Starting phenix.real_space_refine on Sun Aug 24 18:15:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8szc_40908/08_2025/8szc_40908_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8szc_40908/08_2025/8szc_40908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8szc_40908/08_2025/8szc_40908_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8szc_40908/08_2025/8szc_40908_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8szc_40908/08_2025/8szc_40908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8szc_40908/08_2025/8szc_40908.map" } resolution = 3.06 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= 0.029 sd= 0.057 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: 7 Type Number sf(0) Gaussians P 17 5.49 5 Mg 1 5.21 5 S 41 5.16 5 C 6863 2.51 5 N 1670 2.21 5 O 1919 1.98 5 H 9951 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20462 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 10683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 10683 Classifications: {'peptide': 664} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 650} Chain: "C" Number of atoms: 9074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 9074 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 19, 'TRANS': 551} Chain breaks: 1 Chain: "D" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 387 Unusual residues: {' MG': 1, 'ATP': 1, 'POV': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-2': 2, 'POV:plan-3': 3, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 318 Unusual residues: {'ATP': 1, 'HT1': 1, 'POV': 11} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-2': 3, 'POV:plan-3': 7, 'POV:plan-1': 4} Unresolved non-hydrogen planarities: 44 Time building chain proxies: 3.76, per 1000 atoms: 0.18 Number of scatterers: 20462 At special positions: 0 Unit cell: (73.62, 103.886, 155.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 41 16.00 P 17 15.00 Mg 1 11.99 O 1919 8.00 N 1670 7.00 C 6863 6.00 H 9951 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 500.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2292 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 8 sheets defined 65.3% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'D' and resid 2 through 13 removed outlier: 3.637A pdb=" N LEU D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 34 Processing helix chain 'D' and resid 34 through 44 Processing helix chain 'D' and resid 46 through 50 removed outlier: 3.926A pdb=" N ILE D 50 " --> pdb=" O ILE D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 79 removed outlier: 3.975A pdb=" N GLN D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 75 through 79' Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 145 through 195 removed outlier: 3.550A pdb=" N LYS D 195 " --> pdb=" O SER D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 203 removed outlier: 3.634A pdb=" N PHE D 201 " --> pdb=" O PRO D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 249 removed outlier: 4.500A pdb=" N ASP D 216 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR D 217 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 259 through 297 removed outlier: 4.132A pdb=" N TYR D 276 " --> pdb=" O ARG D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.683A pdb=" N PHE D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 336 Processing helix chain 'D' and resid 337 through 362 Processing helix chain 'D' and resid 368 through 384 removed outlier: 3.598A pdb=" N GLN D 384 " --> pdb=" O ASN D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 411 removed outlier: 5.049A pdb=" N GLU D 397 " --> pdb=" O PHE D 393 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU D 398 " --> pdb=" O SER D 394 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 477 Processing helix chain 'D' and resid 495 through 497 No H-bonds generated for 'chain 'D' and resid 495 through 497' Processing helix chain 'D' and resid 498 through 504 Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 535 through 542 removed outlier: 3.541A pdb=" N ALA D 539 " --> pdb=" O GLU D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 550 Processing helix chain 'D' and resid 568 through 584 Processing helix chain 'D' and resid 600 through 613 removed outlier: 3.902A pdb=" N VAL D 604 " --> pdb=" O GLU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 653 Processing helix chain 'D' and resid 655 through 664 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 8 through 15 removed outlier: 3.590A pdb=" N PHE C 12 " --> pdb=" O LEU C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 34 Processing helix chain 'C' and resid 34 through 49 removed outlier: 4.148A pdb=" N LYS C 38 " --> pdb=" O MET C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 103 removed outlier: 3.542A pdb=" N THR C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 112 removed outlier: 3.713A