Starting phenix.real_space_refine on Thu Jul 2 19:13:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wh1_65964/07_2026/9wh1_65964.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wh1_65964/07_2026/9wh1_65964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wh1_65964/07_2026/9wh1_65964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wh1_65964/07_2026/9wh1_65964.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wh1_65964/07_2026/9wh1_65964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wh1_65964/07_2026/9wh1_65964.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 29 5.16 5 C 6056 2.51 5 N 1590 2.21 5 O 1781 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s 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: 9465 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2303 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 6, 'TRANS': 277} Chain: "B" Number of atoms: 6973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6973 Classifications: {'peptide': 851} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 828} Chain: "C" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain breaks: 1 Time building chain proxies: 2.14, per 1000 atoms: 0.23 Number of scatterers: 9465 At special positions: 0 Unit cell: (86.676, 86.676, 137.004, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 9 15.00 O 1781 8.00 N 1590 7.00 C 6056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 273 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 289.4 milliseconds 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2194 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 7 sheets defined 59.2% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.612A pdb=" N ASP A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 297 Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.717A pdb=" N ARG A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 325 Processing helix chain 'A' and resid 330 through 343 removed outlier: 3.580A pdb=" N MET A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 401 Processing helix chain 'A' and resid 402 through 407 removed outlier: 6.191A pdb=" N ARG A 405 " --> pdb=" O PRO A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.524A pdb=" N GLU A 417 " --> pdb=" O THR A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 433 Processing helix chain 'A' and resid 468 through 488 Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 511 through 523 removed outlier: 3.582A pdb=" N LEU A 523 " --> pdb=" O PHE A 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 14 Processing helix chain 'B' and resid 15 through 34 Processing helix chain 'B' and resid 43 through 59 Processing helix chain 'B' and resid 64 through 77 Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 99 through 103 removed outlier: 4.108A pdb=" N ASP B 103 " --> pdb=" O TYR B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 124 Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 158 through 173 removed outlier: 3.597A pdb=" N GLN B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 199 Processing helix chain 'B' and resid 199 through 206 Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 255 through 261 removed outlier: 3.628A pdb=" N LEU B 259 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN B 261 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 283 Processing helix chain 'B' and resid 299 through 305 Processing helix chain 'B' and resid 347 through 353 removed outlier: 3.804A pdb=" N TYR B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR B 352 " --> pdb=" O GLY B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 367 removed outlier: 3.507A pdb=" N PHE B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG B 366 " --> pdb=" O ASN B 362 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS B 367 " --> pdb=" O ILE B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 391 Processing helix chain 'B' and resid 399 through 413 Processing helix chain 'B' and resid 417 through 423 Processing helix chain 'B' and resid 435 through 448 removed outlier: 3.538A pdb=" N LYS B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 removed outlier: 3.636A pdb=" N GLU B 462 " --> pdb=" O PRO B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 500 Processing helix chain 'B' and resid 525 through 530 removed outlier: 4.124A pdb=" N ILE B 528 " --> pdb=" O ASN B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 546 Processing helix chain 'B' and resid 546 through 559 removed outlier: 3.794A pdb=" N ASP B 559 " --> pdb=" O ARG B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 585 removed outlier: 3.908A pdb=" N GLU B 572 " --> pdb=" O ASN B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 591 Processing helix