Starting phenix.real_space_refine on Thu Jul 2 18:33:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z78_73871/07_2026/9z78_73871.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z78_73871/07_2026/9z78_73871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9z78_73871/07_2026/9z78_73871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z78_73871/07_2026/9z78_73871.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9z78_73871/07_2026/9z78_73871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z78_73871/07_2026/9z78_73871.map" } resolution = 2.64 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= 0.136 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 5875 2.51 5 N 1628 2.21 5 O 1874 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 9402 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6274 Classifications: {'peptide': 830} Link IDs: {'PTRANS': 21, 'TRANS': 808} Chain breaks: 8 Chain: "B" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1546 Classifications: {'peptide': 204} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 191} Chain breaks: 2 Chain: "C" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1582 Classifications: {'peptide': 205} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 191} Chain breaks: 3 Time building chain proxies: 1.55, per 1000 atoms: 0.16 Number of scatterers: 9402 At special positions: 0 Unit cell: (73.312, 133.632, 144.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 1874 8.00 N 1628 7.00 C 5875 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS B 203 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " 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: 0.86 Conformation dependent library (CDL) restraints added in 295.8 milliseconds 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2240 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 20 sheets defined 4.0% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 8 through 17 removed outlier: 3.923A pdb=" N PHE A 12 " --> pdb=" O SER A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 removed outlier: 4.208A pdb=" N SER A 52 " --> pdb=" O ASP A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.553A pdb=" N ALA A 302 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 303 " --> pdb=" O LEU A 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 299 through 303' Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'B' and resid 63 through 66 removed outlier: 3.958A pdb=" N ARG B 66 " --> pdb=" O SER B 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 63 through 66' Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.524A pdb=" N THR B 92 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.809A pdb=" N ILE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 6.597A pdb=" N VAL A 3 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.659A pdb=" N GLY A 40 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 67 removed outlier: 3.768A pdb=" N GLY A 98 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 175 removed outlier: 4.057A pdb=" N PHE A 143 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA A 142 " --> pdb=" O TYR A 218 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 146 " --> pdb=" O PRO A 214 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU A 215 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASN A 240 " --> pdb=" O SER A 232 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLY A 234 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLY A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 275 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 288 through 293 current: chain 'A' and resid 388 through 398 removed outlier: 9.109A pdb=" N GLY A 388 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 10.349A pdb=" N ILE A 416 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N LYS A 390 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N SER A 418 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N GLY A 392 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG A 420 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE A 414 " --> pdb=" O SER A 437 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 436 through 438 current: chain 'A' and resid 591 through 602 removed outlier: 5.828A pdb=" N VAL A 592 " --> pdb=" O THR A 633 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ASP A 635 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 9.564A pdb=" N LEU A 594 " --> pdb=" O ASP A 635 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N LEU A 637 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 13.424A pdb=" N GLU A 596 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 14.565A pdb=" N LEU A 639 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 13.405A pdb=" N VAL A 598 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG A 630 " --> pdb=" O HIS A 651 