pdb=" N TYR C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 157 removed outlier: 5.053A pdb=" N LEU C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLN C 126 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET C 146 " --> pdb=" O SER C 142 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET C 147 " --> pdb=" O THR C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 165 removed outlier: 3.591A pdb=" N THR C 162 " --> pdb=" O SER C 158 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE C 163 " --> pdb=" O TRP C 159 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 164 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 207 removed outlier: 3.866A pdb=" N VAL C 171 " --> pdb=" O ILE C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 218 through 243 removed outlier: 3.739A pdb=" N ILE C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 270 removed outlier: 3.532A pdb=" N SER C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 288 through 315 removed outlier: 3.930A pdb=" N MET C 292 " --> pdb=" O MET C 288 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 383 removed outlier: 4.154A pdb=" N ILE C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 427 through 434 Processing helix chain 'C' and resid 441 through 451 removed outlier: 4.109A pdb=" N GLN C 445 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 458 Processing helix chain 'C' and resid 476 through 491 removed outlier: 3.867A pdb=" N ALA C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 521 Processing helix chain 'C' and resid 532 through 536 removed outlier: 3.647A pdb=" N VAL C 536 " --> pdb=" O LEU C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 563 Processing sheet with id=AA1, first strand: chain 'D' and resid 65 through 66 removed outlier: 3.946A pdb=" N SER D 71 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP D 54 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 109 through 112 removed outlier: 3.709A pdb=" N ARG D 126 " --> pdb=" O ILE D 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 452 through 453 removed outlier: 3.615A pdb=" N ASP D 486 " --> pdb=" O ARG D 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 435 through 438 removed outlier: 6.367A pdb=" N VAL D 435 " --> pdb=" O LYS D 447 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS D 447 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE D 437 " --> pdb=" O VAL D 445 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 459 through 460 removed outlier: 6.580A pdb=" N VAL D 459 " --> pdb=" O VAL D 620 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 462 through 463 removed outlier: 6.564A pdb=" N VAL D 462 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE D 634 " --> pdb=" O ARG D 645 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ARG D 645 " --> pdb=" O ILE D 634 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL D 636 " --> pdb=" O VAL D 643 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL D 643 " --> pdb=" O VAL D 636 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 338 through 339 removed outlier: 3.617A pdb=" N VAL C 338 " --> pdb=" O THR C 396 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR C 396 " --> pdb=" O VAL C 338 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 414 through 417 removed outlier: 6.372A pdb=" N GLY C 415 " --> pdb=" O ILE C 497 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ASP C 499 " --> pdb=" O GLY C 415 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C 417 " --> pdb=" O ASP C 499 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 496 " --> pdb=" O THR C 525 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL C 367 " --> pdb=" O ILE C 528 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR C 366 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N LEU C 543 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY C 368 " --> pdb=" O LEU C 543 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET C 545 " --> pdb=" O GLY C 368 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 370 " --> pdb=" O MET C 545 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL C 549 " --> pdb=" O ASP C 546 " (cutoff:3.500A) 611 hydrogen bonds defined for protein. 