Starting phenix.real_space_refine on Fri Jul 3 15:35:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yft_72905/07_2026/9yft_72905.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yft_72905/07_2026/9yft_72905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yft_72905/07_2026/9yft_72905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yft_72905/07_2026/9yft_72905.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yft_72905/07_2026/9yft_72905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yft_72905/07_2026/9yft_72905.map" } resolution = 3.61 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 ------------------------------------------------------------------------------- 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= 0.006 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 8924 2.51 5 N 2370 2.21 5 O 2851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14173 Number of models: 1 Model: "" Number of chains: 3 Chain: "FA" Number of atoms: 5606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5606 Classifications: {'peptide': 716} Link IDs: {'PTRANS': 29, 'TRANS': 686} Chain: "LA" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2315 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 288} Chain: "TA" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 521 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 65} Restraints were copied for chains: TB, TC, TD, TE, TF, TG, TH, TI, TJ, TK, TL Time building chain proxies: 2.31, per 1000 atoms: 0.16 Number of scatterers: 14173 At special positions: 0 Unit cell: (96.714, 105.072, 237.606, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 2851 8.00 N 2370 7.00 C 8924 6.00 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: 1.07 Conformation dependent library (CDL) restraints added in 453.4 milliseconds 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3392 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 51.6% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'FA' and resid 22 through 26 Processing helix chain 'FA' and resid 28 through 37 Processing helix chain 'FA' and resid 45 through 55 Processing helix chain 'FA' and resid 57 through 72 removed outlier: 3.794A pdb=" N ARGFA 63 " --> pdb=" O GLYFA 59 " (cutoff:3.500A) Proline residue: FA 66 - end of helix removed outlier: 3.673A pdb=" N THRFA 71 " --> pdb=" O GLYFA 67 " (cutoff:3.500A) Processing helix chain 'FA' and resid 72 through 78 removed outlier: 3.955A pdb=" N SERFA 76 " --> pdb=" O ASNFA 72 " (cutoff:3.500A) Processing helix chain 'FA' and resid 91 through 99 removed outlier: 4.052A pdb=" N TRPFA 97 " --> pdb=" O GLUFA 93 " (cutoff:3.500A) Processing helix chain 'FA' and resid 118 through 131 Processing helix chain 'FA' and resid 198 through 202 Processing helix chain 'FA' and resid 350 through 355 removed outlier: 3.637A pdb=" N ALAFA 353 " --> pdb=" O VALFA 350 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEUFA 354 " --> pdb=" O LEUFA 351 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHEFA 355 " --> pdb=" O ASPFA 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'FA' and resid 350 through 355' Processing helix chain 'FA' and resid 378 through 392 removed outlier: 4.098A pdb=" N THRFA 383 " --> pdb=" O GLYFA 379 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LEUFA 384 " --> pdb=" O SERFA 380 " (cutoff:3.500A) Processing helix chain 'FA' and resid 396 through 406 Processing helix chain 'FA' and resid 407 through 412 removed outlier: 4.336A pdb=" N GLYFA 411 " --> pdb=" O LYSFA 408 " (cutoff:3.500A) Processing helix chain 'FA' and resid 428 through 446 removed outlier: 3.623A pdb=" N GLNFA 444 " --> pdb=" O GLNFA 440 " (cutoff:3.500A) Processing helix chain 'FA' and resid 459 through 481 removed outlier: 4.157A pdb=" N ALAFA 471 " --> pdb=" O ARGFA 467 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRPFA 475 " --> pdb=" O ALAFA 471 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLYFA 481 " --> pdb=" O GLUFA 477 " (cutoff:3.500A) Processing helix chain 'FA' and resid 611 through 616 Processing helix chain 'FA' and resid 628 through 634 Processing helix chain 'FA' and resid 636 through 645 Processing helix chain 'FA' and resid 667 through 679 removed outlier: 3.802A pdb=" N VALFA 672 " --> pdb=" O PHEFA 668 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VALFA 673 " --> pdb=" O LYSFA 669 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VALFA 674 " --> pdb=" O VALFA 670 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VALFA 675 " --> pdb=" O VALFA 671 " (cutoff:3.500A) Processing helix chain 'FA' and resid 684 through 689 Processing helix chain 'FA' and resid 692 through 703 removed outlier: 3.834A pdb=" N ALAFA 700 " --> pdb=" O ALAFA 696 " (cutoff:3.500A) Processing helix chain 'FA' and resid 704 through 713 removed outlier: 4.399A pdb=" N VALFA 712 " --> pdb=" O ALAFA 708 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLYFA 713 " --> pdb=" O ALAFA 709 " (cutoff:3.500A) Processing helix chain 'LA' and resid 1138 through 1147 Processing helix chain 'LA' and resid 1246 through 1255 Processing helix chain 'LA' and resid 1342 through 1350 Processing helix chain 'TA' and resid 233 through 269 removed outlier: 4.230A pdb=" N LEUTA 259 " --> pdb=" O LYSTA 255 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHETA 260 " --> pdb=" O ALATA 256 " (cutoff:3.500A) Processing helix chain 'TA' and resid 277 through 280 Processing helix chain 'TA' and resid 281 through 297 Processing helix chain 'TB' and resid 233 through 269 removed outlier: 4.231A pdb=" N LEUTB 259 " --> pdb=" O LYSTB 255 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHETB 260 " --> pdb=" O ALATB 256 " (cutoff:3.500A) Processing helix chain 'TB' and resid 277 through 280 Processing helix chain 'TB' and resid 281 through 297 Processing helix chain 'TC' and resid 233 through 269 removed outlier: 4.231A pdb=" N LEUTC 259 " --> pdb=" O LYSTC 255 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHETC 260 " --> pdb=" O ALATC 256 " (cutoff:3.500A) Processing helix chain 'TC' and resid 277 through 280 Processing helix chain 'TC' and resid 281 through 297 Processing helix chain 'TD' and resid 233 through 269 removed outlier: 4.231A pdb=" N LEUTD 259 " --> pdb=" O LYSTD 255 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHETD 260 " --> pdb=" O ALATD 256 " (cutoff:3.500A) Processing helix chain 'TD' and resid 277 through 280 Processing helix chain 'TD' and resid 281 through 297 Processing helix chain 'TE' and resid 233 through 269 removed outlier: 4.231A pdb=" N LEUTE 259 " --> pdb=" O LYSTE 255 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHETE 260 " --> pdb=" O ALATE 256 " (cutoff:3.500A) Processing helix chain 'TE' and resid 277 through 280 Processing helix chain 'TE' and resid 281 through 297 Processing helix chain 'TF' and resid 233 through 269 removed outlier: 4.230A pdb=" N LEUTF 259 " --> pdb=" O LYSTF 255 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHETF 260 " --> pdb=" O ALATF 256 " (cutoff:3.500A) Processing helix chain 'TF' and resid 277 through 280 Processing helix chain 'TF' and resid 281 through 297 Processing helix chain 'TG' and resid 233 through 269 removed outlier: 4.231A pdb=" N LEUTG 259 " --> pdb=" O LYSTG 255 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHETG 260 " --> pdb=" O ALATG 256 " (cutoff:3.500A) Processing helix chain 'TG' and resid 277 through 280 Processing helix chain 'TG' and resid 281 through 297 Processing helix chain 'TH' and resid 233 through 269 removed outlier: 4.230A pdb=" N LEUTH 259 " --> pdb=" O LYSTH 255 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHETH 260 " --> pdb=" O ALATH 256 " (cutoff:3.500A) Processing helix chain 'TH' and resid 277 through 280 Processing helix chain 'TH' and resid 281 through 297 Processing helix chain 'TI' and resid 233 through 269 removed outlier: 4.230A pdb=" N LEUTI 259 " --> pdb=" O LYSTI 255 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHETI 260 " --> pdb=" O ALATI 256 " (cutoff:3.500A) Processing helix chain 'TI' and resid 277 through 280 Processing helix chain 'TI' and resid 281 through 297 Processing helix chain 'TJ' and resid 233 through 269 removed outlier: 4.231A pdb=" N LEUTJ 259 " --> pdb=" O LYSTJ 255 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHETJ 260 " --> pdb=" O ALATJ 256 " (cutoff:3.500A) Processing helix chain 'TJ' and resid 277 through 280 Processing helix chain 'TJ' and resid 281 through 297 Processing helix chain 'TK' and resid 