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N GLN A 653 " --> pdb=" O ARG A 630 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE A 632 " --> pdb=" O GLN A 653 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ASP A 655 " --> pdb=" O PHE A 632 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N MET A 634 " --> pdb=" O ASP A 655 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N SER A 657 " --> pdb=" O MET A 634 " (cutoff:3.500A) removed outlier: 9.503A pdb=" N LYS A 636 " --> pdb=" O SER A 657 " (cutoff:3.500A) removed outlier: 12.088A pdb=" N ALA A 659 " --> pdb=" O LYS A 636 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N ARG A 638 " --> pdb=" O ALA A 659 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 700 through 702 current: chain 'A' and resid 723 through 726 removed outlier: 5.865A pdb=" N ILE A 723 " --> pdb=" O SER A 744 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL A 746 " --> pdb=" O ILE A 723 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA A 725 " --> pdb=" O VAL A 746 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 321 through 322 removed outlier: 6.311A pdb=" N ILE A 321 " --> pdb=" O THR A 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 383 through 384 removed outlier: 5.979A pdb=" N GLY A 383 " --> pdb=" O GLN A 409 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 563 through 565 removed outlier: 6.678A pdb=" N LEU A 586 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE A 644 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A 713 " --> pdb=" O SER A 731 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 729 through 732 current: chain 'A' and resid 863 through 873 removed outlier: 6.315A pdb=" N GLU A 884 " --> pdb=" O MET A 864 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER A 868 " --> pdb=" O LYS A 886 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU A 888 " --> pdb=" O SER A 868 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL A 870 " --> pdb=" O LEU A 888 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ALA A 890 " --> pdb=" O VAL A 870 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET A 872 " --> pdb=" O ALA A 890 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N GLU A 884 " --> pdb=" O VAL A 908 " (cutoff:3.500A) removed outlier: 9.791A pdb=" N GLU A 910 " --> pdb=" O GLU A 884 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS A 886 " --> pdb=" O GLU A 910 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ILE A 912 " --> pdb=" O LYS A 886 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU A 888 " --> pdb=" O ILE A 912 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N SER A 914 " --> pdb=" O LEU A 888 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ALA A 890 " --> pdb=" O SER A 914 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLU A 910 " --> pdb=" O THR A 933 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS A 935 " --> pdb=" O GLU A 910 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ILE A 912 " --> pdb=" O LYS A 935 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLN A 937 " --> pdb=" O ILE A 912 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N SER A 914 " --> pdb=" O GLN A 937 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 611 through 612 Processing sheet with id=AB1, first strand: chain 'A' and resid 670 through 674 Processing sheet with id=AB2, first strand: chain 'A' and resid 795 through 798 removed outlier: 6.810A pdb=" N VAL A 795 " --> pdb=" O TYR A 817 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER A 819 " --> pdb=" O VAL A 795 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER A 797 " --> pdb=" O SER A 819 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY A 816 " --> pdb=" O VAL A 858 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLN A 860 " --> pdb=" O GLY A 816 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU A 818 " --> pdb=" O GLN A 860 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA A 875 " --> pdb=" O GLN A 894 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N GLU A 896 " --> pdb=" O ALA A 875 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TRP A 877 " --> pdb=" O GLU A 896 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'B' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 11 through 12 current: chain 'B' and resid 48 through 53 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 60 through 61 current: chain 'B' and resid 109 through 110 Processing sheet with id=AB5, first strand: chain 'B' and resid 127 through 131 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 144 through 152 current: chain 'B' and resid 183 through 190 Processing sheet with id=AB6, first strand: chain 'B' and resid 158 through 161 removed outlier: 4.591A pdb=" N TYR B 201 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.857A pdb=" N ASP C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.331A pdb=" N LEU C 11 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 54 removed outlier: 5.527A pdb=" N LEU C 46 " --> pdb=" O GLN C 37 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLN C 37 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR C 98 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 115 through 119 removed outlier: 5.764A pdb=" N TYR C 174 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 146 through 150 removed outlier: 4.014A pdb=" N LYS C 146 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR C 198 " --> pdb=" O LYS C 146 " (cutoff:3.500A) 190 hydrogen bonds defined for protein. 