Starting phenix.real_space_refine on Sun Aug 24 18:05:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fmv_29297/08_2025/8fmv_29297_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fmv_29297/08_2025/8fmv_29297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fmv_29297/08_2025/8fmv_29297_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fmv_29297/08_2025/8fmv_29297_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fmv_29297/08_2025/8fmv_29297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fmv_29297/08_2025/8fmv_29297.map" } resolution = 3.34 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= 0.023 sd= 0.049 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 21 5.49 5 Mg 1 5.21 5 S 41 5.16 5 C 6829 2.51 5 N 1681 2.21 5 O 1928 1.98 5 H 9940 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 20441 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 10700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 10700 Classifications: {'peptide': 665} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 651} Chain: "C" Number of atoms: 9038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 9038 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 19, 'TRANS': 549} Chain breaks: 1 Chain: "D" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 376 Unusual residues: {' MG': 1, 'ATP': 1, 'POV': 12} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-1': 4, 'POV:plan-2': 6, 'POV:plan-3': 4} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 327 Unusual residues: {'ATP': 1, 'HT1': 2, 'POV': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-3': 4, 'POV:plan-2': 3} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 3.92, per 1000 atoms: 0.19 Number of scatterers: 20441 At special positions: 0 Unit cell: (71.166, 103.886, 157.056, 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 21 15.00 Mg 1 11.99 O 1928 8.00 N 1681 7.00 C 6829 6.00 H 9940 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: 2.06 Conformation dependent library (CDL) restraints added in 587.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2290 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 7 sheets defined 65.2% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'D' and resid 2 through 13 removed outlier: 3.661A pdb=" N LEU D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 46 Proline residue: D 36 - end of helix Processing helix chain 'D' and resid 47 through 52 removed outlier: 4.097A pdb=" N ILE D 50 " --> pdb=" O ILE D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 142 through 194 removed outlier: 4.137A pdb=" N LYS D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY D 148 " --> pdb=" O PRO D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 203 removed outlier: 3.794A pdb=" N PHE D 201 " --> pdb=" O PRO D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 214 Processing helix chain 'D' and resid 214 through 230 Processing helix chain 'D' and resid 230 through 249 Processing helix chain 'D' and resid 249 through 258 removed outlier: 3.647A pdb=" N VAL D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 297 removed outlier: 3.698A pdb=" N TYR D 276 " --> pdb=" O ARG D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 Processing helix chain 'D' and resid 307 through 336 Processing helix chain 'D' and resid 337 through 362 removed outlier: 3.587A pdb=" N ASN D 362 " --> pdb=" O GLY D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 383 Processing helix chain 'D' and resid 385 through 411 removed outlier: 5.007A pdb=" N GLU D 397 " --> pdb=" O PHE D 393 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU D 398 " --> pdb=" O SER D 394 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 477 removed outlier: 3.769A pdb=" N ILE D 472 " --> pdb=" O GLY D 468 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU D 473 " --> pdb=" O LYS D 469 " (cutoff:3.500A) 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 505 removed outlier: 3.773A pdb=" N HIS D 505 " --> pdb=" O GLU D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 535 through 541 removed outlier: 3.772A pdb=" N ALA D 539 " --> pdb=" O GLU D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 563 removed outlier: 3.845A pdb=" N GLU D 562 " --> pdb=" O PRO D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 584 removed outlier: 3.753A pdb=" N GLN D 573 " --> pdb=" O SER D 569 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP D 584 " --> pdb=" O ALA D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 613 removed