233 through 269 removed outlier: 4.230A pdb=" N LEUTK 259 " --> pdb=" O LYSTK 255 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHETK 260 " --> pdb=" O ALATK 256 " (cutoff:3.500A) Processing helix chain 'TK' and resid 277 through 280 Processing helix chain 'TK' and resid 281 through 297 Processing helix chain 'TL' and resid 233 through 269 removed outlier: 4.231A pdb=" N LEUTL 259 " --> pdb=" O LYSTL 255 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHETL 260 " --> pdb=" O ALATL 256 " (cutoff:3.500A) Processing helix chain 'TL' and resid 277 through 280 Processing helix chain 'TL' and resid 281 through 297 Processing sheet with id=AA1, first strand: chain 'FA' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'FA' and resid 16 through 18 current: chain 'FA' and resid 416 through 423 Processing sheet with id=AA2, first strand: chain 'FA' and resid 358 through 363 removed outlier: 3.808A pdb=" N THRFA 360 " --> pdb=" O GLYFA 82 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N GLYFA 82 " --> pdb=" O THRFA 360 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASNFA 362 " --> pdb=" O ALAFA 80 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALAFA 80 " --> pdb=" O ASNFA 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'FA' and resid 108 through 116 removed outlier: 4.974A pdb=" N ASNFA 176 " --> pdb=" O GLNFA 110 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SERFA 112 " --> pdb=" O TYRFA 174 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYRFA 174 " --> pdb=" O SERFA 112 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILEFA 114 " --> pdb=" O TYRFA 172 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYRFA 172 " --> pdb=" O ILEFA 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'FA' and resid 142 through 143 Processing sheet with id=AA5, first strand: chain 'FA' and resid 184 through 185 WARNING: can't find start of bonding for strands! previous: chain 'FA' and resid 184 through 185 current: chain 'FA' and resid 239 through 264 removed outlier: 16.840A pdb=" N GLUFA 240 " --> pdb=" O VALFA 296 " (cutoff:3.500A) removed outlier: 17.357A pdb=" N VALFA 296 " --> pdb=" O GLUFA 240 " (cutoff:3.500A) removed outlier: 17.538A pdb=" N THRFA 242 " --> pdb=" O THRFA 294 " (cutoff:3.500A) removed outlier: 17.498A pdb=" N THRFA 294 " --> pdb=" O THRFA 242 " (cutoff:3.500A) removed outlier: 17.536A pdb=" N THRFA 244 " --> pdb=" O THRFA 292 " (cutoff:3.500A) removed outlier: 17.605A pdb=" N THRFA 292 " --> pdb=" O THRFA 244 " (cutoff:3.500A) removed outlier: 17.513A pdb=" N GLUFA 246 " --> pdb=" O SERFA 290 " (cutoff:3.500A) removed outlier: 17.301A pdb=" N SERFA 290 " --> pdb=" O GLUFA 246 " (cutoff:3.500A) removed outlier: 17.205A pdb=" N GLNFA 248 " --> pdb=" O THRFA 288 " (cutoff:3.500A) removed outlier: 15.910A pdb=" N THRFA 288 " --> pdb=" O GLNFA 248 " (cutoff:3.500A) removed outlier: 13.017A pdb=" N SERFA 250 " --> pdb=" O VALFA 286 " (cutoff:3.500A) removed outlier: 11.101A pdb=" N VALFA 286 " --> pdb=" O SERFA 250 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N THRFA 252 " --> pdb=" O GLYFA 284 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLYFA 284 " --> pdb=" O THRFA 252 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILEFA 272 " --> pdb=" O GLUFA 264 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILEFA 271 " --> pdb=" O LEUFA 331 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VALFA 303 " --> pdb=" O LEUFA 299 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'FA' and resid 523 through 529 removed outlier: 3.521A pdb=" N METFA 578 " --> pdb=" O ILEFA 590 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLYFA 547 " --> pdb=" O LYSFA 575 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THRFA 577 " --> pdb=" O TYRFA 545 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N TYRFA 545 " --> pdb=" O THRFA 577 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYRFA 579 " --> pdb=" O PHEFA 543 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N PHEFA 543 " --> pdb=" O TYRFA 579 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N THRLA1331 " --> pdb=" O VALFA 550 " (cutoff:3.500A) removed outlier: 9.125A pdb=" N METFA 552 " --> pdb=" O VALLA1329 " (cutoff:3.500A) removed outlier: 11.519A pdb=" N VALLA1329 " --> pdb=" O METFA 552 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYSLA1330 " --> pdb=" O ILELA1320 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VALLA1358 " --> pdb=" O LEULA1321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'FA' and resid 557 through 558 Processing sheet with id=AA8, first strand: chain 'LA' and resid 1086 through 1092 removed outlier: 5.083A pdb=" N GLNLA1087 " --> pdb=" O VALLA1103 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VALLA1103 " --> pdb=" O GLNLA1087 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'LA' and resid 1124 through 1130 removed outlier: 3.543A pdb=" N PHELA1126 " --> pdb=" O ASNLA1115 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILELA1157 " --> pdb=" O THRLA1116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'LA' and resid 1194 through 1197 Processing sheet with id=AB2, first strand: chain 'LA' and resid 1234 through 1238 removed outlier: 3.718A pdb=" N SERLA1262 " --> pdb=" O METLA1225 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'LA' and resid 1294 through 1297 843 hydrogen bonds defined for protein. 2403 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: 2.13 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4645 1.34 - 1.46: 2444 1.46 - 1.57: 7301 1.57 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 14441 Sorted by residual: bond pdb=" C GLYFA 334 " pdb=" N GLYFA 335 " ideal model delta sigma weight residual 1.321 1.331 -0.009 1.24e-02 6.50e+03 5.77e-01 bond pdb=" N ILEFA 499 " pdb=" CA ILEFA 499 " ideal model delta sigma weight residual 1.468 1.460 0.008 1.05e-02 9.07e+03 5.71e-01 bond pdb=" C VALLA1335 " pdb=" O VALLA1335 " ideal model delta sigma weight residual 1.236 1.225 0.010 1.47e-02 4.63e+03 5.07e-01 bond pdb=" CA VALLA1329 " pdb=" CB VALLA1329 " ideal model delta sigma weight residual 1.545 1.539 0.006 9.10e-03 1.21e+04 4.66e-01 bond pdb=" C ARGFA 493 " pdb=" N PROFA 494 " ideal model delta sigma weight residual 1.332 1.341 -0.009 1.34e-02 5.57e+03 4.18e-01 ... (remaining 14436 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 18819 0.98 - 1.96: 618 1.96 - 2.94: 136 2.94 - 3.93: 19 3.93 - 4.91: 9 Bond angle restraints: 19601 Sorted by residual: angle pdb=" N VALLA1329 " pdb=" CA VALLA1329 " pdb=" C VALLA1329 " ideal model delta sigma weight residual 111.48 108.91 2.57 9.40e-01 1.13e+00 7.47e+00 angle pdb=" C THRFA 71 " pdb=" N ASNFA 72 " pdb=" CA ASNFA 72 " ideal model delta sigma weight residual 122.46 117.67 4.79 1.80e+00 3.09e-01 7.07e+00 angle pdb=" C GLNFA 664 " pdb=" N SERFA 665 " pdb=" CA SERFA 665 " ideal model delta sigma weight residual 121.85 117.69 4.16 1.77e+00 3.19e-01 5.54e+00 angle pdb=" C SERFA 665 " pdb=" N GLYFA 666 " pdb=" CA GLYFA 666 " ideal model delta sigma weight residual 121.41 125.54 -4.13 1.96e+00 2.60e-01 4.44e+00 angle pdb=" C LYSFA 603 " pdb=" N ASNFA 604 " pdb=" CA ASNFA 604 " ideal model delta sigma weight residual 121.54 125.45 -3.91 1.91e+00 2.74e-01 4.19e+00 ... (remaining 19596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 8182 16.71 - 33.43: 344 33.43 - 50.14: 78 50.14 - 66.85: 14 66.85 - 83.56: 4 Dihedral angle restraints: 8622 sinusoidal: 3340 harmonic: 5282 Sorted by residual: dihedral pdb=" CA ILEFA 10 " pdb=" C ILEFA 10 " pdb=" N TYRFA 11 " pdb=" CA TYRFA 11 " ideal model delta harmonic sigma weight residual -180.00 -155.04 -24.96 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA TYRFA 11 " pdb=" C TYRFA 11 " pdb=" N VALFA 12 " pdb=" CA VALFA 12 " ideal model delta harmonic sigma weight residual 180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA PHEFA 704 " pdb=" C PHEFA 704 " pdb=" N ALAFA 705 " pdb=" CA ALAFA 705 " ideal model delta harmonic sigma weight residual -180.00 -161.57 -18.43 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 8619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1401 0.028 - 0.056: 556 0.056 - 0.084: 147 0.084 - 0.111: 82 0.111 - 0.139: 28 Chirality restraints: 2214 Sorted by residual: chirality pdb=" CA ILELA1157 " pdb=" N ILELA1157 " pdb=" C ILELA1157 " pdb=" CB ILELA1157 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILELA1333 " pdb=" N ILELA1333 " pdb=" C ILELA1333 " pdb=" CB ILELA1333 