483 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: 1.59 Time building geometry restraints manager: 1.10 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: 3120 1.34 - 1.47: 2259 1.47 - 1.59: 4158 1.59 - 1.71: 0 1.71 - 1.83: 41 Bond restraints: 9578 Sorted by residual: bond pdb=" C LYS B 208 " pdb=" N PRO B 209 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.28e-02 6.10e+03 1.61e+00 bond pdb=" CA ASP B 30 " pdb=" C ASP B 30 " ideal model delta sigma weight residual 1.518 1.566 -0.048 4.01e-02 6.22e+02 1.42e+00 bond pdb=" CG MET A 864 " pdb=" SD MET A 864 " ideal model delta sigma weight residual 1.803 1.832 -0.029 2.50e-02 1.60e+03 1.37e+00 bond pdb=" CB ASP B 30 " pdb=" CG ASP B 30 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.37e+00 bond pdb=" CB ASN A 767 " pdb=" CG ASN A 767 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.32e+00 ... (remaining 9573 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 12901 3.02 - 6.04: 79 6.04 - 9.06: 7 9.06 - 12.07: 1 12.07 - 15.09: 1 Bond angle restraints: 12989 Sorted by residual: angle pdb=" CB MET A 864 " pdb=" CG MET A 864 " pdb=" SD MET A 864 " ideal model delta sigma weight residual 112.70 127.79 -15.09 3.00e+00 1.11e-01 2.53e+01 angle pdb=" C SER A 417 " pdb=" N SER A 418 " pdb=" CA SER A 418 " ideal model delta sigma weight residual 121.54 129.32 -7.78 1.91e+00 2.74e-01 1.66e+01 angle pdb=" C ASP C 50 " pdb=" N ALA C 51 " pdb=" CA ALA C 51 " ideal model delta sigma weight residual 121.54 128.61 -7.07 1.91e+00 2.74e-01 1.37e+01 angle pdb=" CD ARG C 18 " pdb=" NE ARG C 18 " pdb=" CZ ARG C 18 " ideal model delta sigma weight residual 124.40 129.11 -4.71 1.40e+00 5.10e-01 1.13e+01 angle pdb=" CG ARG C 18 " pdb=" CD ARG C 18 " pdb=" NE ARG C 18 " ideal model delta sigma weight residual 112.00 119.00 -7.00 2.20e+00 2.07e-01 1.01e+01 ... (remaining 12984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4912 17.73 - 35.46: 547 35.46 - 53.19: 161 53.19 - 70.92: 36 70.92 - 88.65: 10 Dihedral angle restraints: 5666 sinusoidal: 2159 harmonic: 3507 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 97 " pdb=" CB CYS B 97 " ideal model delta sinusoidal sigma weight residual 93.00 43.23 49.77 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CB CYS B 147 " pdb=" SG CYS B 147 " pdb=" SG CYS B 203 " pdb=" CB CYS B 203 " ideal model delta sinusoidal sigma weight residual 93.00 137.76 -44.76 1 1.00e+01 1.00e-02 2.78e+01 dihedral pdb=" CA GLU A 825 " pdb=" C GLU A 825 " pdb=" N ASN A 826 " pdb=" CA ASN A 826 " ideal model delta harmonic sigma weight residual 180.00 159.41 20.59 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 5663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1152 0.051 - 0.103: 223 0.103 - 0.154: 90 0.154 - 0.205: 5 0.205 - 0.256: 1 Chirality restraints: 1471 Sorted by residual: chirality pdb=" CB ILE B 29 " pdb=" CA ILE B 29 " pdb=" CG1 ILE B 29 " pdb=" CG2 ILE B 29 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CG LEU C 33 " pdb=" CB LEU C 33 " pdb=" CD1 LEU C 33 " pdb=" CD2 LEU C 33 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CB VAL B 69 " pdb=" CA VAL B 69 " pdb=" CG1 VAL B 69 " pdb=" CG2 VAL B 69 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 1468 not shown) Planarity restraints: 1686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 252 " 0.048 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO A 253 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 69 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO A 70 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 18 " -0.204 9.50e-02 1.11e+02 9.22e-02 6.74e+00 pdb=" NE ARG C 18 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG C 18 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG C 18 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C 18 " -0.000 2.00e-02 2.50e+03 ... (remaining 1683 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2047 2.79 - 3.32: 7634 3.32 - 3.85: 16866 3.85 - 4.37: 20417 4.37 - 4.90: 34494 Nonbonded interactions: 81458 Sorted by model distance: nonbonded pdb=" O SER B 86 " pdb=" OG SER B 86 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR A 205 " pdb=" O SER A 235 " model vdw 2.327 3.040 nonbonded pdb=" O SER B 15 " pdb=" OG SER