to fit residues: 10.8064 Evaluate side-chains 78 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 357 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 506 ASN Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 571 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 33 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 38 optimal weight: 30.0000 chunk 72 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** 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 = 0.4538 r_free = 0.4538 target = 0.242135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.227752 restraints weight = 8883.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.182472 restraints weight = 16613.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.177136 restraints weight = 17288.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.174431 restraints weight = 14408.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.172197 restraints weight = 12268.895| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 8257 Z= 0.155 Angle : 0.594 9.685 11271 Z= 0.299 Chirality : 0.048 0.371 1259 Planarity : 0.004 0.047 1443 Dihedral : 6.653 59.298 1322 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.92 % Allowed : 10.35 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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 (0.27), residues: 1000 helix: -1.38 (0.76), residues: 44 sheet: 0.77 (0.30), residues: 367 loop : -1.29 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 99 TYR 0.024 0.001 TYR A 91 PHE 0.016 0.001 PHE B 80 TRP 0.013 0.002 TRP C 424 HIS 0.004 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.15 ( 8236) covalent geometry : angle 0.56778 / 0.29 (11219) SS BOND : bond 0.00490 / 0.25 ( 11) SS BOND : angle 0.92386 / 0.54 ( 22) hydrogen bonds : bond 0.03784 / 2.54 ( 233) hydrogen bonds : angle 5.38233 / 3.74 ( 696) link_NAG-ASN : bond 0.00710 / 0.43 ( 10) link_NAG-ASN : angle 3.38503 / 2.57 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8291 (t0) cc_final: 0.7948 (t0) REVERT: A 104 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8165 (mp) REVERT: B 31 ARG cc_start: 0.8031 (mtt180) cc_final: 0.7435 (tpt170) REVERT: B 187 LEU cc_start: 0.8941 (tt) cc_final: 0.8589 (tt) REVERT: C 85 LYS cc_start: 0.7751 (mttt) cc_final: 0.7216 (mtpt) REVERT: C 210 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7161 (tt) REVERT: C 561 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7632 (t0) outliers start: 26 outliers final: 19 residues processed: 84 average time/residue: 0.0719 time to fit residues: 8.7706 Evaluate side-chains 80 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 357 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 506 ASN Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 571 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 10.0000 chunk 83 optimal weight: 0.1980 chunk 20 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 188 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 = 0.4539 r_free = 0.4539 target = 0.242233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.226159 restraints weight = 9047.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.191557 restraints weight = 22701.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.173714 restraints weight = 16747.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.172388 restraints weight = 14859.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.170687 restraints weight = 12718.413| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 8257 Z= 0.153 Angle : 0.583 9.598 11271 Z= 0.294 Chirality : 0.048 0.371 1259 Planarity : 0.004 0.046 1443 Dihedral : 6.632 59.957 1322 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.37 % Allowed : 10.57 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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 (0.28), residues: 1000 helix: -1.27 (0.77), residues: 44 sheet: 0.76 (0.30), residues: 367 loop : -1.29 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 99 TYR 0.021 0.001 TYR A 91 PHE 0.016 0.001 PHE B 80 TRP 0.013 0.002 TRP C 424 HIS 0.003 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.15 ( 8236) covalent geometry : angle 0.55640 / 0.29 (11219) SS BOND : bond 0.00475 / 0.25 ( 11) SS BOND : angle 0.91169 / 0.53 ( 22) hydrogen bonds : bond 0.03691 / 2.49 ( 233) hydrogen bonds : angle 5.25175 / 3.65 ( 696) link_NAG-ASN : bond 0.00708 / 0.43 ( 10) link_NAG-ASN : angle 3.37864 / 2.56 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 59 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8252 (t0) cc_final: 0.7923 (t0) REVERT: B 31 ARG cc_start: 0.7917 (mtt180) cc_final: 0.7472 (tpt170) REVERT: B 187 LEU cc_start: 0.8913 (tt) cc_final: 0.8569 (tt) REVERT: C 85 LYS cc_start: 0.7774 (mttt) cc_final: 0.7216 (mtpt) REVERT: C 210 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7173 (tt) REVERT: C 561 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7672 (t0) outliers start: 30 outliers final: 25 residues processed: 86 average time/residue: 0.0745 time to fit residues: 9.4379 Evaluate side-chains 84 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 357 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 506 ASN Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 571 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 30.0000 chunk 97 optimal weight: 0.5980 chunk 80 optimal weight: 0.0070 chunk 61 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 85 optimal weight: 0.0870 chunk 12 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 188 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 = 0.4566 r_free = 0.4566 target = 0.246808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.229636 restraints weight = 9113.