outlier: 3.775A pdb=" N ILE D 605 " --> pdb=" O THR D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 654 Processing helix chain 'D' and resid 655 through 664 removed outlier: 3.724A pdb=" N TYR D 659 " --> pdb=" O GLU D 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 8 through 15 Processing helix chain 'C' and resid 16 through 34 Processing helix chain 'C' and resid 34 through 49 removed outlier: 4.272A pdb=" N LYS C 38 " --> pdb=" O MET C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 103 removed outlier: 3.678A pdb=" N THR C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 112 removed outlier: 3.643A pdb=" N TYR C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 123 Processing helix chain 'C' and resid 123 through 144 removed outlier: 4.385A pdb=" N ILE C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 157 Processing helix chain 'C' and resid 159 through 166 Processing helix chain 'C' and resid 167 through 207 removed outlier: 4.089A 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 216 through 243 removed outlier: 3.633A pdb=" N VAL C 221 " --> pdb=" O GLU C 217 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 270 removed outlier: 4.000A pdb=" N SER C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 315 removed outlier: 4.906A pdb=" N TRP C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) Proline residue: C 291 - end of helix removed outlier: 3.902A pdb=" N GLY C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 383 Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 427 through 434 Processing helix chain 'C' and resid 442 through 451 removed outlier: 3.778A pdb=" N GLN C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 459 removed outlier: 3.623A pdb=" N MET C 459 " --> pdb=" O LYS C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 491 removed outlier: 3.970A 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 537 removed outlier: 3.504A pdb=" N VAL C 536 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU C 537 " --> pdb=" O SER C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 562 Processing sheet with id=AA1, first strand: chain 'D' and resid 54 through 56 Processing sheet with id=AA2, first strand: chain 'D' and resid 89 through 93 Processing sheet with id=AA3, first strand: chain 'D' and resid 452 through 453 Processing sheet with id=AA4, first strand: chain 'D' and resid 435 through 437 removed outlier: 7.541A pdb=" N PHE D 437 " --> pdb=" O LYS D 447 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LYS D 447 " --> pdb=" O PHE D 437 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 506 through 509 removed outlier: 6.500A pdb=" N GLY D 507 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL D 636 " --> pdb=" O VAL D 643 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 357 through 361 removed outlier: 7.481A pdb=" N PHE C 359 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N SER C 340 " --> pdb=" O PHE C 359 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL C 361 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL C 338 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 400 " --> pdb=" O PHE C 397 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 414 through 417 removed outlier: 6.433A pdb=" N LEU C 496 " --> pdb=" O PHE C 527 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU C 529 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU C 498 " --> pdb=" O LEU C 529 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N THR C 366 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU C 543 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLY C 368 " --> pdb=" O LEU C 543 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N MET C 545 " --> pdb=" O GLY C 368 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA C 370 " --> pdb=" O MET C 545 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE C 542 " --> pdb=" O ARG C 553 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ARG C 553 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL C 544 " --> pdb=" O ALA C 551 " (cutoff:3.500A) 618 hydrogen bonds defined for protein. 