chain 'B' and resid 592 through 601 Processing helix chain 'B' and resid 604 through 615 removed outlier: 3.688A pdb=" N SER B 608 " --> pdb=" O GLU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 628 removed outlier: 3.596A pdb=" N ILE B 625 " --> pdb=" O PRO B 621 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR B 628 " --> pdb=" O ILE B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 645 Processing helix chain 'B' and resid 647 through 651 removed outlier: 3.506A pdb=" N LYS B 651 " --> pdb=" O VAL B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 672 Processing helix chain 'B' and resid 672 through 677 Processing helix chain 'B' and resid 685 through 699 removed outlier: 4.002A pdb=" N TYR B 689 " --> pdb=" O GLY B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 712 removed outlier: 3.560A pdb=" N ASP B 712 " --> pdb=" O ASN B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 750 Processing helix chain 'B' and resid 753 through 771 removed outlier: 3.980A pdb=" N TYR B 758 " --> pdb=" O PHE B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 786 removed outlier: 3.598A pdb=" N PHE B 782 " --> pdb=" O ASN B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 Processing helix chain 'B' and resid 801 through 810 Processing helix chain 'B' and resid 812 through 816 Processing helix chain 'B' and resid 822 through 825 removed outlier: 3.899A pdb=" N TYR B 825 " --> pdb=" O GLU B 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 822 through 825' Processing helix chain 'B' and resid 831 through 839 Processing helix chain 'B' and resid 845 through 850 Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 271 removed outlier: 3.643A pdb=" N PHE A 506 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU A 447 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N PHE A 505 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE A 449 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL A 507 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 451 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N PHE A 509 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TYR A 453 " --> pdb=" O PHE A 509 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N HIS A 377 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N PHE A 450 " --> pdb=" O HIS A 377 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA A 379 " --> pdb=" O PHE A 450 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N GLY A 452 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE A 381 " --> pdb=" O GLY A 452 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N ASN A 454 " --> pdb=" O PHE A 381 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 348 through 350 removed outlier: 6.402A pdb=" N ALA A 363 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 209 through 211 removed outlier: 6.411A pdb=" N LYS B 209 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE B 230 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 211 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN B 177 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N PHE B 252 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B 179 " --> pdb=" O PHE B 252 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP B 249 " --> pdb=" O LYS B 287 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL B 289 " --> pdb=" O ASP B 249 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 251 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N SER B 291 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 253 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 313 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 321 through 325 removed outlier: 6.678A pdb=" N SER B 321 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE B 513 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ASN B 323 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N CYS B 515 " --> pdb=" O ASN B 323 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR B 325 " --> pdb=" O CYS B 515 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE B 471 " --> pdb=" O PHE B 514 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU B 516 " --> pdb=" O ILE B 471 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE B 473 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET B 371 " --> pdb=" O PHE B 472 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ASN B 474 " --> pdb=" O MET B 371 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR B 373 " --> pdb=" O ASN B 474 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 334 through 337 removed outlier: 4.341A pdb=" N ILE B 334 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 716 through 717 Processing sheet with id=AA7, first strand: chain 