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.226163 restraints weight = 17966.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.200650 restraints weight = 21339.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.186175 restraints weight = 16722.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.179508 restraints weight = 14174.405| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8257 Z= 0.119 Angle : 0.558 9.643 11271 Z= 0.280 Chirality : 0.047 0.369 1259 Planarity : 0.004 0.046 1443 Dihedral : 6.373 59.328 1320 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.15 % Allowed : 11.25 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: -0.70 (0.27), residues: 1000 helix: -1.37 (0.75), residues: 50 sheet: 0.86 (0.30), residues: 360 loop : -1.30 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 99 TYR 0.021 0.001 TYR A 91 PHE 0.013 0.001 PHE B 80 TRP 0.011 0.001 TRP C 424 HIS 0.002 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 8236) covalent geometry : angle 0.53103 / 0.27 (11219) SS BOND : bond 0.00386 / 0.20 ( 11) SS BOND : angle 0.76372 / 0.45 ( 22) hydrogen bonds : bond 0.03376 / 2.29 ( 233) hydrogen bonds : angle 5.09362 / 3.53 ( 696) link_NAG-ASN : bond 0.00711 / 0.44 ( 10) link_NAG-ASN : angle 3.35638 / 2.54 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8207 (t0) cc_final: 0.7899 (t0) REVERT: B 31 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7440 (tpt170) REVERT: B 165 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.4634 (pm20) REVERT: B 187 LEU cc_start: 0.8924 (tt) cc_final: 0.8565 (tt) REVERT: C 85 LYS cc_start: 0.7722 (mttt) cc_final: 0.7188 (mtpt) REVERT: C 210 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7224 (tt) REVERT: C 292 LYS cc_start: 0.8290 (mmmm) cc_final: 0.8069 (tppp) REVERT: C 561 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7559 (t0) outliers start: 28 outliers final: 23 residues processed: 89 average time/residue: 0.0722 time to fit residues: 9.3778 Evaluate side-chains 86 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 357 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 506 ASN Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 571 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 4 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 188 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 = 0.4539 r_free = 0.4539 target = 0.242174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.225422 restraints weight = 8921.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.223542 restraints weight = 22150.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.183078 restraints weight = 18846.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.173406 restraints weight = 15852.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.168864 restraints weight = 16215.565| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 8257 Z= 0.154 Angle : 0.578 9.602 11271 Z= 0.291 Chirality : 0.048 0.370 1259 Planarity : 0.004 0.046 1443 Dihedral : 6.447 59.763 1320 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.60 % Allowed : 11.59 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: -0.73 (0.27), residues: 1000 helix: -1.35 (0.75), residues: 50 sheet: 0.87 (0.30), residues: 358 loop : -1.34 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 99 TYR 0.021 0.001 TYR A 91 PHE 0.016 0.001 PHE B 80 TRP 0.012 0.001 TRP C 424 HIS 0.002 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.15 ( 8236) covalent geometry : angle 0.55094 / 0.29 (11219) SS BOND : bond 0.00460 / 0.24 ( 11) SS BOND : angle 0.91323 / 0.53 ( 22) hydrogen bonds : bond 0.03611 / 2.43 ( 233) hydrogen bonds : angle 5.05856 / 3.51 ( 696) link_NAG-ASN : bond 0.00698 / 0.43 ( 10) link_NAG-ASN : angle 3.35514 / 2.54 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 62 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8239 (m) REVERT: B 31 ARG cc_start: 0.8212 (mtt180) cc_final: 0.7464 (tpt170) REVERT: B 92 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8428 (t) REVERT: B 165 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.4781 (pm20) REVERT: B 187 LEU cc_start: 0.8873 (tt) cc_final: 0.8569 (tt) REVERT: C 85 LYS cc_start: 0.7769 (mttt) cc_final: 0.7210 (mtpt) REVERT: C 292 LYS cc_start: 0.8307 (mmmm) cc_final: 0.8085 (tppp) REVERT: C 561 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7661 (t0) outliers start: 32 outliers final: 24 residues processed: 90 average time/residue: 0.0758 time to fit residues: 9.7105 Evaluate side-chains 86 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 357 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 506 ASN Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 571 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 0.6980 chunk 53 optimal weight: 8.9990 chunk 76 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 20.0000 chunk 68 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 19 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 188 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 = 0.4561 r_free = 0.4561 target = 0.246165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.228403 restraints weight = 9071.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.227544 restraints weight = 17942.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.175437 restraints weight = 16573.