Starting phenix.real_space_refine on Fri Sep 11 05:35:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6lle_0912/09_2026/6lle_0912.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lle_0912/09_2026/6lle_0912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lle_0912/09_2026/6lle_0912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lle_0912/09_2026/6lle_0912.map" model { file = "/net/cci-nas-00/data/ceres_data/6lle_0912/09_2026/6lle_0912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lle_0912/09_2026/6lle_0912.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6lle_0912/09_2026/6lle_0912.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6lle_0912/09_2026/6lle_0912.cif" } resolution = 2.9 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 P 3 5.49 5 Mg 1 5.21 5 S 58 5.16 5 C 5038 2.51 5 N 1319 2.21 5 O 1495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7916 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7882 Classifications: {'peptide': 1020} Link IDs: {'PTRANS': 46, 'TRANS': 973} Chain breaks: 2 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 2, ' MG': 1, 'ACP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.73, per 1000 atoms: 0.22 Number of scatterers: 7916 At special positions: 0 Unit cell: (93.375, 78.435, 141.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 2 19.99 S 58 16.00 P 3 15.00 Mg 1 11.99 O 1495 8.00 N 1319 7.00 C 5038 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: 0.66 Conformation dependent library (CDL) restraints added in 403.1 milliseconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1910 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 52.6% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 8 through 17 removed outlier: 3.874A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 37 Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 59 through 76 Processing helix chain 'A' and resid 88 through 120 removed outlier: 3.801A pdb=" N PHE A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.603A pdb=" N THR A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 274 Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.631A pdb=" N PHE A 279 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN A 280 " --> pdb=" O GLY A 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 276 through 280' Processing helix chain 'A' and resid 287 through 307 removed outlier: 3.512A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 328 Processing helix chain 'A' and resid 335 through 344 removed outlier: 3.715A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR A 341 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LEU A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 420 removed outlier: 3.732A pdb=" N GLU A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 453 Processing helix chain 'A' and resid 469 through 477 Processing helix chain 'A' and resid 516 through 523 removed outlier: 3.602A pdb=" N ARG A 523 " --> pdb=" O GLY A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 554 removed outlier: 3.687A pdb=" N LYS A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 545 " --> pdb=" O LYS A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 575 Processing helix chain 'A' and resid 579 through 586 removed outlier: 4.110A pdb=" N ILE A 584 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 616 removed outlier: 3.511A pdb=" N LYS A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 661 through 672 removed outlier: 4.005A pdb=" N CYS A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 670 " --> pdb=" O ARG A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 693 removed outlier: 3.640A pdb=" N VAL A 687 " --> pdb=" O LYS A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.513A pdb=" N LYS A 712 " --> pdb=" O PRO A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 729 Processing helix chain 'A' and resid 740 through 781 removed outlier: 3.543A pdb=" N ALA A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 769 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 799 Processing helix chain 'A' and resid 800 through 805 Processing helix chain 'A' and resid 806 through 809 Processing helix chain 'A' and resid 829 through 857 removed outlier: 3.683A pdb=" N TRP A 854 " --> pdb=" O ALA A 850 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 871 Processing helix chain 'A' and resid 872 through 875 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 892 through 913 removed outlier: 4.329A pdb=" N MET A 896 " --> pdb=" O SER A 892 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 912 " --> pdb=" O MET A 908 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 913 " --> pdb=" O CYS A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 928 Processing helix chain 'A' and resid 929 through 949 Processing helix chain 'A' and resid 952 through 957 Processing helix chain 'A' and resid 962 through 