B 15 " model vdw 2.375 3.040 nonbonded pdb=" O SER C 77 " pdb=" OG SER C 77 " model vdw 2.376 3.040 nonbonded pdb=" OE2 GLU B 48 " pdb=" NZ LYS B 62 " model vdw 2.422 3.120 ... (remaining 81453 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: 2.040 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.060 Find NCS groups from input model: 0.060 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:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 0.048 9582 Z= 0.158 Angle : 0.677 15.092 12997 Z= 0.361 Chirality : 0.048 0.256 1471 Planarity : 0.006 0.092 1686 Dihedral : 16.868 88.647 3414 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.87 % Allowed : 24.90 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.32 (0.23), residues: 1207 helix: -2.75 (0.88), residues: 22 sheet: -0.72 (0.22), residues: 538 loop : -0.85 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 18 TYR 0.016 0.002 TYR A 9 PHE 0.018 0.002 PHE B 80 TRP 0.014 0.002 TRP B 110 HIS 0.003 0.001 HIS A 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 9578) covalent geometry : angle 0.67679 / 0.36 (12989) SS BOND : bond 0.00415 / 0.17 ( 4) SS BOND : angle 0.58906 / 0.34 ( 8) hydrogen bonds : bond 0.19499 / 12.53 ( 190) hydrogen bonds : angle 9.59921 / 6.34 ( 483) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 208 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7463 (ttpp) REVERT: A 266 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6798 (mm-30) REVERT: A 304 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8383 (mtmt) REVERT: A 638 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8043 (mtt90) REVERT: B 29 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7826 (mp) REVERT: B 216 LYS cc_start: 0.8551 (tppt) cc_final: 0.8039 (tptm) REVERT: C 150 LYS cc_start: 0.5361 (OUTLIER) cc_final: 0.4977 (mmpt) REVERT: C 182 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7343 (pp) outliers start: 30 outliers final: 20 residues processed: 139 average time/residue: 0.4761 time to fit residues: 71.3213 Evaluate side-chains 138 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 852 MET Chi-restraints excluded: chain A residue 862 ASN Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 209 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.168281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133019 restraints weight = 10167.796| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.61 r_work: 0.3555 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9582 Z= 0.167 Angle : 0.509 7.644 12997 Z= 0.269 Chirality : 0.044 0.152 1471 Planarity : 0.005 0.063 1686 Dihedral : 7.220 57.576 1359 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.83 % Allowed : 22.32 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.85 (0.24), residues: 1207 helix: -1.71 (1.05), residues: 22 sheet: -0.35 (0.22), residues: 554 loop : -0.61 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 61 TYR 0.015 0.002 TYR B 54 PHE 0.018 0.001 PHE B 80 TRP 0.011 0.002 TRP B 110 HIS 0.003 0.001 HIS A 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 9578) covalent geometry : angle 0.50823 / 0.27 (12989) SS BOND : bond 0.00493 / 0.16 ( 4) SS BOND : angle 0.97317 / 0.56 ( 8) hydrogen bonds : bond 0.03521 / 2.26 ( 190) hydrogen bonds : angle 7.00687 / 4.70 ( 483) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 119 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 193 ASP cc_start: 0.7797 (t0) cc_final: 0.7432 (t0) REVERT: A 208 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7548 (ttpt) REVERT: A 266 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6819 (mm-30) REVERT: A 304 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8450 (mtmt) REVERT: A 475 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: A 783 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7189 (mt) REVERT: A 872 MET cc_start: 0.7312 (mtp) cc_final: 0.6976 (ttm) REVERT: B 29 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7773 (mp) REVERT: B 150 LYS cc_start: 0.8461 (tttp) cc_final: 0.8144 (tttm) REVERT: C 182 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7153 (pp) REVERT: C 192 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8500 (t) outliers start: 40 outliers final: 18 residues processed: 153 average time/residue: 0.5330 time to fit residues: 87.7552 Evaluate side-chains 135 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 783 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 192 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 16 optimal weight: 0.0770 chunk 7 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.167174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.133906 restraints weight = 10137.301| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.64 r_work: 0.3499 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9582 Z= 0.160 Angle : 0.499 7.326 12997 Z= 0.262 Chirality : 