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILEFA 10 " pdb=" N ILEFA 10 " pdb=" C ILEFA 10 " pdb=" CB ILEFA 10 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 2211 not shown) Planarity restraints: 2536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PROFA 490 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PROFA 491 " 0.056 5.00e-02 4.00e+02 pdb=" CA PROFA 491 " -0.017 5.00e-02 4.00e+02 pdb=" CD PROFA 491 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARGFA 493 " 0.021 5.00e-02 4.00e+02 3.10e-02 1.53e+00 pdb=" N PROFA 494 " -0.054 5.00e-02 4.00e+02 pdb=" CA PROFA 494 " 0.016 5.00e-02 4.00e+02 pdb=" CD PROFA 494 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLYFA 461 " -0.005 2.00e-02 2.50e+03 1.05e-02 1.10e+00 pdb=" C GLYFA 461 " 0.018 2.00e-02 2.50e+03 pdb=" O GLYFA 461 " -0.007 2.00e-02 2.50e+03 pdb=" N PHEFA 462 " -0.006 2.00e-02 2.50e+03 ... (remaining 2533 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1450 2.74 - 3.28: 15109 3.28 - 3.82: 24650 3.82 - 4.36: 27226 4.36 - 4.90: 47133 Nonbonded interactions: 115568 Sorted by model distance: nonbonded pdb=" OG1 THRFA 577 " pdb=" O ILEFA 590 " model vdw 2.206 3.040 nonbonded pdb=" OG1 THRLA1177 " pdb=" ND2 ASNTI 282 " model vdw 2.210 3.120 nonbonded pdb=" OH TYRFA 545 " pdb=" OG1 THRFA 548 " model vdw 2.262 3.040 nonbonded pdb=" O SERFA 529 " pdb=" NE1 TRPFA 587 " model vdw 2.278 3.120 nonbonded pdb=" NH2 ARGFA 479 " pdb=" O ILEFA 487 " model vdw 2.283 3.120 ... (remaining 115563 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 Found NCS groups: ncs_group { reference = chain 'TA' selection = chain 'TB' selection = chain 'TC' selection = chain 'TD' selection = chain 'TE' selection = chain 'TF' selection = chain 'TG' selection = chain 'TH' selection = chain 'TI' selection = chain 'TJ' selection = chain 'TK' selection = chain 'TL' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.470 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 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 : 0.002 0.023 14441 Z= 0.088 Angle : 0.440 4.907 19601 Z= 0.246 Chirality : 0.037 0.139 2214 Planarity : 0.003 0.032 2536 Dihedral : 10.019 83.564 5230 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.87 % Allowed : 6.13 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.21), residues: 1804 helix: 2.54 (0.19), residues: 868 sheet: 0.66 (0.29), residues: 358 loop : -0.01 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGTL 250 TYR 0.015 0.001 TYRFA 178 PHE 0.014 0.001 PHEFA 254 TRP 0.010 0.001 TRPFA 475 HIS 0.005 0.001 HISLA1268 Details of bonding type rmsd/Z covalent geometry : bond 0.00169 / 0.09 (14441) covalent geometry : angle 0.44047 / 0.25 (19601) hydrogen bonds : bond 0.14016 / 8.78 ( 843) hydrogen bonds : angle 5.38878 / 3.69 ( 2403) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 378 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: FA 145 ASP cc_start: 0.7692 (m-30) cc_final: 0.7049 (p0) REVERT: FA 178 TYR cc_start: 0.6306 (OUTLIER) cc_final: 0.5931 (p90) REVERT: FA 282 GLN cc_start: 0.3517 (tt0) cc_final: 0.2211 (tm-30) REVERT: FA 449 ASP cc_start: 0.7052 (t0) cc_final: 0.6583 (t0) REVERT: LA 1146 TYR cc_start: 0.7227 (m-80) cc_final: 0.6642 (m-80) REVERT: LA 1187 MET cc_start: 0.7032 (tmm) cc_final: 0.6315 (tmm) REVERT: TA 262 ASP cc_start: 0.8901 (t0) cc_final: 0.8662 (t0) REVERT: TA 269 THR cc_start: 0.8963 (t) cc_final: 0.8742 (p) REVERT: TC 274 LEU cc_start: 0.6607 (tt) cc_final: 0.6385 (tt) REVERT: TC 298 LEU cc_start: 0.7896 (mt) cc_final: 0.7573 (mp) REVERT: TD 238 LYS cc_start: 0.8492 (mtpt) cc_final: 0.7848 (mttm) REVERT: TD 253 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7804 (mt-10) REVERT: TE 298 LEU cc_start: 0.7560 (mt) cc_final: 0.7338 (mt) REVERT: TF 282 ASN cc_start: 0.7376 (OUTLIER) cc_final: 0.6130 (t0) REVERT: TG 238 LYS cc_start: 0.8927 (mtpt) cc_final: 0.8723 (mttp) REVERT: TG 251 ASP cc_start: 0.9174 (t70) cc_final: 0.8846 (t0) REVERT: TG 271 ASP cc_start: 0.8630 (t0) cc_final: 0.8222 (t70) REVERT: TG 285 LEU cc_start: 0.8960 (mt) cc_final: 0.8754 (mp) REVERT: TH 251 ASP cc_start: 0.8334 (t70) cc_final: 0.7993 (m-30) REVERT: TI 259 LEU cc_start: 0.8761 (mm) cc_final: 0.8499 (mp) REVERT: TJ 244 GLN cc_start: 0.8607 (tt0) cc_final: 0.8375 (tt0) REVERT: TJ 248 TYR cc_start: 0.7181 (m-10) cc_final: 0.6774 (m-10) REVERT: TK 282 ASN cc_start: 0.7246 (OUTLIER) cc_final: 0.6368 (m-40) REVERT: TK 283 SER cc_start: 0.8638 (p) cc_final: 0.8362 (t) REVERT: TL 286 ASP cc_start: 0.8620 (t0) cc_final: 0.8383 (m-30) REVERT: TL 298 LEU cc_start: 0.8989 (mt) cc_final: 0.8756 (mp) outliers start: 29 outliers final: 4 residues processed: 401 average time/residue: 0.1126 time to fit residues: 65.4512 Evaluate side-chains 191 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 184 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FA residue 164 LYS Chi-restraints excluded: chain FA residue 178 TYR Chi-restraints excluded: chain FA residue 679 VAL Chi-restraints excluded: chain LA residue 1310 VAL Chi-restraints excluded: chain LA residue 1350 TYR Chi-restraints excluded: chain TF residue 282 ASN Chi-restraints excluded: chain TK residue 282 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 50.0000 chunk 149 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... FA 37 ASN FA 318 HIS FA 414 GLN FA 464 GLN LA1315 GLN TA 282 ASN TA 294 ASN ** TB 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TB 295 ASN TB 296 ASN TC 295 ASN TD 244 GLN TD 295 ASN TE 237 GLN ** TE 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TE 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 243 GLN TF 282 ASN TF 295 ASN TG 295 ASN ** TH 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TH 295 ASN TI 295 ASN TJ 295 ASN ** TK 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TK 295 ASN TL 295 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.077794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.063676 restraints weight = 99385.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.064588 restraints weight = 56433.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.065206 restraints weight = 36384.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.065596 restraints weight = 26344.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.065884 restraints weight = 21037.272| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14441 Z= 0.154 Angle : 0.616 8.737 19601 Z= 0.331 Chirality : 0.043 0.177 2214 Planarity : 0.004 0.036 2536 Dihedral : 5.361 74.956 1961 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.90 % Allowed : 13.28 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.20), residues: 1804 helix: 2.07 (0.17), residues: 876 sheet: 0.57 (0.29), residues: 345 loop : -0.35 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGTI 250 TYR 0.016 0.001 TYRFA 178 PHE 0.028 0.002 PHEFA 543 TRP 0.021 0.002 TRPFA 208 HIS 0.005 0.001 HISLA1268 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (14441) covalent geometry : angle 0.61605 / 0.33 (19601) hydrogen bonds : bond 0.04348 / 2.87 ( 843) hydrogen bonds : angle 4.68220 / 3.25 ( 2403) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: FA 178 TYR cc_start: 0.6285 (OUTLIER) cc_final: 0.5952 (p90) REVERT: FA 278 MET cc_start: 0.4714 (tpp) cc_final: 0.4471 (tpp) REVERT: FA 449 ASP cc_start: 0.7219 (t0) cc_final: 0.6771 (t0) REVERT: FA 578 MET cc_start: 0.8528 (mmm) cc_final: 0.8185 (mmm) REVERT: LA 1187 MET cc_start: 0.7082 (tmm) cc_final: 0.6456 (tmm) REVERT: LA 1194 TYR cc_start: 0.7974 (p90) cc_final: 0.7748 (p90) REVERT: TK 283 SER cc_start: 0.8365 (p) cc_final: 0.8025 (t) outliers start: 45 outliers final: 26 residues processed: 233 average time/residue: 0.0929 time to fit residues: 33.4762 Evaluate side-chains 179 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FA residue 152 THR Chi-restraints excluded: chain FA residue 164 LYS Chi-restraints excluded: chain FA residue 178 TYR Chi-restraints excluded: chain FA residue 189 VAL Chi-restraints excluded: chain FA residue 211 VAL Chi-restraints excluded: chain FA residue 456 ASP Chi-restraints excluded: chain FA residue 675 VAL Chi-restraints excluded: chain FA residue 679 VAL Chi-restraints excluded: chain LA residue 1113 VAL Chi-restraints excluded: chain LA residue 1132 SER Chi-restraints excluded: chain LA residue 1310 VAL Chi-restraints excluded: chain LA residue 1350 TYR Chi-restraints excluded: chain TA residue 234 VAL Chi-restraints excluded: chain TB residue 248 TYR Chi-restraints excluded: chain TB residue 