Starting phenix.real_space_refine on Thu Jun 19 01:15:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8szc_40908/06_2025/8szc_40908_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8szc_40908/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8szc_40908/06_2025/8szc_40908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8szc_40908/06_2025/8szc_40908.map" model { file = "/net/cci-nas-00/data/ceres_data/8szc_40908/06_2025/8szc_40908_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8szc_40908/06_2025/8szc_40908_trim.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.029 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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-3': 3, 'POV:plan-2': 2, '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-3': 7, 'POV:plan-2': 3, 'POV:plan-1': 4} Unresolved non-hydrogen planarities: 44 Time building chain proxies: 11.38, per 1000 atoms: 0.56 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: 5.30 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.49 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: 7.67 Time building geometry restraints manager: 6.45 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: 0.010 Normalize map: mean=0, sd=1: 154.960 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: 0.520 Extract box with map and model: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 45.550 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 205.010 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.001 TRP C 78 HIS 0.003 0.001 HIS D 505 PHE 0.021 0.001 PHE D 37 TYR 0.019 0.002 TYR C 434 ARG 0.007 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.12502 ( 611) hydrogen bonds : angle 6.11743 ( 1803) covalent geometry : bond 0.01118 (10688) covalent geometry : angle 1.33755 (14302) *********************** 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 : 1.596 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: 0.6153 time to fit residues: 80.0779 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 : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.097079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.077912 restraints weight = 65262.669| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.21 r_work: 0.3418 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.0609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10688 Z= 0.234 Angle : 0.601 8.890 14302 Z= 0.318 Chirality : 0.040 0.159 1552 Planarity : 0.005 0.062 1762 Dihedral : 21.073 160.902 1896 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.24), residues: 1229 helix: 1.03 (0.19), residues: 773 sheet: -2.20 (0.50), residues: 92 loop : -2.01 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 78 HIS 0.005 0.001 HIS C 80 PHE 0.016 0.002 PHE D 166 TYR 0.015 0.002 TYR C 19 ARG 0.007 0.000 ARG C 212 Details of bonding type rmsd hydrogen bonds : bond 0.05254 ( 611) hydrogen bonds : angle 5.04813 ( 1803) covalent geometry : bond 0.00524 (10688) covalent geometry : angle 0.60109 (14302) *********************** 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 106 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 3.019 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: 0.8614 (tpt) cc_final: 0.7974 (tpt) outliers start: 11 outliers final: 7 residues processed: 104 average time/residue: 0.7318 time to fit residues: 111.9664 Evaluate side-chains 99 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 2.106 ------------------------------------------------------------------------------- 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 81 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.097377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.078246 restraints weight = 64745.274| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.20 r_work: 0.3433 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10688 Z= 0.166 Angle : 0.527 8.408 14302 Z= 0.285 Chirality : 0.037 0.154 1552 Planarity : 0.005 0.057 1762 Dihedral : 19.893 167.515 1896 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.51 % Favored : 93.41 % Rotamer: Outliers : 1.24 % Allowed : 20.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.24), residues: 1229 helix: 1.23 (0.19), residues: 775 sheet: -2.24 (0.51), residues: 91 loop : -2.03 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 78 HIS 0.005 0.001 HIS C 452 PHE 0.015 0.001 PHE D 162 TYR 0.014 0.001 TYR C 19 ARG 0.005 0.000 ARG C 212 Details of bonding type rmsd hydrogen bonds : bond 0.04833 ( 611) hydrogen bonds : angle 4.77973 ( 1803) covalent geometry : bond 0.00367 (10688) covalent geometry : angle 0.52742 (14302) *********************** 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 110 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8547 (mt) REVERT: D 436 SER cc_start: 0.6168 (OUTLIER) cc_final: 0.5051 (t) outliers start: 13 outliers final: 9 residues processed: 107 average time/residue: 0.5294 time to fit residues: 79.9551 Evaluate side-chains 104 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.693 ------------------------------------------------------------------------------- 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 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 50 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 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 660 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.097881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.078644 restraints weight = 65233.550| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.22 r_work: 0.3437 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10688 Z= 0.155 Angle : 0.517 8.360 14302 Z= 0.280 Chirality : 0.037 0.155 1552 Planarity : 0.005 0.055 1762 Dihedral : 18.915 174.514 1896 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.08 % Favored : 92.84 % Rotamer: Outliers : 1.33 % Allowed : 20.31 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1229 helix: 1.39 (0.19), residues: 774 sheet: -2.21 (0.52), residues: 91 loop : -2.07 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 78 HIS 0.004 0.001 HIS C 452 PHE 0.014 0.001 PHE D 162 TYR 0.014 0.001 TYR D 659 ARG 0.004 