'B' and resid 818 through 821 removed outlier: 6.159A pdb=" N ASN B 821 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ILE B 827 " --> pdb=" O ASN B 821 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3028 1.34 - 1.46: 2149 1.46 - 1.58: 4446 1.58 - 1.70: 16 1.70 - 1.81: 42 Bond restraints: 9681 Sorted by residual: bond pdb=" C3' DA C 8 " pdb=" C2' DA C 8 " ideal model delta sigma weight residual 1.516 1.530 -0.014 8.00e-03 1.56e+04 3.26e+00 bond pdb=" O4' DA C 8 " pdb=" C1' DA C 8 " ideal model delta sigma weight residual 1.420 1.403 0.017 1.10e-02 8.26e+03 2.26e+00 bond pdb=" N9 DA C 13 " pdb=" C4 DA C 13 " ideal model delta sigma weight residual 1.374 1.383 -0.009 6.00e-03 2.78e+04 2.17e+00 bond pdb=" C3' DA C 6 " pdb=" O3' DA C 6 " ideal model delta sigma weight residual 1.435 1.417 0.018 1.30e-02 5.92e+03 1.99e+00 bond pdb=" C2' DA C 6 " pdb=" C1' DA C 6 " ideal model delta sigma weight residual 1.518 1.532 -0.014 1.00e-02 1.00e+04 1.98e+00 ... (remaining 9676 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 12929 1.95 - 3.89: 147 3.89 - 5.84: 26 5.84 - 7.79: 3 7.79 - 9.73: 1 Bond angle restraints: 13106 Sorted by residual: angle pdb=" N VAL A 267 " pdb=" CA VAL A 267 " pdb=" C VAL A 267 " ideal model delta sigma weight residual 113.71 108.27 5.44 9.50e-01 1.11e+00 3.28e+01 angle pdb=" C LYS B 812 " pdb=" CA LYS B 812 " pdb=" CB LYS B 812 " ideal model delta sigma weight residual 116.54 110.73 5.81 1.15e+00 7.56e-01 2.55e+01 angle pdb=" CA LYS B 812 " pdb=" C LYS B 812 " pdb=" N GLU B 813 " ideal model delta sigma weight residual 119.52 117.08 2.44 7.90e-01 1.60e+00 9.54e+00 angle pdb=" CA GLU A 464 " pdb=" CB GLU A 464 " pdb=" CG GLU A 464 " ideal model delta sigma weight residual 114.10 120.11 -6.01 2.00e+00 2.50e-01 9.02e+00 angle pdb=" CA MET A 249 " pdb=" CB MET A 249 " pdb=" CG MET A 249 " ideal model delta sigma weight residual 114.10 119.67 -5.57 2.00e+00 2.50e-01 7.76e+00 ... (remaining 13101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 5231 16.44 - 32.87: 433 32.87 - 49.31: 149 49.31 - 65.75: 30 65.75 - 82.19: 9 Dihedral angle restraints: 5852 sinusoidal: 2468 harmonic: 3384 Sorted by residual: dihedral pdb=" CA ARG A 271 " pdb=" C ARG A 271 " pdb=" N LEU A 272 " pdb=" CA LEU A 272 " ideal model delta harmonic sigma weight residual -180.00 -157.40 -22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA LYS A 283 " pdb=" C LYS A 283 " pdb=" N ILE A 284 " pdb=" CA ILE A 284 " ideal model delta harmonic sigma weight residual 180.00 163.04 16.96 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA LEU B 231 " pdb=" C LEU B 231 " pdb=" N THR B 232 " pdb=" CA THR B 232 " ideal model delta harmonic sigma weight residual 180.00 164.34 15.66 0 5.00e+00 4.00e-02 9.81e+00 ... (remaining 5849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1028 0.039 - 0.077: 323 0.077 - 0.116: 87 0.116 - 0.155: 15 0.155 - 0.193: 3 Chirality restraints: 1456 Sorted by residual: chirality pdb=" CB ILE A 266 " pdb=" CA ILE A 266 " pdb=" CG1 ILE A 266 " pdb=" CG2 ILE A 266 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA ASN B 568 " pdb=" N ASN B 568 " pdb=" C ASN B 568 " pdb=" CB ASN B 568 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CB THR B 125 " pdb=" CA THR B 125 " pdb=" OG1 THR B 125 " pdb=" CG2 THR B 125 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.08e-01 ... (remaining 1453 not shown) Planarity restraints: 1641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 457 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO B 458 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 458 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 458 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 339 " -0.016 2.00e-02 2.50e+03 1.28e-02 2.86e+00 pdb=" CG PHE A 339 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 339 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 339 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 339 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 339 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 339 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 464 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" C GLU A 464 " 0.026 2.00e-02 2.50e+03 pdb=" O GLU A 464 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN A 465 " -0.009 2.00e-02 2.50e+03 ... (remaining 1638 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 5202 2.99 - 3.47: 10311 3.47 - 3.94: 15999 3.94 - 4.42: 19016 4.42 - 4.90: 29254 Nonbonded interactions: 79782 Sorted by model distance: nonbonded pdb=" O5' DA C 14 " pdb=" O4' DA C 14 " model vdw 2.508 2.432 nonbonded pdb=" N ASP A 423 " pdb=" OD1 ASP A 423 " model vdw 2.523 3.120 nonbonded pdb=" O ARG B 567 " pdb=" OD1 ASN B 568 " model vdw 