261 THR Chi-restraints excluded: chain TD residue 240 LEU Chi-restraints excluded: chain TE residue 259 LEU Chi-restraints excluded: chain TE residue 286 ASP Chi-restraints excluded: chain TF residue 261 THR Chi-restraints excluded: chain TF residue 290 THR Chi-restraints excluded: chain TG residue 234 VAL Chi-restraints excluded: chain TH residue 290 THR Chi-restraints excluded: chain TJ residue 239 GLU Chi-restraints excluded: chain TK residue 247 SER Chi-restraints excluded: chain TK residue 248 TYR Chi-restraints excluded: chain TK residue 298 LEU Chi-restraints excluded: chain TL residue 248 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 133 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 chunk 92 optimal weight: 50.0000 chunk 65 optimal weight: 40.0000 chunk 132 optimal weight: 10.0000 chunk 129 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 41 optimal weight: 40.0000 chunk 108 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... FA 37 ASN ** TA 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 282 ASN ** TB 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TB 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TE 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TG 296 ASN ** TH 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TK 243 GLN ** TK 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.077293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.063125 restraints weight = 101115.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.064007 restraints weight = 57025.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.064602 restraints weight = 36886.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.064996 restraints weight = 26685.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.065227 restraints weight = 21275.430| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14441 Z= 0.140 Angle : 0.599 9.745 19601 Z= 0.320 Chirality : 0.041 0.190 2214 Planarity : 0.003 0.036 2536 Dihedral : 5.280 75.136 1957 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.77 % Allowed : 14.57 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.20), residues: 1804 helix: 1.96 (0.17), residues: 875 sheet: 0.54 (0.29), residues: 350 loop : -0.41 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGTI 250 TYR 0.017 0.001 TYRFA 178 PHE 0.024 0.002 PHETH 280 TRP 0.014 0.001 TRPFA 475 HIS 0.005 0.001 HISLA1268 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (14441) covalent geometry : angle 0.59859 / 0.32 (19601) hydrogen bonds : bond 0.04365 / 2.91 ( 843) hydrogen bonds : angle 4.63374 / 3.23 ( 2403) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: FA 178 TYR cc_start: 0.6569 (OUTLIER) cc_final: 0.6079 (p90) REVERT: FA 460 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6347 (pm20) REVERT: FA 578 MET cc_start: 0.8329 (mmm) cc_final: 0.8036 (mmm) REVERT: LA 1187 MET cc_start: 0.7052 (tmm) cc_final: 0.6380 (tmm) REVERT: LA 1194 TYR cc_start: 0.8059 (p90) cc_final: 0.7820 (p90) REVERT: TB 271 ASP cc_start: 0.7225 (t70) cc_final: 0.6994 (m-30) REVERT: TH 278 ASN cc_start: 0.7119 (p0) cc_final: 0.6671 (m-40) REVERT: TI 294 ASN cc_start: 0.8410 (m-40) cc_final: 0.7864 (p0) REVERT: TK 283 SER cc_start: 0.8344 (p) cc_final: 0.8039 (t) outliers start: 43 outliers final: 32 residues processed: 200 average time/residue: 0.0926 time to fit residues: 28.3882 Evaluate side-chains 181 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FA residue 152 THR Chi-restraints excluded: chain FA residue 164 LYS Chi-restraints excluded: chain FA residue 178 TYR Chi-restraints excluded: chain FA residue 211 VAL Chi-restraints excluded: chain FA residue 306 THR Chi-restraints excluded: chain FA residue 456 ASP Chi-restraints excluded: chain FA residue 460 GLU Chi-restraints excluded: chain FA residue 549 VAL Chi-restraints excluded: chain FA residue 600 ASN Chi-restraints excluded: chain FA residue 675 VAL Chi-restraints excluded: chain FA residue 679 VAL Chi-restraints excluded: chain FA residue 723 ILE Chi-restraints excluded: chain LA residue 1113 VAL Chi-restraints excluded: chain LA residue 1116 THR Chi-restraints excluded: chain LA residue 1132 SER Chi-restraints excluded: chain LA residue 1310 VAL Chi-restraints excluded: chain LA residue 1350 TYR Chi-restraints excluded: chain TA residue 234 VAL Chi-restraints excluded: chain TC residue 289 LEU Chi-restraints excluded: chain TE residue 259 LEU Chi-restraints excluded: chain TE residue 286 ASP Chi-restraints excluded: chain TF residue 261 THR Chi-restraints excluded: chain TF residue 290 THR Chi-restraints excluded: chain TG residue 234 VAL Chi-restraints excluded: chain TH residue 266 THR Chi-restraints excluded: chain TH residue 285 LEU Chi-restraints excluded: chain TH residue 290 THR Chi-restraints excluded: chain TJ residue 239 GLU Chi-restraints excluded: chain TK residue 247 SER Chi-restraints excluded: chain TK residue 248 TYR Chi-restraints excluded: chain TK residue 274 LEU Chi-restraints excluded: chain TK residue 298 LEU Chi-restraints excluded: chain TL residue 248 TYR Chi-restraints excluded: chain TL residue 270 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 130 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 106 optimal weight: 30.0000 chunk 91 optimal weight: 30.0000 chunk 13 optimal weight: 9.9990 chunk 147 optimal weight: 0.0470 overall best weight: 3.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... TA 282 ASN ** TB 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TE 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TG 243 GLN ** TH 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TK 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.077524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.063366 restraints weight = 100283.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.064224 restraints weight = 56305.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.064826 restraints weight = 36299.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.065177 restraints weight = 26189.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.065488 restraints weight = 21003.710| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14441 Z= 0.117 Angle : 0.565 8.729 19601 Z= 0.300 Chirality : 0.040 0.156 2214 Planarity : 0.003 0.037 2536 Dihedral : 5.191 77.247 1957 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.55 % Allowed : 14.96 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.20), residues: 1804 helix: 2.17 (0.17), residues: 856 sheet: 0.59 (0.29), residues: 346 loop : -0.68 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGTI 250 TYR 0.016 0.001 TYRFA 178 PHE 0.020 0.001 PHEFA 254 TRP 0.013 0.001 TRPFA 475 HIS 0.006 0.001 HISFA 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (14441) covalent geometry : angle 0.56497 / 0.30 (19601) hydrogen bonds : bond 0.04020 / 2.68 ( 843) hydrogen bonds : angle 4.42979 / 3.09 ( 2403) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 176 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: FA 336 MET cc_start: 0.7249 (mpp) cc_final: 0.6618 (mpp) REVERT: FA 460 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6378 (pm20) REVERT: FA 578 MET cc_start: 0.8435 (mmm) cc_final: 0.8084 (mmm) REVERT: FA 651 VAL cc_start: 0.6695 (OUTLIER) cc_final: 0.6414 (m) REVERT: LA 1187 MET cc_start: 0.6821 (tmm) cc_final: 0.6076 (tmm) REVERT: LA 1194 TYR cc_start: 0.7884 (p90) cc_final: 0.7662 (p90) REVERT: LA 1225 MET cc_start: 0.5718 (mtp) cc_final: 0.5349 (mmm) REVERT: LA 1378 MET cc_start: 0.5194 (ppp) cc_final: 0.4737 (ppp) REVERT: TA 282 ASN cc_start: 0.7547 (OUTLIER) cc_final: 0.7072 (t0) REVERT: TD 271 ASP cc_start: 0.6160 (t0) cc_final: 0.5948 (t0) REVERT: TF 262 ASP cc_start: 0.7399 (t0) cc_final: 0.7147 (t0) REVERT: TH 278 ASN cc_start: 0.7079 (p0) cc_final: 0.6776 (m-40) REVERT: TI 294 ASN cc_start: 0.8280 (m-40) cc_final: 0.7705 (p0) REVERT: TK 283 SER cc_start: 0.8116 (p) cc_final: 0.7833 (t) outliers start: 55 outliers final: 36 residues processed: 218 average time/residue: 0.0873 time to fit residues: 29.2790 Evaluate side-chains 194 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FA residue 152 THR Chi-restraints excluded: chain FA residue 164 LYS Chi-restraints excluded: chain FA residue 178 TYR Chi-restraints excluded: chain FA residue 211 VAL Chi-restraints excluded: chain FA residue 306 THR Chi-restraints excluded: chain FA residue 456 ASP Chi-restraints excluded: chain FA residue 460 GLU Chi-restraints excluded: chain FA