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.04596 ( 611) hydrogen bonds : angle 4.67332 ( 1803) covalent geometry : bond 0.00345 (10688) covalent geometry : angle 0.51681 (14302) *********************** 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 107 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 1.557 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: 0.6196 (OUTLIER) cc_final: 0.5161 (t) outliers start: 14 outliers final: 10 residues processed: 104 average time/residue: 0.5276 time to fit residues: 77.4661 Evaluate side-chains 104 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.433 ------------------------------------------------------------------------------- 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 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 460 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 96 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.097320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.078106 restraints weight = 65234.564| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.20 r_work: 0.3427 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10688 Z= 0.181 Angle : 0.537 9.064 14302 Z= 0.292 Chirality : 0.038 0.157 1552 Planarity : 0.005 0.055 1762 Dihedral : 18.547 177.736 1896 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.75 % Favored : 93.17 % Rotamer: Outliers : 1.53 % Allowed : 20.21 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.24), residues: 1229 helix: 1.33 (0.19), residues: 774 sheet: -2.22 (0.52), residues: 91 loop : -2.12 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 78 HIS 0.004 0.001 HIS C 80 PHE 0.015 0.001 PHE D 162 TYR 0.014 0.001 TYR D 659 ARG 0.004 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.04707 ( 611) hydrogen bonds : angle 4.64254 ( 1803) covalent geometry : bond 0.00406 (10688) covalent geometry : angle 0.53728 (14302) *********************** 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 112 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.646 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: 0.6227 (OUTLIER) cc_final: 0.5125 (t) outliers start: 16 outliers final: 12 residues processed: 108 average time/residue: 0.7571 time to fit residues: 120.1986 Evaluate side-chains 105 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 1.712 ------------------------------------------------------------------------------- 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 33 GLU 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 97 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 104 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.098056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.078917 restraints weight = 64551.536| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.19 r_work: 0.3446 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10688 Z= 0.138 Angle : 0.505 8.507 14302 Z= 0.273 Chirality : 0.037 0.157 1552 Planarity : 0.005 0.053 1762 Dihedral : 17.568 166.157 1896 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.92 % Favored : 93.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1229 helix: 1.51 (0.19), residues: 773 sheet: -2.18 (0.52), residues: 91 loop : -2.07 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 78 HIS 0.004 0.001 HIS C 452 PHE 0.014 0.001 PHE D 162 TYR 0.014 0.001 TYR C 19 ARG 0.005 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.04417 ( 611) hydrogen bonds : angle 4.52699 ( 1803) covalent geometry : bond 0.00302 (10688) covalent geometry : angle 0.50509 (14302) *********************** 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 110 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.760 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: 0.6245 (OUTLIER) cc_final: 0.5135 (t) outliers start: 13 outliers final: 10 residues processed: 107 average time/residue: 0.6254 time to fit residues: 96.5284 Evaluate side-chains 104 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.601 ------------------------------------------------------------------------------- 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 456 ASP 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 110 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.097974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.078828 restraints weight = 64442.878| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.19 r_work: 0.3449 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10688 Z= 0.144 Angle : 0.504 8.402 14302 Z= 0.273 Chirality : 0.037 0.153 1552 Planarity : 0.005 0.060 1762 Dihedral : 16.792 150.124 1896 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.59 % Favored : 93.33 % Rotamer: Outliers : 1.43 % Allowed : 19.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.25), residues: 1229 helix: 1.55 (0.19), residues: 773 sheet: -2.14 (0.52), residues: 91 loop : -2.10 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 78 HIS 0.003 0.001 HIS C 452 PHE 0.013 0.001 PHE D 162 TYR 0.014 0.001 TYR C 19 ARG 0.006 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.04382 ( 611) hydrogen bonds : angle 4.50447 ( 1803) covalent geometry : bond 0.00318 (10688) covalent geometry : angle 0.50363 (14302) *********************** 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 108 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 1.442 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: 0.6268 (OUTLIER) cc_final: 0.5168 (t) REVERT: C 546 ASP cc_start: 0.7582 (m-30) cc_final: 0.7089 (t0) outliers start: 15 outliers final: 11 residues processed: 105 average time/residue: 0.5640 time to fit residues: 83.5413 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 : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 177 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.0370 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.096701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.077603 restraints weight = 64940.764| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.18 r_work: 0.3415 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10688 Z= 0.233 Angle : 0.565 9.502 14302 Z= 0.305 Chirality : 0.039 0.163 1552 Planarity : 0.005 0.063 1762 Dihedral : 16.916 149.820 1896 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.73 % Favored : 92.19 % Rotamer: Outliers : 1.62 % Allowed : 20.21 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1229 helix: 1.21 (0.18), residues: 774 sheet: -2.27 (0.51), residues: 92 loop : -2.28 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 78 HIS 0.006 0.001 HIS C 80 PHE 0.017 0.002 PHE D 162 TYR 0.015 0.002 TYR C 19 ARG 0.004 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.04788 ( 611) hydrogen bonds : angle 4.67880 ( 1803) covalent geometry : bond 0.00528 (10688) covalent geometry : angle 0.56461 (14302) *********************** 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 115 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 436 SER cc_start: 0.6301 (OUTLIER) cc_final: 0.5192 (t) REVERT: C 430 GLU cc_start: 0.7525 (tp30) cc_final: 0.7323 (tp30) outliers start: 17 outliers final: 13 residues processed: 110 average time/residue: 0.5354 time to fit residues: 83.0581 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 : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 177 SER 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 33 GLU 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 489 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 9 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 82 optimal weight: 0.0970 chunk 93 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.097573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.079088 restraints weight = 63439.611| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.09 r_work: 0.3458 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10688 Z= 0.131 Angle : 0.509 8.692 14302 Z= 0.276 Chirality : 0.037 0.150 1552 Planarity : 0.005 0.058 1762 Dihedral : 16.070 144.068 1896 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.59 % Favored : 93.33 % Rotamer: Outliers : 1.53 % Allowed : 20.50 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.24), residues: 1229 helix: 1.45 (0.18), residues: 773 sheet: -2.16 (0.52), residues: 91 loop : -2.14 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 78 HIS 0.003 0.001 HIS C 80 PHE 0.015 0.001 PHE D 162 TYR 0.014 0.001 TYR C 19 ARG 0.006 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 611) hydrogen bonds : angle 4.51182 ( 1803) covalent geometry : bond 0.00287 (10688) covalent geometry : angle 0.50900 (14302) *********************** 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 107 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 1.572 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: 0.6282 (OUTLIER) cc_final: 0.5179 (t) REVERT: C 546 ASP cc_start: 0.7611 (m-30) cc_final: 0.7100 (t0) REVERT: C 558 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7965 (mp0) outliers start: 16 outliers final: 12 residues processed: 105 average time/residue: 0.5465 time to fit residues: 80.7137 Evaluate side-chains 104 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 177 SER 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 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 460 LEU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 558 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 49 optimal weight: 3.9990 chunk 62 optimal weight: 0.0470 chunk 25 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.097638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.078470 restraints weight = 64520.551| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.20 r_work: 0.3440 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10688 Z= 0.168 Angle : 0.526 8.602 14302 Z= 0.284 Chirality : 0.037 0.153 1552 Planarity : 0.005 0.059 1762 Dihedral : 15.699 138.660 1896 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.08 % Favored : 92.84 % Rotamer: Outliers : 1.24 % Allowed : 21.07 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1229 helix: 1.39 (0.18), residues: 774 sheet: -2.18 (0.52), residues: 91 loop : -2.23 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 78 HIS 0.004 0.001 HIS C 80 PHE 0.014 0.001 PHE D 162 TYR 0.015 0.001 TYR C 19 ARG 0.007 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 611) hydrogen bonds : angle 4.53527 ( 1803) covalent geometry : bond 0.00380 (10688) covalent geometry : angle 0.52573 (14302) ********************** 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 103 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 436 SER cc_start: 0.6297 (OUTLIER) cc_final: 0.5186 (t) REVERT: C 546 ASP cc_start: 0.7581 (m-30) cc_final: 0.7074 (t0) outliers start: 13 outliers final: 10 residues processed: 101 average time/residue: 0.5629 time to fit residues: 79.8149 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 : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 177 SER 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 108 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 87 optimal weight: 0.1980 chunk 75 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.098107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.078937 restraints weight = 64724.164| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.21 r_work: 0.3450 rms_B_bonded: 2.56 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: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10688 Z= 0.135 Angle : 0.505 8.492 14302 Z= 0.273 Chirality : 0.037 0.150 1552 Planarity : 0.005 0.053 1762 Dihedral : 15.189 127.595 1896 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.67 % Favored : 93.17 % Rotamer: Outliers : 1.14 % Allowed : 20.97 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.24), residues: 1229 helix: 1.53 (0.18), residues: 773 sheet: -2.17 (0.52), residues: 91 loop : -2.16 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 78 HIS 0.003 0.001 HIS C 80 PHE 0.013 0.001 PHE D 162 TYR 0.014 0.001 TYR C 19 ARG 0.007 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 611) hydrogen bonds : angle 4.46300 ( 1803) covalent geometry : bond 0.00298 (10688) covalent geometry : angle 0.50462 (14302) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12396.05 seconds wall clock time: 220 minutes 16.37 seconds (13216.37 seconds total)