974 removed outlier: 3.641A pdb=" N MET A 968 " --> pdb=" O THR A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 990 removed outlier: 3.915A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1030 removed outlier: 3.638A pdb=" N LEU A1021 " --> pdb=" O PRO A1017 " (cutoff:3.500A) Proline residue: A1024 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 141 removed outlier: 4.556A pdb=" N LYS A 128 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE A 150 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N MET A 220 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP A 162 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188 removed outlier: 6.294A pdb=" N ARG A 174 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 331 through 333 removed outlier: 6.331A pdb=" N GLY A 716 " --> pdb=" O MET A 732 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU A 734 " --> pdb=" O GLY A 716 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA A 718 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR A 697 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE A 717 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N MET A 699 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N MET A 719 " --> pdb=" O MET A 699 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N GLY A 701 " --> pdb=" O MET A 719 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL A 347 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N THR A 700 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N CYS A 349 " --> pdb=" O THR A 700 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N PHE A 675 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N MET A 622 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE A 652 " --> pdb=" O ALA A 676 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.927A pdb=" N THR A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL A 372 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL A 363 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU A 599 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU A 369 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N VAL A 593 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 14.085A pdb=" N ARG A 371 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 15.739A pdb=" N THR A 591 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N PHE A 592 " --> pdb=" O THR A 565 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N THR A 565 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N SER A 493 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLU A 486 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER A 495 " --> pdb=" O THR A 484 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR A 484 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TYR A 497 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.927A pdb=" N THR A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL A 372 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL A 363 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU A 599 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU A 369 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N VAL A 593 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 14.085A pdb=" N ARG A 371 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 15.739A pdb=" N THR A 591 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU A 590 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY A 594 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 424 through 428 427 hydrogen bonds defined for protein. 1209 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: 1.46 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2592 1.35 - 1.48: 1830 1.48 - 1.61: 3546 1.61 - 1.73: 4 1.73 - 1.86: 92 Bond restraints: 8064 Sorted by residual: bond pdb=" C1' ACP A2001 " pdb=" O4' ACP A2001 " ideal model delta sigma weight residual 1.390 1.617 -0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C1' ACP A2001 " pdb=" C2' ACP A2001 " ideal model delta sigma weight residual 1.527 1.306 0.221 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C4' ACP A2001 " pdb=" O4' ACP A2001 " ideal model delta sigma weight residual 1.428 1.299 0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" C6 ACP A2001 " pdb=" N6 ACP A2001 " ideal model delta sigma weight residual 1.335 1.451 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C2' ACP A2001 " pdb=" O2' ACP A2001 " ideal model delta sigma weight residual 1.401 1.493 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 8059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 10885 3.05 - 6.10: 56 6.10 - 9.14: 5 9.14 - 12.19: 4 12.19 - 15.24: 1 Bond angle restraints: 10951 Sorted by residual: angle pdb=" O3A ACP A2001 " pdb=" PA ACP A2001 " pdb=" O5' ACP A2001 " ideal model delta sigma weight residual 93.75 108.99 -15.24 3.00e+00 1.11e-01 2.58e+01 angle