residue 600 ASN Chi-restraints excluded: chain FA residue 651 VAL Chi-restraints excluded: chain FA residue 675 VAL Chi-restraints excluded: chain FA residue 679 VAL Chi-restraints excluded: chain LA residue 1113 VAL Chi-restraints excluded: chain LA residue 1132 SER Chi-restraints excluded: chain LA residue 1310 VAL Chi-restraints excluded: chain LA residue 1350 TYR Chi-restraints excluded: chain TA residue 234 VAL Chi-restraints excluded: chain TA residue 282 ASN Chi-restraints excluded: chain TB residue 292 LEU Chi-restraints excluded: chain TB residue 294 ASN Chi-restraints excluded: chain TC residue 234 VAL Chi-restraints excluded: chain TC residue 251 ASP Chi-restraints excluded: chain TC residue 289 LEU Chi-restraints excluded: chain TD residue 240 LEU Chi-restraints excluded: chain TD residue 298 LEU Chi-restraints excluded: chain TE residue 259 LEU Chi-restraints excluded: chain TE residue 286 ASP Chi-restraints excluded: chain TF residue 261 THR Chi-restraints excluded: chain TF residue 269 THR Chi-restraints excluded: chain TF residue 290 THR Chi-restraints excluded: chain TF residue 296 ASN Chi-restraints excluded: chain TG residue 234 VAL Chi-restraints excluded: chain TH residue 266 THR Chi-restraints excluded: chain TH residue 285 LEU Chi-restraints excluded: chain TH residue 290 THR Chi-restraints excluded: chain TJ residue 239 GLU Chi-restraints excluded: chain TK residue 247 SER Chi-restraints excluded: chain TK residue 248 TYR Chi-restraints excluded: chain TK residue 274 LEU Chi-restraints excluded: chain TL residue 248 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 99 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 141 optimal weight: 0.0170 chunk 140 optimal weight: 9.9990 chunk 11 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 19 optimal weight: 8.9990 chunk 18 optimal weight: 0.0980 chunk 88 optimal weight: 30.0000 overall best weight: 3.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... FA 505 ASN FA 515 ASN FA 597 HIS ** TB 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TE 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TH 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.077824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.063516 restraints weight = 100885.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.064470 restraints weight = 56212.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.065050 restraints weight = 36067.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.065432 restraints weight = 25927.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.065650 restraints weight = 20684.986| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14441 Z= 0.113 Angle : 0.570 10.251 19601 Z= 0.301 Chirality : 0.040 0.156 2214 Planarity : 0.003 0.039 2536 Dihedral : 5.124 78.409 1957 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.09 % Allowed : 15.73 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.20), residues: 1804 helix: 2.24 (0.17), residues: 849 sheet: 0.71 (0.29), residues: 344 loop : -0.66 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGTB 250 TYR 0.030 0.001 TYRTB 248 PHE 0.019 0.001 PHEFA 254 TRP 0.012 0.001 TRPFA 475 HIS 0.011 0.001 HISFA 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (14441) covalent geometry : angle 0.56976 / 0.30 (19601) hydrogen bonds : bond 0.03928 / 2.62 ( 843) hydrogen bonds : angle 4.37288 / 3.05 ( 2403) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: FA 336 MET cc_start: 0.7188 (mpp) cc_final: 0.6584 (mpp) REVERT: FA 460 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6371 (pm20) REVERT: FA 578 MET cc_start: 0.8487 (mmm) cc_final: 0.8147 (mmm) REVERT: FA 651 VAL cc_start: 0.6843 (OUTLIER) cc_final: 0.6541 (m) REVERT: LA 1187 MET cc_start: 0.6796 (tmm) cc_final: 0.6041 (tmm) REVERT: LA 1194 TYR cc_start: 0.7987 (p90) cc_final: 0.7715 (p90) REVERT: LA 1277 LEU cc_start: 0.7917 (mt) cc_final: 0.7707 (mp) REVERT: LA 1378 MET cc_start: 0.5577 (ppp) cc_final: 0.4902 (ppp) REVERT: TC 258 LYS cc_start: 0.9083 (tptp) cc_final: 0.8874 (tptp) REVERT: TF 262 ASP cc_start: 0.7519 (t0) cc_final: 0.7255 (t0) REVERT: TH 278 ASN cc_start: 0.7183 (p0) cc_final: 0.6956 (m-40) REVERT: TI 269 THR cc_start: 0.8381 (t) cc_final: 0.8135 (p) REVERT: TI 294 ASN cc_start: 0.8447 (m-40) cc_final: 0.7813 (p0) REVERT: TK 283 SER cc_start: 0.8199 (p) cc_final: 0.7927 (t) outliers start: 48 outliers final: 37 residues processed: 200 average time/residue: 0.0996 time to fit residues: 30.4065 Evaluate side-chains 193 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FA residue 152 THR Chi-restraints excluded: chain FA residue 164 LYS Chi-restraints excluded: chain FA residue 178 TYR Chi-restraints excluded: chain FA residue 211 VAL Chi-restraints excluded: chain FA residue 306 THR Chi-restraints excluded: chain FA residue 456 ASP Chi-restraints excluded: chain FA residue 460 GLU Chi-restraints excluded: chain FA residue 549 VAL Chi-restraints excluded: chain FA residue 600 ASN Chi-restraints excluded: chain FA residue 651 VAL Chi-restraints excluded: chain FA residue 675 VAL Chi-restraints excluded: chain FA residue 679 VAL Chi-restraints excluded: chain LA residue 1113 VAL Chi-restraints excluded: chain LA residue 1116 THR Chi-restraints excluded: chain LA residue 1132 SER Chi-restraints excluded: chain LA residue 1310 VAL Chi-restraints excluded: chain LA residue 1350 TYR Chi-restraints excluded: chain TA residue 234 VAL Chi-restraints excluded: chain TC residue 234 VAL Chi-restraints excluded: chain TC residue 250 ARG Chi-restraints excluded: chain TC residue 251 ASP Chi-restraints excluded: chain TC residue 289 LEU Chi-restraints excluded: chain TD residue 240 LEU Chi-restraints excluded: chain TE residue 259 LEU Chi-restraints excluded: chain TE residue 286 ASP Chi-restraints excluded: chain TF residue 261 THR Chi-restraints excluded: chain TF residue 269 THR Chi-restraints excluded: chain TF residue 290 THR Chi-restraints excluded: chain TG residue 234 VAL Chi-restraints excluded: chain TH residue 266 THR Chi-restraints excluded: chain TH residue 285 LEU Chi-restraints excluded: chain TI residue 240 LEU Chi-restraints excluded: chain TJ residue 239 GLU Chi-restraints excluded: chain TK residue 247 SER Chi-restraints excluded: chain TK residue 248 TYR Chi-restraints excluded: chain TK residue 274 LEU Chi-restraints excluded: chain TK residue 298 LEU Chi-restraints excluded: chain TL residue 248 TYR Chi-restraints excluded: chain TL residue 270 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 135 optimal weight: 7.9990 chunk 159 optimal weight: 0.7980 chunk 73 optimal weight: 50.0000 chunk 55 optimal weight: 50.0000 chunk 78 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 35 optimal weight: 40.0000 chunk 143 optimal weight: 20.0000 chunk 171 optimal weight: 0.0070 chunk 6 optimal weight: 6.9990 chunk 106 optimal weight: 30.0000 overall best weight: 5.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LA1110 HIS TA 282 ASN ** TE 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TH 243 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.077226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.062999 restraints weight = 100374.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.063881 restraints weight = 55956.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.064466 restraints weight = 35761.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.064869 restraints weight = 25759.