1803 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: 4.62 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9951 1.03 - 1.23: 32 1.23 - 1.42: 4285 1.42 - 1.62: 6267 1.62 - 1.81: 104 Bond restraints: 20639 Sorted by residual: bond pdb=" C29 POV C 601 " pdb="C210 POV C 601 " ideal model delta sigma weight residual 1.333 1.540 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C29 POV C 603 " pdb="C210 POV C 603 " ideal model delta sigma weight residual 1.333 1.537 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C29 POV D 702 " pdb="C210 POV D 702 " ideal model delta sigma weight residual 1.333 1.534 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C29 POV C 605 " pdb="C210 POV C 605 " ideal model delta sigma weight residual 1.333 1.534 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C29 POV D 706 " pdb="C210 POV D 706 " ideal model delta sigma weight residual 1.333 1.533 -0.200 2.00e-02 2.50e+03 1.01e+02 ... (remaining 20634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.00: 36612 4.00 - 8.00: 176 8.00 - 12.00: 36 12.00 - 16.00: 24 16.00 - 20.00: 20 Bond angle restraints: 36868 Sorted by residual: angle pdb=" C29 POV D 703 " pdb="C210 POV D 703 " pdb="C211 POV D 703 " ideal model delta sigma weight residual 127.67 107.67 20.00 3.00e+00 1.11e-01 4.44e+01 angle pdb=" C28 POV C 603 " pdb=" C29 POV C 603 " pdb="C210 POV C 603 " ideal model delta sigma weight residual 127.79 107.91 19.88 3.00e+00 1.11e-01 4.39e+01 angle pdb=" O13 POV D 710 " pdb=" P POV D 710 " pdb=" O14 POV D 710 " ideal model delta sigma weight residual 121.11 101.33 19.78 3.00e+00 1.11e-01 4.35e+01 angle pdb=" O13 POV C 602 " pdb=" P POV C 602 " pdb=" O14 POV C 602 " ideal model delta sigma weight residual 121.11 101.61 19.50 3.00e+00 1.11e-01 4.23e+01 angle pdb=" O13 POV D 709 " pdb=" P POV D 709 " pdb=" O14 POV D 709 " ideal model delta sigma weight residual 121.11 101.64 19.47 3.00e+00 1.11e-01 4.21e+01 ... (remaining 36863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.39: 9232 32.39 - 64.77: 563 64.77 - 97.16: 34 97.16 - 129.54: 16 129.54 - 161.93: 9 Dihedral angle restraints: 9854 sinusoidal: 5608 harmonic: 4246 Sorted by residual: dihedral pdb=" C29 POV D 710 " pdb="C210 POV D 710 " pdb="C211 POV D 710 " pdb="C212 POV D 710 " ideal model delta sinusoidal sigma weight residual 112.25 -49.68 161.93 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C39 POV D 705 " pdb="C310 POV D 705 " pdb="C311 POV D 705 " pdb="C312 POV D 705 " ideal model delta sinusoidal sigma weight residual -179.51 -17.93 -161.58 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C29 POV C 603 " pdb="C210 POV C 603 " pdb="C211 POV C 603 " pdb="C212 POV C 603 " ideal model delta sinusoidal sigma weight residual 112.25 -86.31 -161.44 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 9851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1338 0.059 - 0.118: 192 0.118 - 0.177: 16 0.177 - 0.235: 0 0.235 - 0.294: 6 Chirality restraints: 1552 Sorted by residual: chirality pdb=" C2' ATP D 711 " pdb=" C1' ATP D 711 " pdb=" C3' ATP D 711 " pdb=" O2' ATP D 711 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C3' ATP D 711 " pdb=" C2' ATP D 711 " pdb=" C4' ATP D 711 " pdb=" O3' ATP D 711 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C2' ATP C 612 " pdb=" C1' ATP C 612 " pdb=" C3' ATP C 612 " pdb=" O2' ATP C 612 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 1549 not shown) Planarity restraints: 2962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV D 708 " -0.284 2.00e-02 2.50e+03 3.22e-01 1.04e+03 pdb=" C29 POV D 708 " 0.215 2.00e-02 2.50e+03 pdb="C210 POV D 708 " 0.412 2.00e-02 2.50e+03 pdb="C211 POV D 708 " -0.343 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 707 " -0.318 2.00e-02 2.50e+03 3.09e-01 9.56e+02 pdb=" C29 POV D 707 " 0.344 2.00e-02 2.50e+03 pdb="C210 POV D 707 " 0.272 2.00e-02 2.50e+03 pdb="C211 POV D 707 " -0.298 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 706 " -0.157 2.00e-02 2.50e+03 2.94e-01 8.65e+02 pdb=" C29 POV D 706 " 0.397 2.00e-02 2.50e+03 pdb="C210 POV D 706 " -0.380 2.00e-02 2.50e+03 pdb="C211 POV D 706 " 0.140 2.00e-02 2.50e+03 ... (remaining 2959 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 514 2.12 - 2.74: 36842 2.74 - 3.36: 60563 3.36 - 3.98: 76628 3.98 - 4.60: 121142 Nonbonded interactions: 295689 Sorted by model distance: nonbonded pdb=" O ARG D 77 " pdb="HH11 ARG D 77 " model vdw 1.498 2.450 nonbonded pdb=" OE2 GLU D 644 " pdb=" H GLN D 657 " model vdw 1.608 2.450 nonbonded pdb=" O GLN D 92 " pdb=" HE ARG D 110 " model vdw 1.653 2.450 nonbonded pdb=" OD1 ASP D 44 " pdb=" H GLY D 370 " model vdw 1.669 2.450 nonbonded pdb="HE22 GLN D 303 " pdb=" O MET C 104 " model vdw 1.669 2.450 ... (remaining 295684 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.940 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: 0.120 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.690 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 : 0.011 0.207 10688 Z= 0.554 Angle : 1.338 20.000 14302 Z= 0.506 Chirality : 0.042 0.294 1552 Planarity : 0.021 0.322 1762 Dihedral : 21.695 161.931 4233 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 20.31 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.24), residues: 1229 helix: 0.99 (0.19), residues: 761 sheet: -1.95 (0.51), residues: 93 loop : -1.75 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 113 TYR 0.019 0.002 TYR C 434 PHE 0.021 0.001 PHE D 37 TRP 0.019 0.001 TRP C 78 HIS 0.003 