0.044 0.156 1471 Planarity : 0.004 0.059 1686 Dihedral : 6.033 58.911 1325 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.02 % Allowed : 22.70 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.48 (0.24), residues: 1207 helix: -1.36 (1.07), residues: 22 sheet: -0.13 (0.22), residues: 560 loop : -0.34 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 18 TYR 0.013 0.002 TYR B 96 PHE 0.016 0.001 PHE B 80 TRP 0.012 0.002 TRP B 110 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 9578) covalent geometry : angle 0.49869 / 0.26 (12989) SS BOND : bond 0.00452 / 0.15 ( 4) SS BOND : angle 0.92269 / 0.52 ( 8) hydrogen bonds : bond 0.03538 / 2.28 ( 190) hydrogen bonds : angle 6.66882 / 4.47 ( 483) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 193 ASP cc_start: 0.7854 (t0) cc_final: 0.7515 (t0) REVERT: A 208 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7570 (ttpt) REVERT: A 266 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6912 (mm-30) REVERT: A 475 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: A 638 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8199 (mtt90) REVERT: A 761 GLN cc_start: 0.7983 (mt0) cc_final: 0.7743 (mt0) REVERT: A 783 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7126 (mt) REVERT: B 29 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7967 (mp) REVERT: B 150 LYS cc_start: 0.8526 (tttp) cc_final: 0.8207 (tttm) REVERT: C 182 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7095 (pp) REVERT: C 192 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8497 (t) outliers start: 42 outliers final: 20 residues processed: 156 average time/residue: 0.5500 time to fit residues: 91.8831 Evaluate side-chains 140 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 783 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 195 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 4 optimal weight: 0.6980 chunk 108 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 103 optimal weight: 0.0020 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 0.0770 chunk 7 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.4346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN A 199 ASN A 204 ASN A 360 GLN A 735 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.168829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133913 restraints weight = 10189.864| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.60 r_work: 0.3567 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9582 Z= 0.102 Angle : 0.447 6.749 12997 Z= 0.237 Chirality : 0.043 0.152 1471 Planarity : 0.004 0.056 1686 Dihedral : 5.363 55.592 1320 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.16 % Allowed : 23.66 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.48 (0.24), residues: 1207 helix: -1.27 (1.03), residues: 22 sheet: -0.11 (0.22), residues: 566 loop : -0.36 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 18 TYR 0.012 0.001 TYR B 54 PHE 0.014 0.001 PHE B 80 TRP 0.010 0.001 TRP B 110 HIS 0.002 0.000 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 9578) covalent geometry : angle 0.44723 / 0.24 (12989) SS BOND : bond 0.00341 / 0.12 ( 4) SS BOND : angle 0.73076 / 0.42 ( 8) hydrogen bonds : bond 0.03001 / 1.93 ( 190) hydrogen bonds : angle 6.36620 / 4.28 ( 483) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 193 ASP cc_start: 0.7848 (t0) cc_final: 0.7484 (t0) REVERT: A 208 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7523 (ttpt) REVERT: A 266 GLU cc_start: 0.7306 (mp0) cc_final: 0.6861 (mm-30) REVERT: A 475 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: A 638 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8095 (mtt90) REVERT: A 761 GLN cc_start: 0.7925 (mt0) cc_final: 0.7578 (mt0) REVERT: A 783 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7064 (mt) REVERT: B 18 LEU cc_start: 0.8151 (tp) cc_final: 0.7850 (tp) REVERT: B 150 LYS cc_start: 0.8363 (tttp) cc_final: 0.8017 (tttm) REVERT: C 182 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7055 (pp) REVERT: C 192 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8515 (t) outliers start: 33 outliers final: 17 residues processed: 145 average time/residue: 0.4856 time to fit residues: 76.0465 Evaluate side-chains 138 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 783 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 192 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 84 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 108 optimal weight: 0.1980 chunk 79 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.166505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.133117 restraints weight = 10178.627| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.53 r_work: 0.3511 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9582 Z= 0.158 Angle : 0.489 7.198 12997 Z= 0.257 Chirality : 0.044 0.156 1471 Planarity : 0.004 0.055 1686 Dihedral : 5.037 