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.065175 restraints weight = 20599.928| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14441 Z= 0.122 Angle : 0.571 9.543 19601 Z= 0.302 Chirality : 0.040 0.162 2214 Planarity : 0.003 0.039 2536 Dihedral : 5.152 78.359 1957 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.93 % Allowed : 15.34 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.20), residues: 1804 helix: 2.16 (0.17), residues: 861 sheet: 0.66 (0.29), residues: 342 loop : -0.67 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGTJ 250 TYR 0.019 0.001 TYRTB 248 PHE 0.019 0.001 PHEFA 254 TRP 0.012 0.001 TRPFA 475 HIS 0.004 0.001 HISFA 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (14441) covalent geometry : angle 0.57082 / 0.30 (19601) hydrogen bonds : bond 0.04013 / 2.68 ( 843) hydrogen bonds : angle 4.35521 / 3.04 ( 2403) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 165 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: FA 278 MET cc_start: 0.6164 (tpp) cc_final: 0.5955 (tpp) REVERT: FA 336 MET cc_start: 0.7211 (mpp) cc_final: 0.6661 (mpp) REVERT: FA 460 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6375 (pm20) REVERT: FA 651 VAL cc_start: 0.6871 (OUTLIER) cc_final: 0.6572 (m) REVERT: LA 1187 MET cc_start: 0.6745 (tmm) cc_final: 0.6435 (tmm) REVERT: LA 1194 TYR cc_start: 0.7998 (p90) cc_final: 0.7688 (p90) REVERT: LA 1225 MET cc_start: 0.5832 (mtp) cc_final: 0.5495 (mmm) REVERT: LA 1378 MET cc_start: 0.5580 (ppp) cc_final: 0.4915 (ppp) REVERT: TA 282 ASN cc_start: 0.7929 (OUTLIER) cc_final: 0.7053 (t0) REVERT: TF 262 ASP cc_start: 0.7652 (t0) cc_final: 0.7382 (t0) REVERT: TG 255 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7901 (mtmm) REVERT: TI 294 ASN cc_start: 0.8477 (m-40) cc_final: 0.7770 (p0) REVERT: TK 283 SER cc_start: 0.8208 (p) cc_final: 0.7950 (t) REVERT: TL 298 LEU cc_start: 0.8087 (mp) cc_final: 0.7629 (mp) outliers start: 61 outliers final: 43 residues processed: 210 average time/residue: 0.1040 time to fit residues: 33.4722 Evaluate side-chains 193 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 146 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FA residue 152 THR Chi-restraints excluded: chain FA residue 164 LYS Chi-restraints excluded: chain FA residue 178 TYR Chi-restraints excluded: chain FA residue 180 ILE Chi-restraints excluded: chain FA residue 211 VAL Chi-restraints excluded: chain FA residue 306 THR Chi-restraints excluded: chain FA residue 442 VAL Chi-restraints excluded: chain FA residue 460 GLU Chi-restraints excluded: chain FA residue 549 VAL Chi-restraints excluded: chain FA residue 600 ASN Chi-restraints excluded: chain FA residue 651 VAL Chi-restraints excluded: chain FA residue 675 VAL Chi-restraints excluded: chain FA residue 723 ILE Chi-restraints excluded: chain LA residue 1113 VAL Chi-restraints excluded: chain LA residue 1116 THR Chi-restraints excluded: chain LA residue 1132 SER Chi-restraints excluded: chain LA residue 1310 VAL Chi-restraints excluded: chain LA residue 1346 ILE Chi-restraints excluded: chain LA residue 1350 TYR Chi-restraints excluded: chain TA residue 234 VAL Chi-restraints excluded: chain TA residue 282 ASN Chi-restraints excluded: chain TB residue 292 LEU Chi-restraints excluded: chain TB residue 294 ASN Chi-restraints excluded: chain TC residue 234 VAL Chi-restraints excluded: chain TC residue 239 GLU Chi-restraints excluded: chain TC residue 250 ARG Chi-restraints excluded: chain TC residue 251 ASP Chi-restraints excluded: chain TC residue 289 LEU Chi-restraints excluded: chain TD residue 240 LEU Chi-restraints excluded: chain TD residue 298 LEU Chi-restraints excluded: chain TE residue 259 LEU Chi-restraints excluded: chain TE residue 286 ASP Chi-restraints excluded: chain TF residue 261 THR Chi-restraints excluded: chain TF residue 269 THR Chi-restraints excluded: chain TF residue 290 THR Chi-restraints excluded: chain TF residue 296 ASN Chi-restraints excluded: chain TG residue 234 VAL Chi-restraints excluded: chain TG residue 255 LYS Chi-restraints excluded: chain TH residue 266 THR Chi-restraints excluded: chain TH residue 285 LEU Chi-restraints excluded: chain TH residue 290 THR Chi-restraints excluded: chain TI residue 240 LEU Chi-restraints excluded: chain TJ residue 239 GLU Chi-restraints excluded: chain TK residue 247 SER Chi-restraints excluded: chain TK residue 248 TYR Chi-restraints excluded: chain TK residue 274 LEU Chi-restraints excluded: chain TL residue 270 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 53 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 45 optimal weight: 50.0000 chunk 142 optimal weight: 0.8980 chunk 161 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 91 optimal weight: 50.0000 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... TA 282 ASN ** TB 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TE 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TJ 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.076615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.062397 restraints weight = 99968.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.063293 restraints weight = 55445.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.063880 restraints weight = 35565.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.064294 restraints weight = 25589.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.064492 restraints weight = 20407.943| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14441 Z= 0.136 Angle : 0.596 10.162 19601 Z= 0.315 Chirality : 0.041 0.199 2214 Planarity : 0.003 0.037 2536 Dihedral : 5.142 78.483 1956 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.61 % Allowed : 16.51 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.20), residues: 1804 helix: 2.05 (0.17), residues: 867 sheet: 0.65 (0.29), residues: 344 loop : -0.67 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGTJ 250 TYR 0.025 0.001 TYRTB 248 PHE 0.020 0.001 PHEFA 254 TRP 0.015 0.001 TRPTK 264 HIS 0.004 0.001 HISFA 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (14441) covalent geometry : angle 0.59649 / 0.31 (19601) hydrogen bonds : bond 0.04241 / 2.82 ( 843) hydrogen bonds : angle 4.38999 / 3.07 ( 2403) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 152 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: FA 336 MET cc_start: 0.7166 (mpp) cc_final: 0.6626 (mpp) REVERT: FA 460 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6352 (pm20) REVERT: FA 578 MET cc_start: 0.8272 (mmm) cc_final: 0.7979 (mmm) REVERT: FA 651 VAL cc_start: 0.6866 (OUTLIER) cc_final: 0.6578 (m) REVERT: LA 1187 MET cc_start: 0.6790 (tmm) cc_final: 0.6479 (tmm) REVERT: LA 1225 MET cc_start: 0.5816 (mtp) cc_final: 0.5441 (mmm) REVERT: LA 1378 MET cc_start: 0.5781 (ppp) cc_final: 0.5086 (ppp) REVERT: TA 282 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.7070 (t0) REVERT: TB 278 ASN cc_start: 0.7340 (p0) cc_final: 0.6611 (p0) REVERT: TC 249 LYS cc_start: 0.9021 (mmmm) cc_final: 0.8750 (mmmm) REVERT: TD 285 LEU cc_start: 0.8643 (mm) cc_final: 0.8403 (tp) REVERT: TF 262 ASP cc_start: 0.7644 (t0) cc_final: 0.7288 (t0) REVERT: TI 294 ASN cc_start: 0.8502 (m-40) cc_final: 0.8205 (m-40) REVERT: TK 283 SER cc_start: 0.8248 (p) cc_final: 0.7957 (t) outliers start: 56 outliers final: 44 residues processed: 194 average time/residue: 0.0934 time to fit residues: 28.1168 Evaluate side-chains 188 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 141 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FA residue 152 THR Chi-restraints excluded: chain FA residue 164 LYS Chi-restraints excluded: chain FA residue 178 TYR Chi-restraints excluded: chain FA residue 180 ILE Chi-restraints excluded: chain FA residue 211 VAL Chi-restraints excluded: chain FA residue 306 THR Chi-restraints excluded: chain FA residue 442 VAL Chi-restraints excluded: chain FA residue 456 ASP Chi-restraints excluded: chain FA residue 460 GLU Chi-restraints excluded: chain FA residue 549 VAL Chi-restraints excluded: chain FA residue 600 ASN Chi-restraints excluded: chain FA residue 651 VAL Chi-restraints excluded: chain FA residue 675 VAL Chi-restraints excluded: chain FA residue 679 VAL Chi-restraints excluded: chain FA residue 723 ILE Chi-restraints excluded: chain LA residue 1113 VAL Chi-restraints excluded: chain LA residue 1116 THR Chi-restraints excluded: chain LA residue 1132 SER Chi-restraints excluded: chain LA residue 1310 VAL Chi-restraints excluded: chain LA residue 1346 ILE Chi-restraints excluded: chain LA residue 1350 TYR Chi-restraints excluded: chain TA residue 234 VAL Chi-restraints excluded: chain TA residue 282 ASN Chi-restraints excluded: chain TB residue 292 LEU Chi-restraints excluded: chain TB residue 294 ASN Chi-restraints excluded: chain TC residue 234 VAL Chi-restraints excluded: chain TC residue 239 GLU Chi-restraints excluded: chain TC residue 250 ARG Chi-restraints excluded: chain TC residue 251 ASP Chi-restraints excluded: chain TD residue 240 LEU Chi-restraints excluded: chain TD residue 298 LEU Chi-restraints excluded: chain TE residue 251 ASP Chi-restraints excluded: chain TE residue 259 LEU Chi-restraints excluded: chain TE residue 286 ASP Chi-restraints excluded: chain TF residue 261 THR Chi-restraints excluded: chain TF residue 269 THR Chi-restraints excluded: chain TF residue 270 ILE Chi-restraints excluded: chain TF residue 290 THR Chi-restraints excluded: chain TF residue 296 ASN Chi-restraints excluded: chain TG residue 234 VAL Chi-restraints excluded: chain TH residue 266 THR Chi-restraints excluded: chain TH residue 285 LEU Chi-restraints excluded: chain TH residue 290 THR Chi-restraints excluded: chain TJ residue 239 GLU Chi-restraints excluded: chain TK residue 247 SER Chi-restraints excluded: chain TK residue 274 LEU Chi-restraints excluded: chain TL residue 270 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 20.0000 chunk 60 optimal weight: 50.0000 chunk 64 optimal weight: 50.0000 chunk 86 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 93 optimal weight: 50.0000 chunk 2 optimal weight: 0.5980 chunk 71 optimal weight: 30.0000 chunk 53 optimal weight: 30.0000 chunk 105 optimal weight: 0.8980 chunk 128 optimal weight: 9.9990 overall best weight: 5.