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.171913 restraints weight = 15025.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.168410 restraints weight = 12532.494| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 8257 Z= 0.138 Angle : 0.572 9.588 11271 Z= 0.288 Chirality : 0.047 0.369 1259 Planarity : 0.004 0.046 1443 Dihedral : 6.402 59.196 1320 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.49 % Allowed : 11.92 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: -0.69 (0.27), residues: 1000 helix: -1.31 (0.76), residues: 50 sheet: 0.94 (0.30), residues: 352 loop : -1.33 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 99 TYR 0.022 0.001 TYR A 91 PHE 0.015 0.001 PHE B 80 TRP 0.012 0.001 TRP C 424 HIS 0.002 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 8236) covalent geometry : angle 0.54571 / 0.28 (11219) SS BOND : bond 0.00415 / 0.22 ( 11) SS BOND : angle 0.81392 / 0.48 ( 22) hydrogen bonds : bond 0.03456 / 2.33 ( 233) hydrogen bonds : angle 4.96770 / 3.46 ( 696) link_NAG-ASN : bond 0.00710 / 0.43 ( 10) link_NAG-ASN : angle 3.33894 / 2.53 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 62 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8060 (t0) cc_final: 0.7811 (t0) REVERT: B 31 ARG cc_start: 0.7811 (mtt180) cc_final: 0.7446 (tpt170) REVERT: B 92 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8465 (t) REVERT: B 165 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.4732 (pm20) REVERT: B 187 LEU cc_start: 0.8756 (tt) cc_final: 0.8502 (tt) REVERT: C 85 LYS cc_start: 0.7798 (mttt) cc_final: 0.7181 (mtpt) outliers start: 31 outliers final: 25 residues processed: 90 average time/residue: 0.0855 time to fit residues: 11.0777 Evaluate side-chains 83 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 56 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 357 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 506 ASN Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 571 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 59 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 15 optimal weight: 50.0000 chunk 64 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN ** B 188 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 = 0.4548 r_free = 0.4548 target = 0.244599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.229165 restraints weight = 9131.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.225864 restraints weight = 13581.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.223109 restraints weight = 17692.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.182193 restraints weight = 20436.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.167373 restraints weight = 16211.575| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 8257 Z= 0.182 Angle : 0.609 9.580 11271 Z= 0.310 Chirality : 0.048 0.371 1259 Planarity : 0.005 0.045 1443 Dihedral : 6.553 59.774 1320 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.37 % Allowed : 11.92 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: -0.77 (0.27), residues: 1000 helix: -1.28 (0.76), residues: 50 sheet: 0.84 (0.30), residues: 358 loop : -1.38 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 99 TYR 0.022 0.002 TYR A 91 PHE 0.017 0.001 PHE B 80 TRP 0.013 0.002 TRP C 424 HIS 0.002 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.18 ( 8236) covalent geometry : angle 0.58384 / 0.30 (11219) SS BOND : bond 0.00509 / 0.27 ( 11) SS BOND : angle 0.99346 / 0.57 ( 22) hydrogen bonds : bond 0.03803 / 2.55 ( 233) hydrogen bonds : angle 5.04182 / 3.50 ( 696) link_NAG-ASN : bond 0.00697 / 0.43 ( 10) link_NAG-ASN : angle 3.36344 / 2.54 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 57 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8155 (mt-10) REVERT: B 31 ARG cc_start: 0.8331 (mtt180) cc_final: 0.7477 (tpt170) REVERT: B 92 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8409 (t) REVERT: B 165 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.4783 (pm20) REVERT: B 187 LEU cc_start: 0.8844 (tt) cc_final: 0.8562 (tt) REVERT: C 85 LYS cc_start: 0.7804 (mttt) cc_final: 0.7189 (mtpt) outliers start: 30 outliers final: 26 residues processed: 83 average time/residue: 0.0725 time to fit residues: 8.6442 Evaluate side-chains 82 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 54 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 357 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 506 ASN Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 571 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 85 optimal weight: 0.0170 chunk 81 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN ** B 188 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 = 0.4559 r_free = 0.4559 target = 0.245930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.229539 restraints weight = 9067.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.227444 restraints weight = 15253.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.224755 restraints weight = 19455.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.196560 restraints weight = 21178.