42.302 1313 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.45 % Allowed : 23.28 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.27 (0.24), residues: 1207 helix: -1.29 (1.02), residues: 22 sheet: 0.04 (0.22), residues: 548 loop : -0.22 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 18 TYR 0.013 0.001 TYR B 96 PHE 0.016 0.001 PHE B 80 TRP 0.010 0.002 TRP B 110 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 9578) covalent geometry : angle 0.48861 / 0.26 (12989) SS BOND : bond 0.00439 / 0.14 ( 4) SS BOND : angle 0.87713 / 0.49 ( 8) hydrogen bonds : bond 0.03266 / 2.08 ( 190) hydrogen bonds : angle 6.34089 / 4.27 ( 483) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 103 ASN cc_start: 0.7801 (m-40) cc_final: 0.7496 (m110) REVERT: A 193 ASP cc_start: 0.7843 (t0) cc_final: 0.7458 (t0) REVERT: A 208 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7575 (ttpt) REVERT: A 266 GLU cc_start: 0.7395 (mp0) cc_final: 0.6954 (mm-30) REVERT: A 475 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: A 638 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8147 (mtt90) REVERT: A 783 ILE cc_start: 0.7532 (OUTLIER) cc_final: 0.7159 (mt) REVERT: B 29 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7960 (mp) REVERT: B 150 LYS cc_start: 0.8409 (tttp) cc_final: 0.8076 (tttm) REVERT: C 150 LYS cc_start: 0.5515 (OUTLIER) cc_final: 0.3429 (mmtt) REVERT: C 182 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7080 (pp) REVERT: C 192 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8443 (t) outliers start: 36 outliers final: 23 residues processed: 143 average time/residue: 0.4774 time to fit residues: 73.5504 Evaluate side-chains 147 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 783 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 197 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 7 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 70 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN A 735 GLN A 860 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.164542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.130894 restraints weight = 10213.446| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.63 r_work: 0.3478 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9582 Z= 0.234 Angle : 0.552 7.766 12997 Z= 0.289 Chirality : 0.046 0.165 1471 Planarity : 0.004 0.053 1686 Dihedral : 5.428 50.018 1313 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.12 % Allowed : 22.61 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.42 (0.24), residues: 1207 helix: -1.33 (1.04), residues: 22 sheet: -0.14 (0.22), residues: 572 loop : -0.24 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 18 TYR 0.014 0.002 TYR B 96 PHE 0.019 0.002 PHE B 80 TRP 0.012 0.002 TRP B 110 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 ( 9578) covalent geometry : angle 0.55111 / 0.29 (12989) SS BOND : bond 0.00563 / 0.17 ( 4) SS BOND : angle 1.09062 / 0.60 ( 8) hydrogen bonds : bond 0.03680 / 2.33 ( 190) hydrogen bonds : angle 6.51806 / 4.38 ( 483) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 193 ASP cc_start: 0.7895 (t0) cc_final: 0.7563 (t0) REVERT: A 208 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7513 (ttpt) REVERT: A 266 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7037 (mm-30) REVERT: A 322 ASP cc_start: 0.8279 (t0) cc_final: 0.7979 (t0) REVERT: A 475 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: A 638 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8148 (mtt90) REVERT: A 761 GLN cc_start: 0.7834 (mt0) cc_final: 0.7585 (mt0) REVERT: A 783 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.7056 (mt) REVERT: B 29 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7972 (mp) REVERT: B 150 LYS cc_start: 0.8470 (tttp) cc_final: 0.8112 (tttm) REVERT: C 150 LYS cc_start: 0.5550 (OUTLIER) cc_final: 0.3505 (mmtt) REVERT: C 182 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7098 (pp) REVERT: C 192 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8476 (t) outliers start: 43 outliers final: 27 residues processed: 150 average time/residue: 0.4767 time to fit residues: 77.0288 Evaluate side-chains 153 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 783 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 197 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 93 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN A 735 GLN A 860 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.170097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.134703 restraints weight = 10126.638| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.60 r_work: 0.3544 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9582 Z= 0.130 Angle : 0.478 7.156 12997 Z= 0.251 Chirality : 0.044 0.156 1471 Planarity : 0.004 0.052 1686 Dihedral : 5.101 45.049 1313 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.02 % Allowed : 22.61 