2.525 3.040 nonbonded pdb=" O5' DA C 9 " pdb=" O4' DA C 9 " model vdw 2.534 2.432 nonbonded pdb=" N VAL A 267 " pdb=" N ASN A 268 " model vdw 2.600 2.560 ... (remaining 79777 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.900 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.290 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9682 Z= 0.171 Angle : 0.553 9.732 13108 Z= 0.313 Chirality : 0.041 0.193 1456 Planarity : 0.003 0.055 1641 Dihedral : 14.222 82.185 3655 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.90 % Favored : 92.84 % Rotamer: Outliers : 2.03 % Allowed : 12.16 % Favored : 85.81 % 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: 0.67 (0.27), residues: 1131 helix: 1.86 (0.22), residues: 606 sheet: -0.73 (0.46), residues: 135 loop : -1.42 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 271 TYR 0.012 0.001 TYR B 273 PHE 0.029 0.001 PHE A 339 TRP 0.011 0.001 TRP B 496 HIS 0.005 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 ( 9681) covalent geometry : angle 0.55265 / 0.31 (13106) SS BOND : bond 0.00536 / 0.28 ( 1) SS BOND : angle 0.87243 / 0.58 ( 2) hydrogen bonds : bond 0.12810 / 7.88 ( 440) hydrogen bonds : angle 5.13183 / 3.59 ( 1272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8740 (mtt) cc_final: 0.8523 (mtp) REVERT: A 303 MET cc_start: 0.8732 (mmm) cc_final: 0.8401 (mmm) REVERT: A 426 GLN cc_start: 0.8976 (tm-30) cc_final: 0.8728 (tm-30) REVERT: A 509 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.7318 (p90) REVERT: B 169 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8538 (tm-30) REVERT: B 309 LYS cc_start: 0.9000 (mtmp) cc_final: 0.8561 (mttp) REVERT: B 439 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.6045 (tmm160) REVERT: B 848 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8267 (mt-10) outliers start: 21 outliers final: 17 residues processed: 75 average time/residue: 0.0926 time to fit residues: 10.0700 Evaluate side-chains 76 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 599 TYR Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 830 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.083324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.065824 restraints weight = 27209.346| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.48 r_work: 0.3060 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.0453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9682 Z= 0.183 Angle : 0.525 9.844 13108 Z= 0.279 Chirality : 0.041 0.169 1456 Planarity : 0.004 0.069 1641 Dihedral : 11.628 82.577 1397 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.25 % Favored : 92.48 % Rotamer: Outliers : 3.57 % Allowed : 12.26 % Favored : 84.17 % 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: 0.64 (0.27), residues: 1131 helix: 1.79 (0.22), residues: 613 sheet: -0.54 (0.48), residues: 128 loop : -1.50 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 271 TYR 0.013 0.001 TYR B 668 PHE 0.014 0.001 PHE B 598 TRP 0.012 0.001 TRP B 697 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 9681) covalent geometry : angle 0.52514 / 0.28 (13106) SS BOND : bond 0.00452 / 0.24 ( 1) SS BOND : angle 1.36829 / 0.91 ( 2) hydrogen bonds : bond 0.04150 / 2.73 ( 440) hydrogen bonds : angle 4.43599 / 3.12 ( 1272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 60 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8758 (mtt) cc_final: 0.8534 (mtp) REVERT: A 426 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8723 (tm-30) REVERT: A 509 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7367 (p90) REVERT: B 169 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8569 (tm-30) REVERT: B 309 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8567 (mttp) REVERT: B 439 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.6123 (tmm160) REVERT: B 848 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8285 (mm-30) outliers start: 37 outliers final: 18 residues processed: 92 average time/residue: 0.0725 time to fit residues: 10.1933 Evaluate side-chains 78 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 599 TYR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 844 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 39 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 3 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.083758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.066324 restraints weight = 27097.713| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.46 r_work: 0.3068 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.0590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9682 Z= 0.158 Angle : 0.506 7.461 13108 Z= 0.268 Chirality : 0.040 0.168 1456 Planarity : 0.003 0.058 1641 Dihedral : 11.502 81.921 1385 