pdb=" C3B ACP A2001 " pdb=" PB ACP A2001 " pdb=" O3A ACP A2001 " ideal model delta sigma weight residual 98.05 110.24 -12.19 3.00e+00 1.11e-01 1.65e+01 angle pdb=" O1B ACP A2001 " pdb=" PB ACP A2001 " pdb=" O2B ACP A2001 " ideal model delta sigma weight residual 119.60 109.22 10.38 3.00e+00 1.11e-01 1.20e+01 angle pdb=" N1 ACP A2001 " pdb=" C6 ACP A2001 " pdb=" N6 ACP A2001 " ideal model delta sigma weight residual 119.32 109.04 10.28 3.00e+00 1.11e-01 1.17e+01 angle pdb=" O1A ACP A2001 " pdb=" PA ACP A2001 " pdb=" O2A ACP A2001 " ideal model delta sigma weight residual 118.95 108.80 10.15 3.00e+00 1.11e-01 1.14e+01 ... (remaining 10946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.50: 4672 23.50 - 47.00: 171 47.00 - 70.49: 19 70.49 - 93.99: 6 93.99 - 117.49: 1 Dihedral angle restraints: 4869 sinusoidal: 1923 harmonic: 2946 Sorted by residual: dihedral pdb=" CA ILE A 153 " pdb=" C ILE A 153 " pdb=" N ALA A 154 " pdb=" CA ALA A 154 " ideal model delta harmonic sigma weight residual 180.00 152.82 27.18 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" O1A ACP A2001 " pdb=" O3A ACP A2001 " pdb=" PA ACP A2001 " pdb=" PB ACP A2001 " ideal model delta sinusoidal sigma weight residual -48.75 68.74 -117.49 1 3.00e+01 1.11e-03 1.56e+01 dihedral pdb=" CA VAL A 949 " pdb=" C VAL A 949 " pdb=" N GLU A 950 " pdb=" CA GLU A 950 " ideal model delta harmonic sigma weight residual -180.00 -162.47 -17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 4866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1184 0.079 - 0.158: 97 0.158 - 0.237: 1 0.237 - 0.316: 0 0.316 - 0.395: 1 Chirality restraints: 1283 Sorted by residual: chirality pdb=" C2' ACP A2001 " pdb=" C1' ACP A2001 " pdb=" C3' ACP A2001 " pdb=" O2' ACP A2001 " both_signs ideal model delta sigma weight residual False -2.75 -2.36 -0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CB ILE A 153 " pdb=" CA ILE A 153 " pdb=" CG1 ILE A 153 " pdb=" CG2 ILE A 153 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA ILE A 623 " pdb=" N ILE A 623 " pdb=" C ILE A 623 " pdb=" CB ILE A 623 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 1280 not shown) Planarity restraints: 1390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A1016 " -0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO A1017 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A1017 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1017 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 661 " -0.021 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO A 662 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 662 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 662 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 974 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO A 975 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " -0.017 5.00e-02 4.00e+02 ... (remaining 1387 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 91 2.62 - 3.19: 6955 3.19 - 3.76: 12323 3.76 - 4.33: 17608 4.33 - 4.90: 29040 Nonbonded interactions: 66017 Sorted by model distance: nonbonded pdb=" OD2 ASP A 351 " pdb="MG MG A2002 " model vdw 2.050 2.170 nonbonded pdb=" O THR A 353 " pdb="MG MG A2002 " model vdw 2.114 2.170 nonbonded pdb=" OD1 ASP A 351 " pdb="MG MG A2002 " model vdw 2.170 2.170 nonbonded pdb=" O3G ACP A2001 " pdb="MG MG A2002 " model vdw 2.171 2.170 nonbonded pdb=" OD1 ASP A 702 " pdb="MG MG A2002 " model vdw 2.192 2.170 ... (remaining 66012 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.310 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.110 Find NCS groups from input model: 0.030 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:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 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 : 0.005 0.227 8064 Z= 0.260 Angle : 0.632 15.238 10951 Z= 0.315 Chirality : 0.043 0.395 1283 Planarity : 0.004 0.036 1390 Dihedral : 12.591 117.490 2959 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.24), residues: 1014 helix: -0.83 (0.22), residues: 472 sheet: -1.09 (0.47), residues: 104 loop : -1.62 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 677 TYR 0.015 0.001 TYR A 842 PHE 0.012 0.001 PHE A 367 TRP 0.009 0.001 TRP A 793 HIS 0.007 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.26 ( 8064) covalent geometry : angle 0.63241 / 0.32 (10951) hydrogen bonds : bond 0.14837 / 9.65 ( 415) hydrogen bonds : angle 6.66692 / 4.63 ( 1209) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.301 Fit side-chains REVERT: A 251 GLN cc_start: 0.7762 (mt0) cc_final: 0.7538 (mt0) REVERT: A 394 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7073 (mt-10) REVERT: A 439 GLU cc_start: 0.7554 (tt0) cc_final: 0.7331 (tt0) REVERT: A 479 MET cc_start: 0.7209 (mtt) cc_final: 0.6970 (mtp) REVERT: A 531 SER cc_start: 0.9135 (p) cc_final: 0.8890 (p) REVERT: A 545 MET cc_start: 0.8044 (mmm) cc_final: 0.7714 (mmm) REVERT: A 572 ARG cc_start: 0.6945 (tpt90) cc_final: 0.6681 (tpt-90) REVERT: A 575 MET cc_start: 0.9284 (mtt) cc_final: 0.8931 (mtt) REVERT: A 667 ASP cc_start: 0.7962 (t0) cc_final: 0.7745 (t0) REVERT: A 816 MET cc_start: 0.8749 (mmm) cc_final: 0.8485 (mmm) REVERT: A 917 GLU cc_start: 0.7797 (tt0) cc_final: 0.7484 (tt0) REVERT: A 940 MET cc_start: 0.8639 (mmm) cc_final: 0.8180 (mmm) REVERT: A 1023 MET cc_start: 0.6803 (tpp) cc_final: 0.6589 (tpp) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.5969 time to fit residues: 115.4467 Evaluate side-chains 126 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 HIS A 190 HIS A 275 ASN A 469 ASN A 817 ASN A 913 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.141075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.109741 restraints weight = 8446.153| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.65 r_work: 0.2940 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8064 Z= 0.147 Angle : 0.547 6.795 10951 Z= 0.282 Chirality : 0.043 0.151 1283 Planarity : 0.004 0.035 1390 Dihedral : 6.334 138.520 1082 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.21 % Allowed : 11.91 % Favored : 84.88 % 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: -0.64 (0.26), residues: 1014 helix: 0.41 (0.24), residues: 485 sheet: -0.91 (0.44), residues: 117 loop : -1.20 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 365 TYR 0.015 0.002 TYR A 842 PHE 0.019 0.001 PHE A 367 TRP 0.009 0.001 TRP A 793 HIS 0.007 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 8064) covalent geometry : angle 0.54736 / 0.28 (10951) hydrogen bonds : bond 0.04028 / 2.72 ( 415) hydrogen bonds : angle 4.68039 / 3.23 ( 1209) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.371 Fit side-chains REVERT: A 31 LYS cc_start: 0.7743 (mtpt) cc_final: 0.7448 (mtmm) REVERT: A 40 GLU cc_start: 0.8513 (pt0) cc_final: 0.8311 (pt0) REVERT: A 51 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7553 (pt0) REVERT: A 135 LYS cc_start: 0.8729 (tptp) cc_final: 0.8289 (mtpp) REVERT: A 251 GLN cc_start: 0.8006 (mt0) cc_final: 0.7729 (mt0) REVERT: A 280 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7823 (p0) REVERT: A 309 GLU cc_start: 0.8834 (pm20) cc_final: 0.8506 (pm20) REVERT: A 394 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7598 (mt-10) REVERT: A 479 MET cc_start: 0.7271 (mtt) cc_final: 0.6971 (mtp) REVERT: A 531 SER cc_start: 0.9131 (p) cc_final: 0.8912 (p) REVERT: A 545 MET cc_start: 0.8222 (mmm) cc_final: 0.7864 (mmm) REVERT: A 572 ARG cc_start: 0.7021 (tpt90) cc_final: 0.6727 (tpt-90) REVERT: A 575 MET cc_start: 0.9190 (mtt) cc_final: 0.8788 (mtt) REVERT: A 599 LEU cc_start: 0.8979 (pp) cc_final: 0.8614 (pt) REVERT: A 816 MET cc_start: 0.8902 (mmm) cc_final: 0.8597 (mmm) REVERT: A 917 GLU cc_start: 0.8441 (tt0) cc_final: 0.8027 (tt0) outliers start: 28 outliers final: 10 residues processed: 140 average time/residue: 0.5111 time to fit residues: 76.2827 Evaluate side-chains 124 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 661 ASN Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 967 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 100 optimal weight: 0.4980 chunk 78 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.141797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.110605 restraints weight = 8563.805| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.64 r_work: 0.2988 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8064 Z= 0.118 Angle : 0.523 6.936 10951 Z= 0.267 Chirality : 0.042 0.192 1283 Planarity : 0.004 0.038 1390 Dihedral : 6.258 138.740 1082 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.44 % Allowed : 12.94 % Favored : 83.62 % 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: 0.08 (0.27), residues: 1014 helix: 1.06 (0.24), residues: 488 sheet: -0.47 (0.46), residues: 114 loop : -0.98 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 174 TYR 0.014 0.001 TYR A 842 PHE 0.016 0.001 PHE A 367 TRP 0.009 0.001 TRP A 793 HIS 0.004 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 8064) covalent geometry : angle 0.52301 / 0.27 (10951) hydrogen bonds : bond 0.03510 / 2.40 ( 415) hydrogen bonds : angle 4.41568 / 3.04 ( 1209) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.308 Fit side-chains REVERT: A 31 LYS cc_start: 0.7755 (mtpt) cc_final: 0.7482 (mtmt) REVERT: A 51 GLU cc_start: 0.7971 (tt0) cc_final: 0.7558 (pt0) REVERT: A 135 LYS cc_start: 0.8717 (tptp) cc_final: 0.8293 (mtmt) REVERT: A 198 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7410 (mmp80) REVERT: A 251 GLN cc_start: 0.7998 (mt0) cc_final: 0.7764 (mt0) REVERT: A 280 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7884 (p0) REVERT: A 309 GLU cc_start: 0.8835 (pm20) cc_final: 0.8622 (pm20) REVERT: A 394 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7558 (mt-10) REVERT: A 479 MET cc_start: 0.7214 (mtt) cc_final: 0.6874 (mtp) REVERT: A 531 SER cc_start: 0.9137 (p) cc_final: 0.8929 (p) REVERT: A 545 MET cc_start: 0.8282 (mmm) cc_final: 0.7914 (mmm) REVERT: A 572 ARG cc_start: 0.6910 (tpt90) cc_final: 0.6701 (tpt-90) REVERT: A 575 MET cc_start: 0.9096 (mtt) cc_final: 0.8654 (mtt) REVERT: A 623 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8734 (mt) REVERT: A 816 MET cc_start: 0.8919 (mmm) cc_final: 0.8628 (mmm) REVERT: A 940 MET cc_start: 0.8748 (mmm) cc_final: 0.8390 (mmm) REVERT: A 979 MET cc_start: 0.8654 (ttm) cc_final: 0.8366 (ttm) outliers start: 30 outliers final: 11 residues processed: 142 average time/residue: 0.4978 time to fit residues: 75.6443 Evaluate side-chains 123 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 967 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 2 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 50 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 93 optimal weight: 0.2980 chunk 100 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.146900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.116444 restraints weight = 8605.524| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.63 r_work: 0.3071 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8064 Z= 0.107 Angle : 0.506 7.495 10951 Z= 0.258 Chirality : 0.041 0.159 1283 Planarity : 0.003 0.038 1390 Dihedral : 6.177 138.816 1082 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.55 % Allowed : 14.43 % Favored : 82.02 % 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: 0.45 (0.27), residues: 1014 helix: 1.44 (0.24), residues: 487 sheet: -0.44 (0.46), residues: 114 loop : -0.83 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 365 TYR 0.014 0.001 TYR A 842 PHE 0.016 0.001 PHE A 367 TRP 0.008 0.001 TRP A 927 HIS 0.003 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 8064) covalent geometry : angle 0.50639 / 0.26 (10951) hydrogen bonds : bond 0.03232 / 2.22 ( 415) hydrogen bonds : angle 4.23923 / 2.92 ( 1209) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.302 Fit side-chains REVERT: A 31 LYS cc_start: 0.7772 (mtpt) cc_final: 0.7519 (mtmt) REVERT: A 51 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7628 (pt0) REVERT: A 77 TRP cc_start: 0.6775 (OUTLIER) cc_final: 0.5952 (m100) REVERT: A 135 LYS cc_start: 0.8749 (tptp) cc_final: 0.8352 (mtpp) REVERT: A 198 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7411 (mmp80) REVERT: A 251 GLN cc_start: 0.8035 (mt0) cc_final: 0.7782 (mt0) REVERT: A 309 GLU cc_start: 0.8840 (pm20) cc_final: 0.8571 (pm20) REVERT: A 394 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7560 (mt-10) REVERT: A 479 MET cc_start: 0.7205 (mtt) cc_final: 0.6854 (mtp) REVERT: A 531 SER cc_start: 0.9181 (p) cc_final: 0.8967 (p) REVERT: A 545 MET cc_start: 0.8362 (mmm) cc_final: 0.8008 (mmm) REVERT: A 575 MET cc_start: 0.9107 (mtt) cc_final: 0.8675 (mtt) REVERT: A 623 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8791 (mt) REVERT: A 812 ASP cc_start: 0.7313 (m-30) cc_final: 0.7107 (m-30) REVERT: A 816 MET cc_start: 0.8913 (mmm) cc_final: 0.8640 (mmm) REVERT: A 940 MET cc_start: 0.8815 (mmm) cc_final: 0.8465 (mmm) REVERT: A 979 MET cc_start: 0.8682 (ttm) cc_final: 0.8399 (ttm) outliers start: 31 outliers final: 8 residues processed: 139 average time/residue: 0.5096 time to fit residues: 75.5990 Evaluate side-chains 128 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 77 TRP Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 967 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 32 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 78 optimal weight: 0.0030 chunk 98 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.148587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.118199 restraints weight = 8561.337| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.61 r_work: 0.2956 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8064 Z= 0.113 Angle : 0.514 7.672 10951 Z= 0.260 Chirality : 0.041 0.146 1283 Planarity : 0.003 0.038 1390 Dihedral : 6.202 140.804 1082 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.86 % Allowed : 16.27 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.27), residues: 1014 helix: 1.66 (0.25), residues: 486 sheet: -0.31 (0.46), residues: 114 loop : -0.77 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 572 TYR 0.014 0.001 TYR A 842 PHE 0.017 0.001 PHE A 367 TRP 0.008 0.001 TRP A 927 HIS 0.003 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 8064) covalent geometry : angle 0.51415 / 0.26 (10951) hydrogen bonds : bond 0.03266 / 2.24 ( 415) hydrogen bonds : angle 4.20072 / 2.89 ( 1209) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.311 Fit side-chains REVERT: A 31 LYS cc_start: 0.7758 (mtpt) cc_final: 0.7508 (mtmt) REVERT: A 33 LYS cc_start: 0.7983 (tttt) cc_final: 0.7588 (ttmt) REVERT: A 51 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7624 (pt0) REVERT: A 135 LYS cc_start: 