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... TA 282 ASN ** TB 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TE 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TJ 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TJ 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.076587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.062242 restraints weight = 101048.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.063134 restraints weight = 55338.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.063708 restraints weight = 35159.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 72)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.064105 restraints weight = 25320.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.064322 restraints weight = 20290.755| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14441 Z= 0.130 Angle : 0.601 12.824 19601 Z= 0.316 Chirality : 0.040 0.200 2214 Planarity : 0.003 0.038 2536 Dihedral : 5.131 79.395 1956 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.29 % Allowed : 17.09 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.20), residues: 1804 helix: 2.02 (0.17), residues: 867 sheet: 0.59 (0.29), residues: 344 loop : -0.72 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGFA 371 TYR 0.023 0.001 TYRTB 248 PHE 0.019 0.001 PHEFA 254 TRP 0.020 0.001 TRPFA 208 HIS 0.003 0.001 HISFA 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (14441) covalent geometry : angle 0.60144 / 0.32 (19601) hydrogen bonds : bond 0.04238 / 2.81 ( 843) hydrogen bonds : angle 4.39307 / 3.08 ( 2403) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 149 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: FA 208 TRP cc_start: 0.2074 (m-10) cc_final: 0.1690 (m100) REVERT: FA 336 MET cc_start: 0.7113 (mpp) cc_final: 0.6564 (mpp) REVERT: FA 460 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.6354 (pm20) REVERT: FA 578 MET cc_start: 0.8400 (mmm) cc_final: 0.8123 (mmm) REVERT: FA 651 VAL cc_start: 0.6849 (OUTLIER) cc_final: 0.6576 (m) REVERT: LA 1187 MET cc_start: 0.6790 (tmm) cc_final: 0.6273 (tmm) REVERT: LA 1225 MET cc_start: 0.5697 (mtp) cc_final: 0.5264 (mmm) REVERT: LA 1378 MET cc_start: 0.5770 (ppp) cc_final: 0.5059 (ppp) REVERT: TB 278 ASN cc_start: 0.7438 (p0) cc_final: 0.6779 (p0) REVERT: TD 285 LEU cc_start: 0.8708 (mm) cc_final: 0.8380 (tp) REVERT: TF 262 ASP cc_start: 0.7824 (t0) cc_final: 0.7446 (t0) REVERT: TI 294 ASN cc_start: 0.8466 (m-40) cc_final: 0.8164 (m-40) REVERT: TK 283 SER cc_start: 0.8231 (p) cc_final: 0.7944 (t) REVERT: TL 251 ASP cc_start: 0.7996 (m-30) cc_final: 0.7739 (m-30) outliers start: 51 outliers final: 39 residues processed: 188 average time/residue: 0.0990 time to fit residues: 28.9512 Evaluate side-chains 181 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FA residue 126 PHE Chi-restraints excluded: chain FA residue 152 THR Chi-restraints excluded: chain FA residue 164 LYS Chi-restraints excluded: chain FA residue 178 TYR Chi-restraints excluded: chain FA residue 180 ILE Chi-restraints excluded: chain FA residue 211 VAL Chi-restraints excluded: chain FA residue 306 THR Chi-restraints excluded: chain FA residue 460 GLU Chi-restraints excluded: chain FA residue 549 VAL Chi-restraints excluded: chain FA residue 600 ASN Chi-restraints excluded: chain FA residue 651 VAL Chi-restraints excluded: chain FA residue 675 VAL Chi-restraints excluded: chain FA residue 679 VAL Chi-restraints excluded: chain LA residue 1113 VAL Chi-restraints excluded: chain LA residue 1116 THR Chi-restraints excluded: chain LA residue 1132 SER Chi-restraints excluded: chain LA residue 1310 VAL Chi-restraints excluded: chain LA residue 1346 ILE Chi-restraints excluded: chain LA residue 1350 TYR Chi-restraints excluded: chain TA residue 234 VAL Chi-restraints excluded: chain TB residue 294 ASN Chi-restraints excluded: chain TC residue 234 VAL Chi-restraints excluded: chain TC residue 239 GLU Chi-restraints excluded: chain TC residue 251 ASP Chi-restraints excluded: chain TD residue 240 LEU Chi-restraints excluded: chain TE residue 251 ASP Chi-restraints excluded: chain TE residue 259 LEU Chi-restraints excluded: chain TE residue 286 ASP Chi-restraints excluded: chain TF residue 261 THR Chi-restraints excluded: chain TF residue 269 THR Chi-restraints excluded: chain TF residue 270 ILE Chi-restraints excluded: chain TF residue 290 THR Chi-restraints excluded: chain TF residue 296 ASN Chi-restraints excluded: chain TG residue 234 VAL Chi-restraints excluded: chain TH residue 266 THR Chi-restraints excluded: chain TH residue 290 THR Chi-restraints excluded: chain TI residue 274 LEU Chi-restraints excluded: chain TJ residue 239 GLU Chi-restraints excluded: chain TK residue 247 SER Chi-restraints excluded: chain TK residue 274 LEU Chi-restraints excluded: chain TL residue 270 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 1 optimal weight: 30.0000 chunk 44 optimal weight: 7.9990 chunk 86 optimal weight: 40.0000 chunk 141 optimal weight: 8.9990 chunk 134 optimal weight: 40.0000 chunk 41 optimal weight: 30.0000 chunk 77 optimal weight: 30.0000 chunk 108 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 93 optimal weight: 50.0000 overall best weight: 10.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... FA 248 GLN LA1266 GLN TA 282 ASN TB 243 GLN TE 295 ASN ** TJ 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TJ 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.074685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.060650 restraints weight = 101274.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.061533 restraints weight = 55852.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.062066 restraints weight = 35916.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.062439 restraints weight = 25785.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.062625 restraints weight = 20539.443| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14441 Z= 0.192 Angle : 0.671 12.692 19601 Z= 0.358 Chirality : 0.043 0.173 2214 Planarity : 0.004 0.037 2536 Dihedral : 5.533 79.916 1956 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.61 % Allowed : 16.89 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.20), residues: 1804 helix: 1.54 (0.17), residues: 888 sheet: 0.34 (0.28), residues: 343 loop : -0.59 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGFA 371 TYR 0.020 0.002 TYRTB 248 PHE 0.025 0.002 PHEFA 254 TRP 0.013 0.002 TRPFA 320 HIS 0.006 0.001 HISLA1226 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (14441) covalent geometry : angle 0.67130 / 0.36 (19601) hydrogen bonds : bond 0.04966 / 3.29 ( 843) hydrogen bonds : angle 4.77243 / 3.33 ( 2403) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 138 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: FA 460 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6335 (pm20) REVERT: LA 1225 MET cc_start: 0.5803 (mtp) cc_final: 0.5481 (mmm) REVERT: TA 282 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8143 (t0) REVERT: TB 278 ASN cc_start: 0.7524 (p0) cc_final: 0.6804 (p0) REVERT: TF 262 ASP cc_start: 0.7614 (t0) cc_final: 0.7254 (t0) REVERT: TK 283 SER cc_start: 0.8537 (p) cc_final: 0.8284 (t) outliers start: 56 outliers final: 43 residues processed: 182 average time/residue: 0.0946 time to fit residues: 26.8569 Evaluate side-chains 174 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FA residue 126 PHE Chi-restraints excluded: chain FA residue 152 THR Chi-restraints excluded: chain FA residue 164 LYS Chi-restraints excluded: chain FA residue 178 TYR Chi-restraints excluded: chain FA residue 278 MET Chi-restraints excluded: chain FA residue 442 VAL Chi-restraints excluded: chain FA residue 460 GLU Chi-restraints excluded: chain FA residue 549 VAL