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.07 % Favored : 92.66 % Rotamer: Outliers : 2.99 % Allowed : 12.84 % Favored : 84.17 % 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: 0.64 (0.26), residues: 1131 helix: 1.81 (0.22), residues: 613 sheet: -0.53 (0.47), residues: 128 loop : -1.53 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 271 TYR 0.012 0.001 TYR B 668 PHE 0.016 0.001 PHE A 339 TRP 0.012 0.001 TRP B 697 HIS 0.003 0.001 HIS B 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 9681) covalent geometry : angle 0.50571 / 0.27 (13106) SS BOND : bond 0.00341 / 0.18 ( 1) SS BOND : angle 1.32605 / 0.88 ( 2) hydrogen bonds : bond 0.03807 / 2.50 ( 440) hydrogen bonds : angle 4.29551 / 3.02 ( 1272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 57 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8763 (mtt) cc_final: 0.8544 (mtp) REVERT: A 303 MET cc_start: 0.8697 (mmm) cc_final: 0.8381 (mmm) REVERT: A 426 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8720 (tm-30) REVERT: A 472 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8947 (mm) REVERT: A 509 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.7361 (p90) REVERT: B 169 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8558 (tm-30) REVERT: B 309 LYS cc_start: 0.9008 (mtmp) cc_final: 0.8567 (mttp) REVERT: B 439 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.6096 (tmm160) REVERT: B 848 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8255 (mm-30) outliers start: 31 outliers final: 19 residues processed: 84 average time/residue: 0.0865 time to fit residues: 11.0033 Evaluate side-chains 78 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 599 TYR Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 844 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 5 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.082456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.064931 restraints weight = 27504.808| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.47 r_work: 0.3036 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9682 Z= 0.216 Angle : 0.546 9.811 13108 Z= 0.288 Chirality : 0.042 0.172 1456 Planarity : 0.004 0.059 1641 Dihedral : 11.460 81.608 1381 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.05 % Favored : 91.60 % Rotamer: Outliers : 3.47 % Allowed : 13.51 % Favored : 83.01 % 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: 0.58 (0.26), residues: 1131 helix: 1.75 (0.21), residues: 613 sheet: -0.59 (0.48), residues: 129 loop : -1.53 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.015 0.001 TYR B 273 PHE 0.019 0.001 PHE B 598 TRP 0.013 0.001 TRP B 697 HIS 0.004 0.001 HIS B 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.22 ( 9681) covalent geometry : angle 0.54554 / 0.29 (13106) SS BOND : bond 0.00362 / 0.19 ( 1) SS BOND : angle 1.26958 / 0.85 ( 2) hydrogen bonds : bond 0.03881 / 2.57 ( 440) hydrogen bonds : angle 4.31873 / 3.05 ( 1272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 61 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8760 (mtt) cc_final: 0.8542 (mtp) REVERT: A 426 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8697 (tm-30) REVERT: A 472 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8922 (mm) REVERT: A 509 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7430 (p90) REVERT: B 169 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8589 (tm-30) REVERT: B 309 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8545 (mttp) REVERT: B 439 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.6098 (tmm160) REVERT: B 848 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8234 (mm-30) outliers start: 36 outliers final: 22 residues processed: 92 average time/residue: 0.0856 time to fit residues: 11.9170 Evaluate side-chains 81 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 55 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 844 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 69 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 chunk 37 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.083765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.066152 restraints weight = 27192.774| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 3.50 r_work: 0.3067 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9682 Z= 0.127 Angle : 0.519 15.741 13108 Z= 0.268 Chirality : 0.040 0.168 1456 Planarity : 0.003 0.056 1641 Dihedral : 11.403 82.209 1379 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.54 % Favored : 93.10 % Rotamer: Outliers : 3.38 % Allowed : 14.38 % Favored : 82.24 % 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: 0.70 (0.27), residues: 1131 helix: 1.79 (0.22), residues: 620 sheet: -0.51 (0.49), residues: 123 loop : -1.43 