1812 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: 4.84 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 3268 1.05 - 1.24: 8003 1.24 - 1.43: 3059 1.43 - 1.63: 6212 1.63 - 1.82: 82 Bond restraints: 20624 Sorted by residual: bond pdb=" NE1 TRP D 266 " pdb=" HE1 TRP D 266 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP D 54 " pdb=" HE1 TRP D 54 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP C 565 " pdb=" HE1 TRP C 565 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP C 10 " pdb=" HE1 TRP C 10 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP C 16 " pdb=" HE1 TRP C 16 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 20619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.06: 36691 4.06 - 8.13: 183 8.13 - 12.19: 5 12.19 - 16.26: 2 16.26 - 20.32: 2 Bond angle restraints: 36883 Sorted by residual: angle pdb=" PB ATP C 609 " pdb=" O3B ATP C 609 " pdb=" PG ATP C 609 " ideal model delta sigma weight residual 139.87 119.55 20.32 1.00e+00 1.00e+00 4.13e+02 angle pdb=" PA ATP D 713 " pdb=" O3A ATP D 713 " pdb=" PB ATP D 713 " ideal model delta sigma weight residual 136.83 117.71 19.12 1.00e+00 1.00e+00 3.65e+02 angle pdb=" PB ATP D 713 " pdb=" O3B ATP D 713 " pdb=" PG ATP D 713 " ideal model delta sigma weight residual 139.87 130.47 9.40 1.00e+00 1.00e+00 8.83e+01 angle pdb=" PA ATP C 609 " pdb=" O3A ATP C 609 " pdb=" PB ATP C 609 " ideal model delta sigma weight residual 136.83 128.65 8.18 1.00e+00 1.00e+00 6.70e+01 angle pdb=" N GLU D 655 " pdb=" CA GLU D 655 " pdb=" C GLU D 655 " ideal model delta sigma weight residual 108.00 117.55 -9.55 1.48e+00 4.57e-01 4.16e+01 ... (remaining 36878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.69: 9178 27.69 - 55.37: 506 55.37 - 83.06: 100 83.06 - 110.74: 18 110.74 - 138.43: 10 Dihedral angle restraints: 9812 sinusoidal: 5569 harmonic: 4243 Sorted by residual: dihedral pdb=" C29 POV C 608 " pdb="C210 POV C 608 " pdb="C211 POV C 608 " pdb="C212 POV C 608 " ideal model delta sinusoidal sigma weight residual 112.25 -109.32 -138.43 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" C27 POV D 706 " pdb=" C28 POV D 706 " pdb=" C29 POV D 706 " pdb="C210 POV D 706 " ideal model delta sinusoidal sigma weight residual 127.48 -3.34 130.82 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" C29 POV C 605 " pdb="C210 POV C 605 " pdb="C211 POV C 605 " pdb="C212 POV C 605 " ideal model delta sinusoidal sigma weight residual 112.25 -119.19 -128.56 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 9809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1427 0.075 - 0.151: 112 0.151 - 0.226: 12 0.226 - 0.301: 1 0.301 - 0.377: 1 Chirality restraints: 1553 Sorted by residual: chirality pdb=" CA THR C 466 " pdb=" N THR C 466 " pdb=" C THR C 466 " pdb=" CB THR C 466 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA GLU D 655 " pdb=" N GLU D 655 " pdb=" C GLU D 655 " pdb=" CB GLU D 655 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA THR D 458 " pdb=" N THR D 458 " pdb=" C THR D 458 " pdb=" CB THR D 458 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1550 not shown) Planarity restraints: 2957 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV D 709 " 0.110 2.00e-02 2.50e+03 2.45e-01 6.02e+02 pdb=" C29 POV D 709 " -0.341 2.00e-02 2.50e+03 pdb="C210 POV D 709 " 0.323 2.00e-02 2.50e+03 pdb="C211 POV D 709 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C 606 " 0.224 2.00e-02 2.50e+03 2.44e-01 5.96e+02 pdb=" C29 POV C 606 " -0.182 2.00e-02 2.50e+03 pdb="C210 POV C 606 " -0.299 2.00e-02 2.50e+03 pdb="C211 POV C 606 " 0.257 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 701 " -0.196 2.00e-02 2.50e+03 1.99e-01 3.97e+02 pdb=" C29 POV D 701 " 0.188 2.00e-02 2.50e+03 pdb="C210 POV D 701 " 0.210 2.00e-02 2.50e+03 pdb="C211 POV D 701 " -0.202 2.00e-02 2.50e+03 ... (remaining 2954 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 757 2.08 - 2.71: 31965 2.71 - 3.34: 59644 3.34 - 3.97: 79390 3.97 - 4.60: 121279 Nonbonded interactions: 293035 Sorted by model distance: nonbonded pdb=" HE2 TYR C 179 " pdb=" HG1 THR C 248 " model vdw 1.447 2.100 nonbonded pdb=" HH TYR C 179 " pdb=" HG1 THR C 248 " model vdw 1.477 2.100 nonbonded pdb=" HE2 MET C 144 " pdb=" HG1 THR C 148 " model vdw 1.477 2.270 nonbonded pdb=" HB3 GLU D 420 " pdb=" HG SER D 498 " model vdw 1.482 2.270 nonbonded pdb="HG13 ILE D 119 " pdb=" HG SER D 125 " model vdw 1.535 2.270 ... (remaining 293030 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: 5.240 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: 0.130 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 21.190 Find NCS groups from input model: 0.090 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.007 0.165 10684 Z= 0.396 Angle : 0.862 20.320 14342 Z= 0.542 Chirality : 0.044 0.377 1553 Planarity : 0.013 0.245 1758 Dihedral : 19.285 138.429 4196 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.10 % Allowed : 15.17 % Favored : 84.73 % 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 (0.24), residues: 1228 helix: 1.36 (0.19), residues: 766 sheet: -0.35 (0.68), residues: 74 loop : -1.94 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 567 TYR 0.020 0.001 TYR D 237 PHE 0.015 0.001 PHE D 106 TRP 0.016 0.001 TRP C 78 HIS 0.006 0.001 HIS D 307 Details of bonding type rmsd covalent geometry : bond 0.00723 (10684) covalent geometry : angle 0.86218 (14342) hydrogen bonds : bond 0.12161 ( 618) hydrogen bonds : angle 5.96920 ( 1812) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.489 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 106 PHE cc_start: 0.5997 (m-80) cc_final: 0.5684 (m-10) REVERT: C 430 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7788 (mp0) outliers start: 1 outliers final: 1 residues processed: 94 average time/residue: 0.3178 time to fit residues: 39.7873 Evaluate side-chains 88 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 543 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.089427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.066404 restraints weight = 71492.496| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.26 r_work: 0.3116 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10684 Z= 0.160 Angle : 0.539 6.061 14342 Z= 0.285 Chirality : 0.038 0.144 1553 Planarity : 0.004 0.041 1758 Dihedral : 17.863 129.192 1862 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.29 % Favored : 94.63 % Rotamer: Outliers : 0.38 % Allowed : 14.79 % Favored : 84.83 % 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: 0.58 (0.24), residues: 1228 helix: 1.42 (0.19), residues: 777 sheet: -0.35 (0.64), residues: 80 loop : -1.71 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 541 TYR 0.012 0.001 TYR D 156 PHE 0.011 0.001 PHE C 187 TRP 0.015 0.001 TRP C 78 HIS 0.003 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00350 (10684) covalent geometry : angle 0.53886 (14342) hydrogen bonds : bond 0.04863 ( 618) hydrogen bonds : angle 4.92214 ( 1812) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 430 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7757 (mp0) REVERT: C 467 MET cc_start: 0.7614 (mmm) cc_final: 0.7265 (mmm) outliers start: 4 outliers final: 2 residues processed: 95 average time/residue: 0.3193 time to fit residues: 39.9706 Evaluate side-chains 89 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 67 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 ASN C 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.088447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.065373 restraints weight = 71910.874| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.29 r_work: 0.3098 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10684 Z= 0.209 Angle : 0.521 5.857 14342 Z= 0.281 Chirality : 0.039 0.138 1553 Planarity : 0.004 0.043 1758 Dihedral : 16.909 146.153 1861 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.67 % Allowed : 15.36 % Favored : 83.97 % 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: 0.51 (0.24), residues: 1228 helix: 1.36 (0.18), residues: 776 sheet: -0.56 (0.63), residues: 80 loop : -1.66 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 624 TYR 0.014 0.001 TYR D 156 PHE 0.013 0.001 PHE D 323 TRP 0.016 0.001 TRP C 78 HIS 0.003 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00469 (10684) covalent geometry : angle 0.52123 (14342) hydrogen bonds : bond 0.04648 ( 618) hydrogen bonds : angle 4.83768 ( 1812) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 106 PHE cc_start: 0.6629 (m-80) cc_final: 0.6171 (m-10) REVERT: C 430 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7940 (mp0) REVERT: C 467 MET cc_start: 0.7637 (mmm) cc_final: 0.7290 (mmm) outliers start: 7 outliers final: 4 residues processed: 95 average time/residue: 0.2958 time to fit residues: 37.2861 Evaluate side-chains 92 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain C residue 538 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.088691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.066093 restraints weight = 71922.902| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.25 r_work: 0.3107 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10684 Z= 0.193 Angle : 0.508 5.174 14342 Z= 0.277 Chirality : 0.038 0.138 1553 Planarity : 0.004 0.041 1758 Dihedral : 16.531 154.306 1861 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.95 % Allowed : 14.79 % Favored : 84.26 % 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: 