Chi-restraints excluded: chain FA residue 600 ASN Chi-restraints excluded: chain FA residue 675 VAL Chi-restraints excluded: chain FA residue 723 ILE Chi-restraints excluded: chain LA residue 1113 VAL Chi-restraints excluded: chain LA residue 1116 THR Chi-restraints excluded: chain LA residue 1132 SER Chi-restraints excluded: chain LA residue 1310 VAL Chi-restraints excluded: chain LA residue 1346 ILE Chi-restraints excluded: chain TA residue 234 VAL Chi-restraints excluded: chain TA residue 282 ASN Chi-restraints excluded: chain TB residue 292 LEU Chi-restraints excluded: chain TB residue 294 ASN Chi-restraints excluded: chain TC residue 234 VAL Chi-restraints excluded: chain TC residue 239 GLU Chi-restraints excluded: chain TC residue 251 ASP Chi-restraints excluded: chain TC residue 298 LEU Chi-restraints excluded: chain TD residue 240 LEU Chi-restraints excluded: chain TD residue 298 LEU Chi-restraints excluded: chain TE residue 251 ASP Chi-restraints excluded: chain TE residue 259 LEU Chi-restraints excluded: chain TE residue 286 ASP Chi-restraints excluded: chain TF residue 261 THR Chi-restraints excluded: chain TF residue 269 THR Chi-restraints excluded: chain TF residue 270 ILE Chi-restraints excluded: chain TF residue 290 THR Chi-restraints excluded: chain TF residue 296 ASN Chi-restraints excluded: chain TG residue 234 VAL Chi-restraints excluded: chain TH residue 266 THR Chi-restraints excluded: chain TH residue 290 THR Chi-restraints excluded: chain TI residue 245 ILE Chi-restraints excluded: chain TI residue 274 LEU Chi-restraints excluded: chain TI residue 298 LEU Chi-restraints excluded: chain TJ residue 239 GLU Chi-restraints excluded: chain TK residue 247 SER Chi-restraints excluded: chain TK residue 274 LEU Chi-restraints excluded: chain TL residue 270 ILE Chi-restraints excluded: chain TL residue 298 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 90 optimal weight: 30.0000 chunk 22 optimal weight: 30.0000 chunk 53 optimal weight: 40.0000 chunk 76 optimal weight: 0.6980 chunk 93 optimal weight: 40.0000 chunk 16 optimal weight: 20.0000 chunk 163 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 35 optimal weight: 30.0000 chunk 129 optimal weight: 0.0980 chunk 43 optimal weight: 30.0000 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... FA 37 ASN LA1266 GLN ** TJ 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TJ 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.074714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.060625 restraints weight = 100151.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.061491 restraints weight = 54898.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.062045 restraints weight = 35012.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.062357 restraints weight = 25286.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.062571 restraints weight = 20501.854| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.235 14441 Z= 0.239 Angle : 0.878 59.198 19601 Z= 0.496 Chirality : 0.046 0.679 2214 Planarity : 0.004 0.083 2536 Dihedral : 5.444 79.946 1954 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.03 % Allowed : 17.67 % Favored : 79.30 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.20), residues: 1804 helix: 1.51 (0.17), residues: 888 sheet: 0.31 (0.28), residues: 343 loop : -0.61 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGTJ 250 TYR 0.021 0.002 TYRLA1352 PHE 0.024 0.002 PHEFA 254 TRP 0.013 0.002 TRPFA 475 HIS 0.006 0.001 HISLA1226 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.24 (14441) covalent geometry : angle 0.87764 / 0.50 (19601) hydrogen bonds : bond 0.04912 / 3.26 ( 843) hydrogen bonds : angle 4.76876 / 3.33 ( 2403) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 129 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: FA 460 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6332 (pm20) REVERT: LA 1225 MET cc_start: 0.5755 (mtp) cc_final: 0.5429 (mmm) REVERT: TB 278 ASN cc_start: 0.7505 (p0) cc_final: 0.6775 (p0) REVERT: TF 262 ASP cc_start: 0.7588 (t0) cc_final: 0.7229 (t0) REVERT: TK 283 SER cc_start: 0.8509 (p) cc_final: 0.8255 (t) outliers start: 47 outliers final: 46 residues processed: 164 average time/residue: 0.0862 time to fit residues: 22.2823 Evaluate side-chains 176 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 129 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FA residue 126 PHE Chi-restraints excluded: chain FA residue 152 THR Chi-restraints excluded: chain FA residue 164 LYS Chi-restraints excluded: chain FA residue 178 TYR Chi-restraints excluded: chain FA residue 442 VAL Chi-restraints excluded: chain FA residue 456 ASP Chi-restraints excluded: chain FA residue 460 GLU Chi-restraints excluded: chain FA residue 549 VAL Chi-restraints excluded: chain FA residue 600 ASN Chi-restraints excluded: chain FA residue 675 VAL Chi-restraints excluded: chain FA residue 723 ILE Chi-restraints excluded: chain LA residue 1113 VAL Chi-restraints excluded: chain LA residue 1116 THR Chi-restraints excluded: chain LA residue 1132 SER Chi-restraints excluded: chain LA residue 1310 VAL Chi-restraints excluded: chain LA residue 1346 ILE Chi-restraints excluded: chain LA residue 1350 TYR Chi-restraints excluded: chain TA residue 234 VAL Chi-restraints excluded: chain TB residue 292 LEU Chi-restraints excluded: chain TB residue 294 ASN Chi-restraints excluded: chain TC residue 234 VAL Chi-restraints excluded: chain TC residue 239 GLU Chi-restraints excluded: chain TC residue 251 ASP Chi-restraints excluded: chain TC residue 298 LEU Chi-restraints excluded: chain TD residue 240 LEU Chi-restraints excluded: chain TD residue 262 ASP Chi-restraints excluded: chain TD residue 285 LEU Chi-restraints excluded: chain TD residue 298 LEU Chi-restraints excluded: chain TE residue 251 ASP Chi-restraints excluded: chain TE residue 259 LEU Chi-restraints excluded: chain TE residue 286 ASP Chi-restraints excluded: chain TF residue 261 THR Chi-restraints excluded: chain TF residue 269 THR Chi-restraints excluded: chain TF residue 270 ILE Chi-restraints excluded: chain TF residue 290 THR Chi-restraints excluded: chain TF residue 296 ASN Chi-restraints excluded: chain TG residue 234 VAL Chi-restraints excluded: chain TH residue 266 THR Chi-restraints excluded: chain TH residue 290 THR Chi-restraints excluded: chain TI residue 245 ILE Chi-restraints excluded: chain TI residue 274 LEU Chi-restraints excluded: chain TI residue 298 LEU Chi-restraints excluded: chain TJ residue 239 GLU Chi-restraints excluded: chain TK residue 247 SER Chi-restraints excluded: chain TK residue 274 LEU Chi-restraints excluded: chain TL residue 270 ILE Chi-restraints excluded: chain TL residue 298 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 162 optimal weight: 20.0000 chunk 145 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 117 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LA1266 GLN ** TJ 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TJ 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.074725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.060601 restraints weight = 100427.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.061478 restraints weight = 55378.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.062042 restraints weight = 35298.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.062356 restraints weight = 25452.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.062670 restraints weight = 20581.949| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.235 14441 Z= 0.239 Angle : 0.878 59.198 19601 Z= 0.496 Chirality : 0.046 0.679 2214 Planarity : 0.004 0.083 2536 Dihedral : 5.444 79.946 1954 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.03 % Allowed : 17.79 % Favored : 79.17 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.20), residues: 1804 helix: 1.51 (0.17), residues: 888 sheet: 0.31 (0.28), residues: 343 loop : -0.61 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGTJ 250 TYR 0.021 0.002 TYRLA1352 PHE 0.024 0.002 PHEFA 254 TRP 0.013 0.002 TRPFA 475 HIS 0.006 0.001 HISLA1226 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.24 (14441) covalent geometry : angle 0.87764 / 0.50 (19601) hydrogen bonds : bond 0.04912 / 3.26 ( 843) hydrogen bonds : angle 4.76876 / 3.33 ( 2403) =============================================================================== Job complete usr+sys time: 2984.77 seconds wall clock time: 52 minutes 11.70 seconds (3131.70 seconds total)