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 802 TYR 0.012 0.001 TYR B 668 PHE 0.013 0.001 PHE B 598 TRP 0.011 0.001 TRP B 697 HIS 0.002 0.001 HIS B 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 9681) covalent geometry : angle 0.51861 / 0.27 (13106) SS BOND : bond 0.00318 / 0.17 ( 1) SS BOND : angle 0.95049 / 0.63 ( 2) hydrogen bonds : bond 0.03495 / 2.32 ( 440) hydrogen bonds : angle 4.21729 / 2.97 ( 1272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 58 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8740 (mtt) cc_final: 0.8502 (mtp) REVERT: A 303 MET cc_start: 0.8706 (mmm) cc_final: 0.8379 (mmm) REVERT: A 426 GLN cc_start: 0.9057 (tm-30) cc_final: 0.8722 (tm-30) REVERT: A 472 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8948 (mm) REVERT: A 509 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.7388 (p90) REVERT: B 169 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8565 (tm-30) REVERT: B 309 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8558 (mttp) REVERT: B 439 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6053 (tmm160) REVERT: B 848 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8235 (mm-30) outliers start: 35 outliers final: 16 residues processed: 86 average time/residue: 0.0843 time to fit residues: 11.1541 Evaluate side-chains 74 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 844 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 25 optimal weight: 0.0170 chunk 77 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 0.0980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 ASN ** B 636 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 = 0.3584 r_free = 0.3584 target = 0.083894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.066399 restraints weight = 27262.778| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.50 r_work: 0.3068 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9682 Z= 0.123 Angle : 0.514 14.743 13108 Z= 0.266 Chirality : 0.040 0.166 1456 Planarity : 0.003 0.057 1641 Dihedral : 11.284 82.693 1377 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.90 % Favored : 92.75 % Rotamer: Outliers : 2.99 % Allowed : 14.77 % Favored : 82.24 % 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: 0.77 (0.27), residues: 1131 helix: 1.84 (0.22), residues: 620 sheet: -0.42 (0.50), residues: 122 loop : -1.41 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 271 TYR 0.012 0.001 TYR B 668 PHE 0.014 0.001 PHE A 506 TRP 0.011 0.001 TRP B 697 HIS 0.002 0.001 HIS B 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 9681) covalent geometry : angle 0.51363 / 0.27 (13106) SS BOND : bond 0.00288 / 0.15 ( 1) SS BOND : angle 1.00100 / 0.67 ( 2) hydrogen bonds : bond 0.03398 / 2.26 ( 440) hydrogen bonds : angle 4.14946 / 2.92 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 57 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8704 (mtt) cc_final: 0.8434 (mtp) REVERT: A 303 MET cc_start: 0.8692 (mmm) cc_final: 0.8362 (mmm) REVERT: A 426 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8704 (tm-30) REVERT: A 509 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.7305 (p90) REVERT: B 169 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8574 (tm-30) REVERT: B 309 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8585 (mttp) REVERT: B 439 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.5942 (tmm160) REVERT: B 848 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8220 (mm-30) outliers start: 31 outliers final: 21 residues processed: 81 average time/residue: 0.0790 time to fit residues: 9.9209 Evaluate side-chains 78 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 844 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 83 optimal weight: 0.7980 chunk 95 optimal weight: 0.0980 chunk 87 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.083589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.066118 restraints weight = 27380.578| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.49 r_work: 0.3065 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9682 Z= 0.142 Angle : 0.521 14.664 13108 Z= 0.268 Chirality : 0.040 0.164 1456 Planarity : 0.003 0.058 1641 Dihedral : 11.215 83.038 1375 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.81 % Favored : 92.84 % Rotamer: Outliers : 2.99 % Allowed : 14.86 % Favored : 82.14 % 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: 0.74 (0.27), residues: 1131 helix: 1.84 (0.22), residues: 620 sheet: -0.47 (0.51), residues: 123 loop : -1.43 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 271 TYR 0.012 0.001 TYR B 668 PHE 0.025 0.001 PHE B 598 TRP 0.011 0.001 TRP B 697 HIS 0.003 0.001 HIS B 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 9681) covalent geometry : angle 0.52115 / 0.27 (13106) SS BOND : bond 0.00395 / 0.21 ( 1) SS BOND : angle 0.85443 / 0.57 ( 2) hydrogen bonds : bond 0.03413 / 2.27 ( 440) hydrogen bonds : angle 4.13441 / 2.91 ( 1272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 56 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8670 (mtt) cc_final: 0.8360 (mtp) REVERT: A 303 MET cc_start: 0.8703 (mmm) cc_final: 0.8388 (mmm) REVERT: A 426 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8700 (tm-30) REVERT: A 472 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8958 (mm) REVERT: A 509 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7233 (p90) REVERT: B 169 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8578 (tm-30) REVERT: B 309 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8582 (mttp) REVERT: B 439 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.6014 (tmm160) REVERT: B 466 MET cc_start: 0.8939 (tpp) cc_final: 0.8616 (tpp) REVERT: B 848 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8219 (mm-30) outliers start: 31 outliers final: 21 residues processed: 82 average time/residue: 0.0871 time to fit residues: 10.9860 Evaluate side-chains 78 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 844 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 0.0470 chunk 77 optimal weight: 0.1980 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 0.0170 chunk 0 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 480 ASN ** B 636 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 = 0.3602 r_free = 0.3602 target = 0.084823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.067185 restraints weight = 26991.339| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.52 r_work: 0.3089 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9682 Z= 0.106 Angle : 0.513 14.585 13108 Z= 0.264 Chirality : 0.039 0.163 1456 Planarity : 0.004 0.073 1641 Dihedral : 11.190 83.841 1375 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.45 % Favored : 93.19 % Rotamer: Outliers : 2.70 % Allowed : 15.83 % Favored : 81.47 % 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: 0.78 (0.27), residues: 1131 helix: 1.88 (0.22), residues: 621 sheet: -0.45 (0.50), residues: 122 loop : -1.45 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 254 TYR 0.012 0.001 TYR A 270 PHE 0.018 0.001 PHE B 598 TRP 0.011 0.001 TRP B 697 HIS 0.003 0.000 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 9681) covalent geometry : angle 0.51312 / 0.26 (13106) SS BOND : bond 0.00356 / 0.19 ( 1) SS BOND : angle 1.06154 / 0.71 ( 2) hydrogen bonds : bond 0.03186 / 2.12 ( 440) hydrogen bonds : angle 4.05960 / 2.86 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8542 (mtt) cc_final: 0.8318 (mtt) REVERT: A 303 MET cc_start: 0.8683 (mmm) cc_final: 0.8365 (mmm) REVERT: A 426 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8685 (tm-30) REVERT: A 472 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8977 (mm) REVERT: A 509 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.7064 (p90) REVERT: B 169 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8571 (tm-30) REVERT: B 309 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8577 (mttp) REVERT: B 439 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.5961 (tmm160) REVERT: B 466 MET cc_start: 0.8931 (tpp) cc_final: 0.8605 (tpp) REVERT: B 800 ILE cc_start: 0.9546 (mp) cc_final: 0.9343 (pt) REVERT: B 848 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8215 (mm-30) outliers start: 28 outliers final: 20 residues processed: 81 average time/residue: 0.0836 time to fit residues: 10.4356 Evaluate side-chains 78 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 844 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 41 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 112 optimal weight: 0.1980 chunk 77 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.083617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.066111 restraints weight = 27185.634| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.48 r_work: 0.3061 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9682 Z= 0.160 Angle : 0.533 14.303 13108 Z= 0.274 Chirality : 0.040 0.164 1456 Planarity : 0.003 0.058 1641 Dihedral : 11.185 83.923 1375 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.34 % Favored : 92.31 % Rotamer: Outliers : 2.80 % Allowed : 16.02 % Favored : 81.18 % 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: 0.74 (0.27), residues: 1131 helix: 1.85 (0.22), residues: 620 sheet: -0.51 (0.51), residues: 123 loop : -1.47 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 271 TYR 0.012 0.001 TYR B 668 PHE 0.026 0.001 PHE B 598 TRP 0.011 0.001 TRP B 496 HIS 0.003 0.001 HIS B 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 9681) covalent geometry : angle 0.53282 / 0.27 (13106) SS BOND : bond 0.00362 / 0.19 ( 1) SS BOND : angle 1.06113 / 0.71 ( 2) hydrogen bonds : bond 0.03402 / 2.26 ( 440) hydrogen bonds : angle 4.10342 / 2.89 ( 1272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 54 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8742 (mmm) cc_final: 0.8407 (mmm) REVERT: A 426 GLN cc_start: 0.9073 (tm-30) cc_final: 0.8690 (tm-30) REVERT: A 472 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8957 (mm) REVERT: A 509 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.7157 (p90) REVERT: B 169 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8579 (tm-30) REVERT: B 309 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8583 (mttp) REVERT: B 439 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.6095 (tmm160) REVERT: B 466 MET cc_start: 0.8962 (tpp) cc_final: 0.8616 (tpp) REVERT: B 848 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8196 (mm-30) outliers start: 29 outliers final: 22 residues processed: 79 average time/residue: 0.0872 time to fit residues: 10.6059 Evaluate side-chains 79 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 53 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 844 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 105 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 109 optimal weight: 0.4980 chunk 45 optimal weight: 0.2980 chunk 47 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.084174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.066679 restraints weight = 26910.510| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.48 r_work: 0.3075 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9682 Z= 0.131 Angle : 0.527 14.256 13108 Z= 0.271 Chirality : 0.040 0.163 1456 Planarity : 0.003 0.057 1641 Dihedral : 11.183 84.366 1375 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.54 % Favored : 93.10 % Rotamer: Outliers : 2.32 % Allowed : 16.80 % Favored : 80.89 % 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: 0.72 (0.27), residues: 1131 helix: 1.85 (0.22), residues: 621 sheet: -0.45 (0.51), residues: 122 loop : -1.52 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 802 TYR 0.012 0.001 TYR B 668 PHE 0.013 0.001 PHE A 339 TRP 0.010 0.001 TRP B 496 HIS 0.002 0.001 HIS B 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 9681) covalent geometry : angle 0.52655 / 0.27 (13106) SS BOND : bond 0.00336 / 0.18 ( 1) SS BOND : angle 0.87667 / 0.58 ( 2) hydrogen bonds : bond 0.03303 / 2.20 ( 440) hydrogen bonds : angle 4.07397 / 2.87 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8706 (mmm) cc_final: 0.8370 (mmm) REVERT: A 426 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8681 (tm-30) REVERT: A 472 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8978 (mm) REVERT: A 509 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7096 (p90) REVERT: B 169 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8584 (tm-30) REVERT: B 439 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.6102 (tmm160) REVERT: B 466 MET cc_start: 0.8970 (tpp) cc_final: 0.8633 (tpp) REVERT: B 848 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8190 (mm-30) outliers start: 24 outliers final: 20 residues processed: 73 average time/residue: 0.0796 time to fit residues: 9.0322 Evaluate side-chains 75 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 844 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 1 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 57 optimal weight: 0.0570 chunk 56 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.084259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.066775 restraints weight = 26828.924| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.48 r_work: 0.3078 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9682 Z= 0.126 Angle : 0.532 14.214 13108 Z= 0.272 Chirality : 0.040 0.163 1456 Planarity : 0.003 0.057 1641 Dihedral : 11.175 84.757 1375 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.81 % Favored : 92.84 % Rotamer: Outliers : 2.22 % Allowed : 16.80 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.74 (0.27), residues: 1131 helix: 1.86 (0.22), residues: 621 sheet: -0.44 (0.51), residues: 122 loop : -1.51 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 254 TYR 0.012 0.001 TYR B 668 PHE 0.021 0.001 PHE B 598 TRP 0.010 0.001 TRP B 496 HIS 0.002 0.000 HIS B 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 9681) covalent geometry : angle 0.53174 / 0.27 (13106) SS BOND : bond 0.00361 / 0.19 ( 1) SS BOND : angle 0.84350 / 0.56 ( 2) hydrogen bonds : bond 0.03256 / 2.16 ( 440) hydrogen bonds : angle 4.06411 / 2.86 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2101.28 seconds wall clock time: 37 minutes 8.89 seconds (2228.89 seconds total)