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.181336 restraints weight = 17357.980| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8257 Z= 0.134 Angle : 0.579 9.596 11271 Z= 0.293 Chirality : 0.047 0.371 1259 Planarity : 0.004 0.046 1443 Dihedral : 6.446 59.422 1320 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.49 % Allowed : 11.92 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: -0.70 (0.27), residues: 1000 helix: -1.22 (0.76), residues: 50 sheet: 0.90 (0.30), residues: 358 loop : -1.35 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 99 TYR 0.022 0.001 TYR A 91 PHE 0.014 0.001 PHE B 80 TRP 0.013 0.001 TRP C 424 HIS 0.002 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.13 ( 8236) covalent geometry : angle 0.55271 / 0.29 (11219) SS BOND : bond 0.00403 / 0.21 ( 11) SS BOND : angle 0.76725 / 0.45 ( 22) hydrogen bonds : bond 0.03415 / 2.31 ( 233) hydrogen bonds : angle 4.93840 / 3.43 ( 696) link_NAG-ASN : bond 0.00708 / 0.43 ( 10) link_NAG-ASN : angle 3.35098 / 2.54 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 56 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 31 ARG cc_start: 0.7826 (mtt180) cc_final: 0.7394 (tpt170) REVERT: B 165 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.4706 (pm20) REVERT: B 187 LEU cc_start: 0.8911 (tt) cc_final: 0.8617 (tt) REVERT: C 85 LYS cc_start: 0.7744 (mttt) cc_final: 0.7177 (mtpt) outliers start: 31 outliers final: 27 residues processed: 83 average time/residue: 0.0696 time to fit residues: 8.4590 Evaluate side-chains 84 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 56 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 357 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 506 ASN Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 571 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 51 optimal weight: 0.0770 chunk 34 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 30.0000 chunk 20 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN ** B 188 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 = 0.4558 r_free = 0.4558 target = 0.245617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.221436 restraints weight = 9050.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.217725 restraints weight = 15835.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.215133 restraints weight = 17651.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.213311 restraints weight = 17644.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.185479 restraints weight = 17732.340| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 8257 Z= 0.148 Angle : 0.586 9.517 11271 Z= 0.298 Chirality : 0.047 0.370 1259 Planarity : 0.005 0.046 1443 Dihedral : 6.437 59.373 1320 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.15 % Allowed : 12.26 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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 (0.27), residues: 1000 helix: -1.24 (0.76), residues: 50 sheet: 0.94 (0.30), residues: 352 loop : -1.37 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 99 TYR 0.023 0.001 TYR A 91 PHE 0.015 0.001 PHE B 80 TRP 0.012 0.001 TRP C 424 HIS 0.002 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 ( 8236) covalent geometry : angle 0.56008 / 0.29 (11219) SS BOND : bond 0.00429 / 0.23 ( 11) SS BOND : angle 0.82894 / 0.48 ( 22) hydrogen bonds : bond 0.03515 / 2.38 ( 233) hydrogen bonds : angle 4.92112 / 3.42 ( 696) link_NAG-ASN : bond 0.00706 / 0.43 ( 10) link_NAG-ASN : angle 3.34443 / 2.53 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 59 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 31 ARG cc_start: 0.7156 (mtt180) cc_final: 0.6780 (tpt170) REVERT: B 165 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.4782 (pm20) REVERT: B 187 LEU cc_start: 0.8924 (tt) cc_final: 0.8626 (tt) REVERT: C 85 LYS cc_start: 0.7707 (mttt) cc_final: 0.7173 (mtpt) outliers start: 28 outliers final: 27 residues processed: 83 average time/residue: 0.0722 time to fit residues: 8.7235 Evaluate side-chains 84 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 56 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 357 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 506 ASN Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 571 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 85 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 83 optimal weight: 0.1980 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN ** B 188 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 = 0.4550 r_free = 0.4550 target = 0.244882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.221812 restraints weight = 9003.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.216908 restraints weight = 13992.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.214925 restraints weight = 16727.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.212637 restraints weight = 18369.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.210231 restraints weight = 17564.824| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 8257 Z= 0.177 Angle : 0.610 9.470 11271 Z= 0.311 Chirality : 0.048 0.369 1259 Planarity : 0.005 0.045 1443 Dihedral : 6.517 59.911 1320 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.26 % Allowed : 12.37 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: -0.79 (0.27), residues: 1000 helix: -1.25 (0.76), residues: 50 sheet: 0.79 (0.30), residues: 359 loop : -1.38 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 99 TYR 0.023 0.002 TYR A 91 PHE 0.017 0.001 PHE B 80 TRP 0.013 0.002 TRP C 424 HIS 0.002 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 ( 8236) covalent geometry : angle 0.58444 / 0.31 (11219) SS BOND : bond 0.00486 / 0.26 ( 11) SS BOND : angle 0.93116 / 0.54 ( 22) hydrogen bonds : bond 0.03801 / 2.58 ( 233) hydrogen bonds : angle 4.97624 / 3.45 ( 696) link_NAG-ASN : bond 0.00707 / 0.43 ( 10) link_NAG-ASN : angle 3.34977 / 2.54 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1317.53 seconds wall clock time: 23 minutes 28.51 seconds (1408.51 seconds total)