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.01118 (10688) covalent geometry : angle 1.33755 (14302) hydrogen bonds : bond 0.12502 ( 611) hydrogen bonds : angle 6.11743 ( 1803) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 329 MET cc_start: 0.8623 (tpt) cc_final: 0.8003 (tpt) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2806 time to fit residues: 35.9639 Evaluate side-chains 92 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 326 GLN D 327 ASN C 479 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.097160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.078036 restraints weight = 65232.161| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.20 r_work: 0.3420 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.0593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10688 Z= 0.225 Angle : 0.597 8.819 14302 Z= 0.316 Chirality : 0.039 0.159 1552 Planarity : 0.005 0.063 1762 Dihedral : 21.064 162.397 1896 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 1.05 % Allowed : 19.92 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.24), residues: 1229 helix: 1.05 (0.19), residues: 773 sheet: -2.16 (0.51), residues: 91 loop : -1.96 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 212 TYR 0.014 0.002 TYR C 19 PHE 0.016 0.002 PHE D 166 TRP 0.014 0.001 TRP C 78 HIS 0.005 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00505 (10688) covalent geometry : angle 0.59723 (14302) hydrogen bonds : bond 0.05290 ( 611) hydrogen bonds : angle 5.03330 ( 1803) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 103 average time/residue: 0.2410 time to fit residues: 34.1436 Evaluate side-chains 98 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 460 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 91 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 326 GLN D 660 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.096974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.078535 restraints weight = 64779.940| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.11 r_work: 0.3440 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10688 Z= 0.157 Angle : 0.522 8.263 14302 Z= 0.282 Chirality : 0.037 0.154 1552 Planarity : 0.005 0.057 1762 Dihedral : 19.855 166.031 1896 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.59 % Favored : 93.33 % Rotamer: Outliers : 1.24 % Allowed : 20.11 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.24), residues: 1229 helix: 1.27 (0.19), residues: 775 sheet: -2.20 (0.51), residues: 91 loop : -2.00 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 212 TYR 0.014 0.001 TYR C 19 PHE 0.014 0.001 PHE D 162 TRP 0.014 0.001 TRP C 78 HIS 0.005 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00344 (10688) covalent geometry : angle 0.52236 (14302) hydrogen bonds : bond 0.04794 ( 611) hydrogen bonds : angle 4.77363 ( 1803) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8565 (mt) REVERT: D 436 SER cc_start: 0.6144 (OUTLIER) cc_final: 0.5035 (t) REVERT: C 236 MET cc_start: 0.7494 (mmp) cc_final: 0.7107 (mmp) outliers start: 13 outliers final: 10 residues processed: 106 average time/residue: 0.2659 time to fit residues: 39.4938 Evaluate side-chains 104 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 544 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 8 optimal weight: 0.0980 chunk 100 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.097285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.077543 restraints weight = 65306.001| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.27 r_work: 0.3440 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10688 Z= 0.138 Angle : 0.507 8.227 14302 Z= 0.276 Chirality : 0.037 0.152 1552 Planarity : 0.005 0.055 1762 Dihedral : 18.934 172.494 1896 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.83 % Favored : 93.08 % Rotamer: Outliers : 1.33 % Allowed : 19.92 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.25), residues: 1229 helix: 1.47 (0.19), residues: 775 sheet: -2.19 (0.52), residues: 91 loop : -2.01 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 113 TYR 0.013 0.001 TYR D 659 PHE 0.014 0.001 PHE D 162 TRP 0.016 0.001 TRP C 78 HIS 0.004 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00298 (10688) covalent geometry : angle 0.50734 (14302) hydrogen bonds : bond 0.04546 ( 611) hydrogen bonds : angle 4.66873 ( 1803) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 436 SER cc_start: 0.6137 (OUTLIER) cc_final: 0.5060 (t) outliers start: 14 outliers final: 9 residues processed: 105 average time/residue: 0.2694 time to fit residues: 39.3709 Evaluate side-chains 100 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 460 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 0.0060 chunk 80 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.098305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.079116 restraints