0.55 (0.24), residues: 1228 helix: 1.40 (0.18), residues: 776 sheet: -0.66 (0.62), residues: 80 loop : -1.61 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 572 TYR 0.019 0.001 TYR D 662 PHE 0.012 0.001 PHE D 323 TRP 0.016 0.001 TRP C 78 HIS 0.003 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00430 (10684) covalent geometry : angle 0.50807 (14342) hydrogen bonds : bond 0.04557 ( 618) hydrogen bonds : angle 4.76434 ( 1812) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 106 PHE cc_start: 0.6537 (m-80) cc_final: 0.6129 (m-10) REVERT: D 109 ASN cc_start: 0.8062 (m110) cc_final: 0.7731 (m110) REVERT: D 662 TYR cc_start: 0.7939 (t80) cc_final: 0.7730 (t80) REVERT: C 430 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7937 (mp0) REVERT: C 467 MET cc_start: 0.7639 (mmm) cc_final: 0.7334 (mmm) outliers start: 10 outliers final: 6 residues processed: 96 average time/residue: 0.3303 time to fit residues: 42.2859 Evaluate side-chains 94 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 205 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 17 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 26 optimal weight: 0.0270 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.089096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.066291 restraints weight = 71236.671| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.26 r_work: 0.3121 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10684 Z= 0.142 Angle : 0.477 5.072 14342 Z= 0.259 Chirality : 0.037 0.137 1553 Planarity : 0.004 0.043 1758 Dihedral : 15.966 167.280 1861 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.86 % Allowed : 15.08 % Favored : 84.06 % 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: 0.68 (0.24), residues: 1228 helix: 1.54 (0.18), residues: 780 sheet: -0.70 (0.58), residues: 89 loop : -1.70 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 572 TYR 0.010 0.001 TYR D 156 PHE 0.010 0.001 PHE D 323 TRP 0.017 0.001 TRP C 78 HIS 0.002 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00308 (10684) covalent geometry : angle 0.47721 (14342) hydrogen bonds : bond 0.04319 ( 618) hydrogen bonds : angle 4.61070 ( 1812) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 106 PHE cc_start: 0.6622 (m-80) cc_final: 0.6118 (m-10) REVERT: D 299 MET cc_start: 0.8137 (tpp) cc_final: 0.7917 (tpp) REVERT: D 329 MET cc_start: 0.8800 (tpt) cc_final: 0.8538 (tpt) REVERT: D 662 TYR cc_start: 0.7986 (t80) cc_final: 0.7764 (t80) REVERT: C 47 MET cc_start: 0.8363 (mtt) cc_final: 0.8078 (mtt) REVERT: C 430 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7935 (mp0) REVERT: C 467 MET cc_start: 0.7638 (mmm) cc_final: 0.7345 (mmm) outliers start: 9 outliers final: 6 residues processed: 96 average time/residue: 0.3256 time to fit residues: 41.3167 Evaluate side-chains 91 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 205 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 86 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.088624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.065747 restraints weight = 71094.072| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.26 r_work: 0.3112 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10684 Z= 0.181 Angle : 0.490 5.007 14342 Z= 0.266 Chirality : 0.038 0.137 1553 Planarity : 0.004 0.043 1758 Dihedral : 15.921 174.308 1861 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.34 % Allowed : 14.79 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.24), residues: 1228 helix: 1.50 (0.18), residues: 780 sheet: -0.73 (0.62), residues: 80 loop : -1.63 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 572 TYR 0.013 0.001 TYR D 156 PHE 0.011 0.001 PHE D 356 TRP 0.016 0.001 TRP C 78 HIS 0.002 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00406 (10684) covalent geometry : angle 0.48963 (14342) hydrogen bonds : bond 0.04377 ( 618) hydrogen bonds : angle 4.63347 ( 1812) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 106 PHE cc_start: 0.6494 (m-80) cc_final: 0.6052 (m-10) REVERT: D 662 TYR cc_start: 0.7951 (t80) cc_final: 0.7743 (t80) REVERT: C 47 MET cc_start: 0.8380 (mtt) cc_final: 0.8105 (mtt) REVERT: C 430 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7775 (mp0) REVERT: C 467 MET cc_start: 0.7586 (mmm) cc_final: 0.7351 (tpp) REVERT: C 565 TRP cc_start: 0.5188 (OUTLIER) cc_final: 0.3688 (m100) outliers start: 14 outliers final: 12 residues processed: 96 average time/residue: 0.2857 time to fit residues: 36.5476 Evaluate side-chains 97 