0.8726 (tptp) cc_final: 0.8320 (mtmt) REVERT: A 198 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7416 (mmp80) REVERT: A 251 GLN cc_start: 0.8014 (mt0) cc_final: 0.7767 (mt0) REVERT: A 309 GLU cc_start: 0.8866 (pm20) cc_final: 0.8561 (pm20) REVERT: A 394 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7555 (mt-10) REVERT: A 479 MET cc_start: 0.7203 (mtt) cc_final: 0.6837 (mtp) REVERT: A 531 SER cc_start: 0.9170 (p) cc_final: 0.8947 (p) REVERT: A 545 MET cc_start: 0.8364 (mmm) cc_final: 0.7970 (mmm) REVERT: A 575 MET cc_start: 0.9112 (mtt) cc_final: 0.8757 (mtt) REVERT: A 623 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8847 (mt) REVERT: A 812 ASP cc_start: 0.7343 (m-30) cc_final: 0.6935 (m-30) REVERT: A 816 MET cc_start: 0.8871 (mmm) cc_final: 0.8563 (mmm) REVERT: A 940 MET cc_start: 0.8803 (mmm) cc_final: 0.8449 (mmm) outliers start: 25 outliers final: 11 residues processed: 138 average time/residue: 0.5483 time to fit residues: 80.5167 Evaluate side-chains 131 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 967 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.147696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.116950 restraints weight = 8437.365| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.63 r_work: 0.2905 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8064 Z= 0.126 Angle : 0.524 7.910 10951 Z= 0.265 Chirality : 0.042 0.160 1283 Planarity : 0.003 0.039 1390 Dihedral : 6.221 140.827 1082 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.55 % Allowed : 16.15 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.27), residues: 1014 helix: 1.72 (0.24), residues: 485 sheet: -0.35 (0.46), residues: 117 loop : -0.69 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 572 TYR 0.015 0.001 TYR A 842 PHE 0.019 0.001 PHE A 367 TRP 0.008 0.001 TRP A 793 HIS 0.004 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 8064) covalent geometry : angle 0.52383 / 0.27 (10951) hydrogen bonds : bond 0.03399 / 2.33 ( 415) hydrogen bonds : angle 4.17603 / 2.87 ( 1209) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.451 Fit side-chains REVERT: A 31 LYS cc_start: 0.7610 (mtpt) cc_final: 0.7329 (mtmt) REVERT: A 33 LYS cc_start: 0.7938 (tttt) cc_final: 0.7492 (ttmt) REVERT: A 51 GLU cc_start: 0.7953 (tt0) cc_final: 0.7534 (pt0) REVERT: A 71 ILE cc_start: 0.8643 (mt) cc_final: 0.8399 (mt) REVERT: A 77 TRP cc_start: 0.6626 (OUTLIER) cc_final: 0.6104 (m100) REVERT: A 135 LYS cc_start: 0.8606 (tptp) cc_final: 0.8244 (mtmt) REVERT: A 198 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7404 (mmp80) REVERT: A 251 GLN cc_start: 0.7906 (mt0) cc_final: 0.7703 (mt0) REVERT: A 394 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7554 (mt-10) REVERT: A 479 MET cc_start: 0.7222 (mtt) cc_final: 0.6838 (mtp) REVERT: A 531 SER cc_start: 0.9153 (p) cc_final: 0.8938 (p) REVERT: A 545 MET cc_start: 0.8338 (mmm) cc_final: 0.7961 (mmm) REVERT: A 575 MET cc_start: 0.9074 (mtt) cc_final: 0.8728 (mtt) REVERT: A 623 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8821 (mt) REVERT: A 812 ASP cc_start: 0.7346 (m-30) cc_final: 0.6871 (m-30) REVERT: A 816 MET cc_start: 0.8842 (mmm) cc_final: 0.8537 (mmm) REVERT: A 940 MET cc_start: 0.8717 (mmm) cc_final: 0.8479 (mmm) outliers start: 31 outliers final: 15 residues processed: 139 average time/residue: 0.5067 time to fit residues: 75.2619 Evaluate side-chains 134 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 77 TRP Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 967 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 74 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.143019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.111574 restraints weight = 8456.970| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.66 r_work: 0.2941 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8064 Z= 0.110 Angle : 0.511 8.217 10951 Z= 0.258 Chirality : 0.041 0.132 1283 Planarity : 0.003 0.038 1390 Dihedral : 6.194 141.149 1082 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.32 % Allowed : 16.84 % Favored : 79.84 % 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: 0.86 (0.27), residues: 1014 helix: 1.79 (0.24), residues: 486 sheet: -0.26 (0.47), residues: 117 loop : -0.64 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 572 TYR 0.016 0.001 TYR A 122 PHE 0.017 0.001 PHE A 367 TRP 0.008 0.001 TRP A 927 HIS 0.003 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 8064) covalent geometry : angle 0.51123 / 0.26 (10951) hydrogen bonds : bond 0.03187 / 2.19 ( 415) hydrogen bonds : angle 4.10122 / 2.82 ( 1209) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.317 Fit side-chains REVERT: A 31 LYS cc_start: 0.7666 (mtpt) cc_final: 0.7391 (mtmt) REVERT: A 33 LYS cc_start: 0.7951 (tttt) cc_final: 0.7541 (ttmt) REVERT: A 51 GLU cc_start: 0.8006 (tt0) cc_final: 0.7601 (pt0) REVERT: A 71 ILE cc_start: 0.8686 (mt) cc_final: 0.8448 (mt) REVERT: A 135 LYS cc_start: 0.8650 (tptp) cc_final: 0.8265 (mtpp) REVERT: A 198 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7408 (mmp80) REVERT: A 251 GLN cc_start: 0.7947 (mt0) cc_final: 0.7746 (mt0) REVERT: A 280 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7696 (p0) REVERT: A 394 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7609 (mt-10) REVERT: A 479 MET cc_start: 0.7258 (mtt) cc_final: 0.6883 (mtp) REVERT: A 531 SER cc_start: 0.9157 (p) cc_final: 0.8945 (p) REVERT: A 545 MET cc_start: 0.8394 (mmm) cc_final: 0.8035 (mmm) REVERT: A 575 MET cc_start: 0.9088 (mtt) cc_final: 0.8767 (mtt) REVERT: A 623 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8821 (mt) REVERT: A 812 ASP cc_start: 0.7357 (m-30) cc_final: 0.7002 (m-30) REVERT: A 816 MET cc_start: 0.8873 (mmm) cc_final: 0.8560 (mmm) REVERT: A 940 MET cc_start: 0.8739 (mmm) cc_final: 0.8359 (mmm) REVERT: A 979 MET cc_start: 0.8644 (ttm) cc_final: 0.8355 (ttm) outliers start: 29 outliers final: 18 residues processed: 139 average time/residue: 0.5315 time to fit residues: 78.8784 Evaluate side-chains 134 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 967 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.142902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.111534 restraints weight = 8477.088| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.65 r_work: 0.2941 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8064 Z= 0.113 Angle : 0.522 10.416 10951 Z= 0.263 Chirality : 0.041 0.131 1283 Planarity : 0.003 0.038 1390 Dihedral : 6.196 141.306 1082 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.21 % Allowed : 17.75 % Favored : 79.04 % 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: 0.91 (0.27), residues: 1014 helix: 1.81 (0.24), residues: 486 sheet: -0.25 (0.48), residues: 116 loop : -0.56 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 572 TYR 0.014 0.001 TYR A 842 PHE 0.017 0.001 PHE A 367 TRP 0.007 0.001 TRP A 927 HIS 0.003 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 ( 8064) covalent geometry : angle 0.52159 / 0.26 (10951) hydrogen bonds : bond 0.03233 / 2.22 ( 415) hydrogen bonds : angle 4.11204 / 2.83 ( 1209) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.330 Fit side-chains REVERT: A 31 LYS cc_start: 0.7675 (mtpt) cc_final: 0.7394 (mtmt) REVERT: A 33 LYS cc_start: 0.7937 (tttt) cc_final: 0.7526 (ttmt) REVERT: A 51 GLU cc_start: 0.8004 (tt0) cc_final: 0.7597 (pt0) REVERT: A 71 ILE cc_start: 0.8714 (mt) cc_final: 0.8481 (mt) REVERT: A 135 LYS cc_start: 0.8751 (tptp) cc_final: 0.8341 (mtpp) REVERT: A 198 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7386 (mmp80) REVERT: A 280 ASN cc_start: 0.8038 (OUTLIER) cc_final: 0.7729 (p0) REVERT: A 394 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7624 (mt-10) REVERT: A 479 MET cc_start: 0.7255 (mtt) cc_final: 0.6867 (mtp) REVERT: A 531 SER cc_start: 0.9148 (p) cc_final: 0.8944 (p) REVERT: A 545 MET cc_start: 0.8459 (mmm) cc_final: 0.8090 (mmm) REVERT: A 575 MET cc_start: 0.9085 (mtt) cc_final: 0.8771 (mtt) REVERT: A 623 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8839 (mt) REVERT: A 812 ASP cc_start: 0.7352 (m-30) cc_final: 0.6998 (m-30) REVERT: A 816 MET cc_start: 0.8874 (mmm) cc_final: 0.8571 (mmm) REVERT: A 940 MET cc_start: 0.8729 (mmm) cc_final: 0.8473 (mmm) REVERT: A 1023 MET cc_start: 0.6445 (tpt) cc_final: 0.6092 (tpp) outliers start: 28 outliers final: 20 residues processed: 141 average time/residue: 0.5149 time to fit residues: 77.6383 Evaluate side-chains 140 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 967 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 45 optimal weight: 0.1980 chunk 96 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 GLN 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 = 0.144233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.113420 restraints weight = 8480.385| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.61 r_work: 0.3055 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8064 Z= 0.127 Angle : 0.539 11.455 10951 Z= 0.272 Chirality : 0.042 0.143 1283 Planarity : 0.003 0.038 1390 Dihedral : 6.235 141.028 1082 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.75 % Allowed : 18.44 % Favored : 78.81 % 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: 0.91 (0.27), residues: 1014 helix: 1.79 (0.24), residues: 484 sheet: -0.20 (0.48), residues: 116 loop : -0.55 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 666 TYR 0.015 0.001 TYR A 842 PHE 0.018 0.001 PHE A 367 TRP 0.007 0.001 TRP A 107 HIS 0.004 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 8064) covalent geometry : angle 0.53886 / 0.27 (10951) hydrogen bonds : bond 0.03406 / 2.34 ( 415) hydrogen bonds : angle 4.18814 / 2.89 ( 1209) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.347 Fit side-chains REVERT: A 31 LYS cc_start: 0.7777 (mtpt) cc_final: 0.7500 (mtmt) REVERT: A 33 LYS cc_start: 0.7972 (tttt) cc_final: 0.7607 (ttmt) REVERT: A 51 GLU cc_start: 0.8086 (tt0) cc_final: 0.7696 (pt0) REVERT: A 71 ILE cc_start: 0.8807 (mt) cc_final: 0.8582 (mt) REVERT: A 135 LYS cc_start: 0.8743 (tptp) cc_final: 0.7829 (tttp) REVERT: A 198 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7383 (mmp80) REVERT: A 394 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7611 (mt-10) REVERT: A 479 MET cc_start: 0.7295 (mtt) cc_final: 0.6993 (mtp) REVERT: A 545 MET cc_start: 0.8532 (mmm) cc_final: 0.8164 (mmm) REVERT: A 575 MET cc_start: 0.9118 (mtt) cc_final: 0.8786 (mtt) REVERT: A 623 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8865 (mt) REVERT: A 812 ASP cc_start: 0.7471 (m-30) cc_final: 0.7118 (m-30) REVERT: A 816 MET cc_start: 0.8915 (mmm) cc_final: 0.8596 (mmm) REVERT: A 940 MET cc_start: 0.8810 (mmm) cc_final: 0.8544 (mmm) REVERT: A 1023 MET cc_start: 0.6655 (tpt) cc_final: 0.6260 (tpp) outliers start: 24 outliers final: 19 residues processed: 137 average time/residue: 0.4940 time to fit residues: 72.2436 Evaluate side-chains 137 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 967 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 9 optimal weight: 0.0980 chunk 2 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 566 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.147036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.116334 restraints weight = 8489.260| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.61 r_work: 0.3043 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8064 Z= 0.141 Angle : 0.554 12.068 10951 Z= 0.281 Chirality : 0.043 0.165 1283 Planarity : 0.003 0.038 1390 Dihedral : 6.287 141.090 1082 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.52 % Allowed : 19.13 % Favored : 78.35 % 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: 0.86 (0.27), residues: 1014 helix: 1.73 (0.24), residues: 484 sheet: -0.19 (0.47), residues: 116 loop : -0.55 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 666 TYR 0.015 0.002 TYR A 842 PHE 0.019 0.001 PHE A 367 TRP 0.008 0.001 TRP A 107 HIS 0.005 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 ( 8064) covalent geometry : angle 0.55351 / 0.28 (10951) hydrogen bonds : bond 0.03544 / 2.43 ( 415) hydrogen bonds : angle 4.26804 / 2.95 ( 1209) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.364 Fit side-chains REVERT: A 31 LYS cc_start: 0.7791 (mtpt) cc_final: 0.7494 (mtmm) REVERT: A 33 LYS cc_start: 0.8015 (tttt) cc_final: 0.7625 (ttmt) REVERT: A 51 GLU cc_start: 0.8108 (tt0) cc_final: 0.7743 (pt0) REVERT: A 71 ILE cc_start: 0.8773 (mt) cc_final: 0.8529 (mt) REVERT: A 135 LYS cc_start: 0.8755 (tptp) cc_final: 0.8412 (mttt) REVERT: A 198 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7364 (mmp80) REVERT: A 394 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7615 (mt-10) REVERT: A 479 MET cc_start: 0.7316 (mtt) cc_final: 0.6961 (mtp) REVERT: A 545 MET cc_start: 0.8492 (mmm) cc_final: 0.8120 (mmm) REVERT: A 575 MET cc_start: 0.9107 (mtt) cc_final: 0.8780 (mtt) REVERT: A 623 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8875 (mt) REVERT: A 812 ASP cc_start: 0.7478 (m-30) cc_final: 0.7161 (m-30) REVERT: A 816 MET cc_start: 0.8932 (mmm) cc_final: 0.8604 (mmm) REVERT: A 940 MET cc_start: 0.8798 (mmm) cc_final: 0.8528 (mmm) REVERT: A 1023 MET cc_start: 0.6726 (tpt) cc_final: 0.6339 (tpp) outliers start: 22 outliers final: 18 residues processed: 133 average time/residue: 0.4987 time to fit residues: 70.8431 Evaluate side-chains 136 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 967 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 60 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 54 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.141962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.110492 restraints weight = 8427.228| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.65 r_work: 0.2945 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8064 Z= 0.110 Angle : 0.525 11.952 10951 Z= 0.266 Chirality : 0.041 0.143 1283 Planarity : 0.003 0.037 1390 Dihedral : 6.206 141.295 1082 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.41 % Allowed : 19.59 % Favored : 78.01 % 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: 1.00 (0.27), residues: 1014 helix: 1.83 (0.24), residues: 487 sheet: -0.20 (0.47), residues: 116 loop : -0.46 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 666 TYR 0.014 0.001 TYR A 295 PHE 0.016 0.001 PHE A 367 TRP 0.009 0.001 TRP A 793 HIS 0.001 0.000 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 8064) covalent geometry : angle 0.52461 / 0.27 (10951) hydrogen bonds : bond 0.03189 / 2.20 ( 415) hydrogen bonds : angle 4.13505 / 2.85 ( 1209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2805.99 seconds wall clock time: 48 minutes 37.54 seconds (2917.54 seconds total)