weight = 64576.613| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.20 r_work: 0.3448 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10688 Z= 0.136 Angle : 0.504 9.820 14302 Z= 0.272 Chirality : 0.037 0.167 1552 Planarity : 0.005 0.053 1762 Dihedral : 18.197 179.962 1896 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.51 % Favored : 93.41 % Rotamer: Outliers : 1.62 % Allowed : 19.73 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.25), residues: 1229 helix: 1.55 (0.19), residues: 775 sheet: -2.15 (0.52), residues: 91 loop : -2.01 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 113 TYR 0.018 0.001 TYR D 659 PHE 0.013 0.001 PHE D 162 TRP 0.019 0.001 TRP C 78 HIS 0.004 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00297 (10688) covalent geometry : angle 0.50355 (14302) hydrogen bonds : bond 0.04441 ( 611) hydrogen bonds : angle 4.55728 ( 1803) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 436 SER cc_start: 0.6203 (OUTLIER) cc_final: 0.5113 (t) outliers start: 17 outliers final: 10 residues processed: 108 average time/residue: 0.2554 time to fit residues: 38.5314 Evaluate side-chains 101 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 544 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.098214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.079035 restraints weight = 64672.774| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.20 r_work: 0.3447 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10688 Z= 0.152 Angle : 0.510 8.896 14302 Z= 0.276 Chirality : 0.037 0.161 1552 Planarity : 0.005 0.053 1762 Dihedral : 17.674 172.996 1896 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.83 % Favored : 93.08 % Rotamer: Outliers : 1.14 % Allowed : 19.92 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.25), residues: 1229 helix: 1.57 (0.19), residues: 773 sheet: -2.13 (0.53), residues: 91 loop : -2.07 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 113 TYR 0.013 0.001 TYR C 19 PHE 0.013 0.001 PHE D 162 TRP 0.008 0.001 TRP C 78 HIS 0.003 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00338 (10688) covalent geometry : angle 0.50967 (14302) hydrogen bonds : bond 0.04442 ( 611) hydrogen bonds : angle 4.55827 ( 1803) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 436 SER cc_start: 0.6232 (OUTLIER) cc_final: 0.5138 (t) outliers start: 12 outliers final: 9 residues processed: 105 average time/residue: 0.2718 time to fit residues: 39.4627 Evaluate side-chains 102 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 544 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 61 optimal weight: 0.2980 chunk 42 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.098236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.079078 restraints weight = 64554.793| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.20 r_work: 0.3450 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10688 Z= 0.144 Angle : 0.503 8.235 14302 Z= 0.273 Chirality : 0.037 0.165 1552 Planarity : 0.005 0.057 1762 Dihedral : 17.016 159.401 1896 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.67 % Favored : 93.25 % Rotamer: Outliers : 1.14 % Allowed : 19.83 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.25), residues: 1229 helix: 1.58 (0.19), residues: 774 sheet: -2.12 (0.53), residues: 91 loop : -2.08 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 113 TYR 0.014 0.001 TYR C 19 PHE 0.013 0.001 PHE D 162 TRP 0.007 0.001 TRP C 78 HIS 0.003 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00319 (10688) covalent geometry : angle 0.50334 (14302) hydrogen bonds : bond 0.04397 ( 611) hydrogen bonds : angle 4.49611 ( 1803) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 436 SER cc_start: 0.6249 (OUTLIER) cc_final: 0.5149 (t) REVERT: C 546 ASP cc_start: 0.7626 (m-30) cc_final: 0.7088 (t0) outliers start: 12 outliers final: 9 residues processed: 104 average time/residue: 0.2424 time to fit residues: 35.2703 Evaluate side-chains 101 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 544 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 43 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 431 ASN ** C 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.097901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.078785 restraints weight = 64823.972| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.19 r_work: 0.3439 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10688 Z= 0.160 Angle : 0.511 8.357 14302 Z= 0.277 Chirality : 0.037 0.158 1552 Planarity : 0.005 0.057 1762 Dihedral : 16.567 145.605 1896 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.59 % Favored : 93.33 % Rotamer: Outliers : 1.14 % Allowed : 19.64 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.24), residues: 1229 helix: 1.52 (0.19), residues: 774 sheet: -2.13 (0.52), residues: 91 loop : -2.10 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 