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 606 GLN Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 565 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 118 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 384 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.088895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.066022 restraints weight = 70846.586| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.29 r_work: 0.3121 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10684 Z= 0.150 Angle : 0.476 5.073 14342 Z= 0.259 Chirality : 0.037 0.139 1553 Planarity : 0.004 0.044 1758 Dihedral : 15.492 159.353 1861 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.54 % Rotamer: Outliers : 1.62 % Allowed : 14.79 % Favored : 83.59 % 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: 0.77 (0.25), residues: 1228 helix: 1.59 (0.18), residues: 780 sheet: -0.66 (0.63), residues: 79 loop : -1.60 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG D 629 TYR 0.011 0.001 TYR D 156 PHE 0.010 0.001 PHE D 323 TRP 0.016 0.001 TRP C 78 HIS 0.013 0.001 HIS D 648 Details of bonding type rmsd covalent geometry : bond 0.00328 (10684) covalent geometry : angle 0.47619 (14342) hydrogen bonds : bond 0.04259 ( 618) hydrogen bonds : angle 4.54588 ( 1812) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 106 PHE cc_start: 0.6591 (m-80) cc_final: 0.6128 (m-10) REVERT: D 329 MET cc_start: 0.8791 (tpt) cc_final: 0.8516 (tpt) REVERT: D 662 TYR cc_start: 0.8060 (t80) cc_final: 0.7835 (t80) REVERT: C 47 MET cc_start: 0.8376 (mtt) cc_final: 0.8146 (mtt) REVERT: C 430 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7792 (mp0) REVERT: C 565 TRP cc_start: 0.5166 (OUTLIER) cc_final: 0.3654 (m100) outliers start: 17 outliers final: 14 residues processed: 101 average time/residue: 0.3334 time to fit residues: 44.3502 Evaluate side-chains 101 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 606 GLN Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 565 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 21 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 384 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 = 0.3759 r_free = 0.3759 target = 0.089317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.066359 restraints weight = 71390.933| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.29 r_work: 0.3131 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10684 Z= 0.137 Angle : 0.475 8.678 14342 Z= 0.257 Chirality : 0.037 0.137 1553 Planarity : 0.004 0.044 1758 Dihedral : 15.141 143.005 1861 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.54 % Favored : 94.38 % Rotamer: Outliers : 1.43 % Allowed : 14.89 % Favored : 83.68 % 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: 0.84 (0.25), residues: 1228 helix: 1.66 (0.18), residues: 780 sheet: -0.70 (0.62), residues: 79 loop : -1.60 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 572 TYR 0.010 0.001 TYR D 156 PHE 0.009 0.001 PHE D 323 TRP 0.016 0.001 TRP C 78 HIS 0.011 0.001 HIS D 648 Details of bonding type rmsd covalent geometry : bond 0.00297 (10684) covalent geometry : angle 0.47492 (14342) hydrogen bonds : bond 0.04167 ( 618) hydrogen bonds : angle 4.49275 ( 1812) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 106 PHE cc_start: 0.6588 (m-80) cc_final: 0.6135 (m-10) REVERT: D 329 MET cc_start: 0.8793 (tpt) cc_final: 0.8518 (tpt) REVERT: D 662 TYR cc_start: 0.8022 (t80) cc_final: 0.7764 (t80) REVERT: C 47 MET cc_start: 0.8382 (mtt) cc_final: 0.8176 (mtt) REVERT: C 430 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7755 (mp0) REVERT: C 565 TRP cc_start: 0.5135 (OUTLIER) cc_final: 0.3614 (m100) outliers start: 15 outliers final: 14 residues processed: 99 average time/residue: 0.3052 time to fit residues: 40.5152 Evaluate side-chains 99 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 606 GLN Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 565 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 114 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 0.0470 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.089167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.066566 restraints weight = 71228.126| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.26 r_work: 0.3134 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10684 Z= 0.135 Angle : 0.465 5.152 14342 Z= 0.253 Chirality : 0.037 0.138 1553 Planarity : 0.004 0.055 1758 Dihedral : 14.672 122.619 1861 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.21 % Favored : 94.71 % Rotamer: Outliers : 1.34 % Allowed : 15.17 % Favored : 83.49 % 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: 0.90 (0.25), residues: 1228 helix: 1.73 (0.19), residues: 780 sheet: -0.68 (0.62), residues: 79 loop : -1.62 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 572 TYR 0.010 0.001 TYR D 156 PHE 0.009 0.001 PHE D 323 TRP 0.016 0.001 TRP C 78 HIS 0.008 0.001 HIS D 648 Details of bonding type rmsd covalent geometry : bond 0.00291 (10684) covalent geometry : angle 0.46492 (14342) hydrogen bonds : bond 0.04106 ( 618) hydrogen bonds : angle 4.44565 ( 1812) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 106 PHE cc_start: 0.6502 (m-80) cc_final: 0.6089 (m-10) REVERT: D 329 MET cc_start: 0.8784 (tpt) cc_final: 0.8508 (tpt) REVERT: C 430 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7764 (mp0) REVERT: C 565 TRP cc_start: 0.5160 (OUTLIER) cc_final: 0.3628 (m100) outliers start: 14 outliers final: 13 residues processed: 97 average time/residue: 0.3315 time to fit residues: 42.8695 Evaluate side-chains 99 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 606 GLN Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 565 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 99 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 384 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 = 0.3767 r_free = 0.3767 target = 0.089423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.066792 restraints weight = 71436.248| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.28 r_work: 0.3130 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10684 Z= 0.138 Angle : 0.464 5.194 14342 Z= 0.253 Chirality : 0.037 0.137 1553 Planarity : 0.004 0.059 1758 Dihedral : 14.435 109.724 1861 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.54 % Favored : 94.38 % Rotamer: Outliers : 1.43 % Allowed : 14.89 % Favored : 83.68 % 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: 0.90 (0.25), residues: 1228 helix: 1.74 (0.19), residues: 780 sheet: -0.72 (0.62), residues: 79 loop : -1.64 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 629 TYR 0.010 0.001 TYR D 156 PHE 0.012 0.001 PHE C 397 TRP 0.016 0.001 TRP C 78 HIS 0.007 0.001 HIS D 648 Details of bonding type rmsd covalent geometry : bond 0.00301 (10684) covalent geometry : angle 0.46422 (14342) hydrogen bonds : bond 0.04083 ( 618) hydrogen bonds : angle 4.43789 ( 1812) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.512 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 106 PHE cc_start: 0.6558 (m-80) cc_final: 0.6154 (m-10) REVERT: D 329 MET cc_start: 0.8786 (tpt) cc_final: 0.8505 (tpt) REVERT: C 430 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7763 (mp0) REVERT: C 565 TRP cc_start: 0.5128 (OUTLIER) cc_final: 0.3594 (m100) outliers start: 15 outliers final: 13 residues processed: 99 average time/residue: 0.2824 time to fit residues: 37.8242 Evaluate side-chains 100 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 606 GLN Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 565 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 48 optimal weight: 0.8980 chunk 12 optimal weight: 0.0070 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 104 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 648 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 = 0.3766 r_free = 0.3766 target = 0.089280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.066753 restraints weight = 71415.528| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.26 r_work: 0.3139 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10684 Z= 0.131 Angle : 0.460 5.306 14342 Z= 0.251 Chirality : 0.037 0.137 1553 Planarity : 0.004 0.044 1758 Dihedral : 14.158 96.971 1861 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.21 % Favored : 94.71 % Rotamer: Outliers : 1.43 % Allowed : 15.27 % Favored : 83.30 % 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: 0.93 (0.25), residues: 1228 helix: 1.76 (0.19), residues: 781 sheet: -0.71 (0.61), residues: 79 loop : -1.63 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 572 TYR 0.011 0.001 TYR D 662 PHE 0.010 0.001 PHE C 397 TRP 0.016 0.001 TRP C 78 HIS 0.009 0.001 HIS D 648 Details of bonding type rmsd covalent geometry : bond 0.00282 (10684) covalent geometry : angle 0.46017 (14342) hydrogen bonds : bond 0.04042 ( 618) hydrogen bonds : angle 4.40317 ( 1812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5197.57 seconds wall clock time: 88 minutes 54.74 seconds (5334.74 seconds total)