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.35 (0.24), residues: 1207 helix: -1.19 (1.05), residues: 22 sheet: -0.09 (0.22), residues: 580 loop : -0.19 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 18 TYR 0.011 0.001 TYR B 54 PHE 0.015 0.001 PHE B 80 TRP 0.012 0.001 TRP B 110 HIS 0.002 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 9578) covalent geometry : angle 0.47725 / 0.25 (12989) SS BOND : bond 0.00385 / 0.13 ( 4) SS BOND : angle 0.83732 / 0.47 ( 8) hydrogen bonds : bond 0.03118 / 2.00 ( 190) hydrogen bonds : angle 6.31419 / 4.25 ( 483) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 193 ASP cc_start: 0.7826 (t0) cc_final: 0.7482 (t0) REVERT: A 208 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7454 (ttpt) REVERT: A 266 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6945 (mm-30) REVERT: A 638 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8094 (mtt90) REVERT: A 783 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.7022 (mt) REVERT: B 29 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7881 (mp) REVERT: B 150 LYS cc_start: 0.8337 (tttp) cc_final: 0.7980 (tttm) REVERT: C 150 LYS cc_start: 0.5484 (OUTLIER) cc_final: 0.3470 (mmtt) REVERT: C 182 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7029 (pp) REVERT: C 192 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8371 (t) outliers start: 42 outliers final: 25 residues processed: 149 average time/residue: 0.4254 time to fit residues: 68.6745 Evaluate side-chains 149 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 783 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 197 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 100 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.169447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133896 restraints weight = 10146.153| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.60 r_work: 0.3535 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9582 Z= 0.159 Angle : 0.498 7.264 12997 Z= 0.261 Chirality : 0.044 0.156 1471 Planarity : 0.004 0.052 1686 Dihedral : 5.143 45.496 1313 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.54 % Allowed : 23.08 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.33 (0.24), residues: 1207 helix: -1.21 (1.04), residues: 22 sheet: -0.06 (0.22), residues: 576 loop : -0.20 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 18 TYR 0.012 0.002 TYR B 96 PHE 0.017 0.001 PHE B 80 TRP 0.012 0.002 TRP B 110 HIS 0.002 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 9578) covalent geometry : angle 0.49800 / 0.26 (12989) SS BOND : bond 0.00439 / 0.14 ( 4) SS BOND : angle 0.90022 / 0.50 ( 8) hydrogen bonds : bond 0.03227 / 2.05 ( 190) hydrogen bonds : angle 6.29575 / 4.23 ( 483) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8195 (tt0) cc_final: 0.7986 (tt0) REVERT: A 193 ASP cc_start: 0.7819 (t0) cc_final: 0.7471 (t0) REVERT: A 208 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7454 (ttpt) REVERT: A 224 LYS cc_start: 0.8309 (pttm) cc_final: 0.8097 (pttt) REVERT: A 266 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6961 (mm-30) REVERT: A 638 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8103 (mtt90) REVERT: A 761 GLN cc_start: 0.7767 (mt0) cc_final: 0.7490 (mt0) REVERT: A 783 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.7019 (mt) REVERT: B 29 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7886 (mp) REVERT: B 150 LYS cc_start: 0.8302 (tttp) cc_final: 0.7937 (tttm) REVERT: C 150 LYS cc_start: 0.5488 (OUTLIER) cc_final: 0.3508 (mmtt) REVERT: C 182 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.6995 (pp) REVERT: C 192 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8372 (t) outliers start: 37 outliers final: 25 residues processed: 147 average time/residue: 0.4503 time to fit residues: 71.3892 Evaluate side-chains 150 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 783 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 197 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 66 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 ASN A 735 GLN A 860 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.164606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.131486 restraints weight = 10008.653| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.53 r_work: 0.3491 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9582 Z= 0.187 Angle : 0.520 7.451 12997 Z= 0.272 Chirality : 0.045 0.164 1471 Planarity : 0.004 0.052 1686 Dihedral : 5.270 48.287 1313 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.93 % Allowed : 22.32 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.40 (0.24), residues: 1207 helix: -1.25 (1.05), residues: 22 sheet: -0.12 (0.22), residues: 569 loop : -0.23 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 18 TYR 0.013 0.002 TYR B 96 PHE 0.017 0.001 PHE B 80 TRP 0.011 0.002 TRP B 110 