113 TYR 0.013 0.001 TYR C 19 PHE 0.014 0.001 PHE D 162 TRP 0.007 0.001 TRP C 78 HIS 0.003 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00356 (10688) covalent geometry : angle 0.51118 (14302) hydrogen bonds : bond 0.04433 ( 611) hydrogen bonds : angle 4.51113 ( 1803) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 436 SER cc_start: 0.6278 (OUTLIER) cc_final: 0.5186 (t) REVERT: C 546 ASP cc_start: 0.7662 (m-30) cc_final: 0.7107 (t0) outliers start: 12 outliers final: 10 residues processed: 102 average time/residue: 0.2812 time to fit residues: 39.8385 Evaluate side-chains 101 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 544 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.097882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.078716 restraints weight = 64464.906| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.20 r_work: 0.3442 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10688 Z= 0.162 Angle : 0.515 8.416 14302 Z= 0.279 Chirality : 0.037 0.156 1552 Planarity : 0.005 0.059 1762 Dihedral : 16.183 142.293 1896 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.75 % Favored : 93.17 % Rotamer: Outliers : 1.05 % Allowed : 19.92 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.24), residues: 1229 helix: 1.50 (0.18), residues: 774 sheet: -2.15 (0.52), residues: 91 loop : -2.12 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 113 TYR 0.015 0.001 TYR C 19 PHE 0.014 0.001 PHE D 162 TRP 0.008 0.001 TRP C 78 HIS 0.003 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00361 (10688) covalent geometry : angle 0.51516 (14302) hydrogen bonds : bond 0.04446 ( 611) hydrogen bonds : angle 4.52045 ( 1803) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 436 SER cc_start: 0.6269 (OUTLIER) cc_final: 0.5180 (t) REVERT: C 546 ASP cc_start: 0.7622 (m-30) cc_final: 0.7084 (t0) outliers start: 11 outliers final: 10 residues processed: 100 average time/residue: 0.2843 time to fit residues: 39.1047 Evaluate side-chains 102 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 544 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 89 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 660 GLN ** C 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.098082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.078982 restraints weight = 64356.027| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.19 r_work: 0.3441 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10688 Z= 0.146 Angle : 0.506 8.426 14302 Z= 0.273 Chirality : 0.037 0.153 1552 Planarity : 0.005 0.056 1762 Dihedral : 15.557 137.018 1896 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.59 % Favored : 93.33 % Rotamer: Outliers : 1.05 % Allowed : 20.02 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.25), residues: 1229 helix: 1.56 (0.19), residues: 775 sheet: -2.13 (0.52), residues: 91 loop : -2.11 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 113 TYR 0.014 0.001 TYR C 19 PHE 0.014 0.001 PHE D 162 TRP 0.009 0.001 TRP C 78 HIS 0.003 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00323 (10688) covalent geometry : angle 0.50557 (14302) hydrogen bonds : bond 0.04359 ( 611) hydrogen bonds : angle 4.48991 ( 1803) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 436 SER cc_start: 0.6284 (OUTLIER) cc_final: 0.5206 (t) REVERT: C 546 ASP cc_start: 0.7622 (m-30) cc_final: 0.7071 (t0) outliers start: 11 outliers final: 9 residues processed: 100 average time/residue: 0.2627 time to fit residues: 36.1499 Evaluate side-chains 101 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 544 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 19 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 326 GLN ** C 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.096988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.078532 restraints weight = 64071.067| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.06 r_work: 0.3430 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10688 Z= 0.210 Angle : 0.552 8.898 14302 Z= 0.298 Chirality : 0.038 0.161 1552 Planarity : 0.005 0.051 1762 Dihedral : 15.653 135.602 1896 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.16 % Favored : 92.68 % Rotamer: Outliers : 1.14 % Allowed : 20.11 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.24), residues: 1229 helix: 1.35 (0.18), residues: 774 sheet: -2.22 (0.51), residues: 92 loop : -2.25 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 113 TYR 0.016 0.002 TYR C 19 PHE 0.016 0.002 PHE C 145 TRP 0.007 0.001 TRP C 78 HIS 0.004 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00477 (10688) covalent geometry : angle 0.55175 (14302) hydrogen bonds : bond 0.04637 ( 611) hydrogen bonds : angle 4.61431 ( 1803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5568.26 seconds wall clock time: 95 minutes 8.69 seconds (5708.69 seconds total)