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 ( 9578) covalent geometry : angle 0.51965 / 0.27 (12989) SS BOND : bond 0.00489 / 0.15 ( 4) SS BOND : angle 0.95455 / 0.53 ( 8) hydrogen bonds : bond 0.03387 / 2.15 ( 190) hydrogen bonds : angle 6.35815 / 4.27 ( 483) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8208 (tt0) cc_final: 0.7999 (tt0) REVERT: A 193 ASP cc_start: 0.7926 (t0) cc_final: 0.7651 (t0) REVERT: A 208 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7892 (mptt) REVERT: A 224 LYS cc_start: 0.8426 (pttm) cc_final: 0.8133 (pttt) REVERT: A 266 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7048 (mm-30) REVERT: A 475 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: A 638 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8135 (mtt90) REVERT: A 761 GLN cc_start: 0.7866 (mt0) cc_final: 0.7582 (mt0) REVERT: A 783 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.7047 (mt) REVERT: B 29 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7907 (mp) REVERT: B 150 LYS cc_start: 0.8355 (tttp) cc_final: 0.8019 (tttm) REVERT: C 146 LYS cc_start: 0.8569 (pttm) cc_final: 0.8351 (pttp) REVERT: C 150 LYS cc_start: 0.5566 (OUTLIER) cc_final: 0.3534 (mmtt) REVERT: C 182 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7101 (pp) REVERT: C 192 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8418 (t) outliers start: 41 outliers final: 27 residues processed: 147 average time/residue: 0.4954 time to fit residues: 78.3400 Evaluate side-chains 150 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 783 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 6 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 45 optimal weight: 0.4980 chunk 110 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 GLN A 860 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.170010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.134569 restraints weight = 10106.375| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.60 r_work: 0.3543 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9582 Z= 0.138 Angle : 0.480 7.122 12997 Z= 0.252 Chirality : 0.044 0.155 1471 Planarity : 0.004 0.051 1686 Dihedral : 5.050 44.236 1313 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.74 % Allowed : 22.70 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.36 (0.24), residues: 1207 helix: -1.17 (1.06), residues: 22 sheet: -0.11 (0.22), residues: 573 loop : -0.19 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 18 TYR 0.012 0.001 TYR B 54 PHE 0.016 0.001 PHE B 80 TRP 0.012 0.001 TRP B 110 HIS 0.002 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 9578) covalent geometry : angle 0.48018 / 0.25 (12989) SS BOND : bond 0.00394 / 0.13 ( 4) SS BOND : angle 0.82482 / 0.46 ( 8) hydrogen bonds : bond 0.03087 / 1.97 ( 190) hydrogen bonds : angle 6.22304 / 4.18 ( 483) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 193 ASP cc_start: 0.7826 (t0) cc_final: 0.7495 (t0) REVERT: A 208 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7871 (mptt) REVERT: A 224 LYS cc_start: 0.8349 (pttm) cc_final: 0.8080 (pttt) REVERT: A 266 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6961 (mm-30) REVERT: A 638 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8054 (mtt90) REVERT: A 783 ILE cc_start: 0.7397 (OUTLIER) cc_final: 0.7018 (mt) REVERT: B 29 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7874 (mp) REVERT: B 150 LYS cc_start: 0.8274 (tttp) cc_final: 0.7918 (tttm) REVERT: C 150 LYS cc_start: 0.5508 (OUTLIER) cc_final: 0.3546 (mmtt) REVERT: C 182 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7002 (pp) REVERT: C 192 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8361 (t) outliers start: 39 outliers final: 28 residues processed: 145 average time/residue: 0.5068 time to fit residues: 79.4697 Evaluate side-chains 149 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 783 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 114 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 67 optimal weight: 0.0870 chunk 29 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN ** A 100 ASN ** 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 = 0.3983 r_free = 0.3983 target = 0.170172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.134780 restraints weight = 10059.116| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.59 r_work: 0.3545 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9582 Z= 0.137 Angle : 0.480 7.059 12997 Z= 0.252 Chirality : 0.044 0.156 1471 Planarity : 0.004 0.051 1686 Dihedral : 5.012 42.407 1313 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.02 % Allowed : 22.61 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.35 (0.24), residues: 1207 helix: -1.19 (1.04), residues: 22 sheet: -0.10 (0.22), residues: 571 loop : -0.18 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 18 TYR 0.012 0.001 TYR B 60 PHE 0.015 0.001 PHE B 80 TRP 0.012 0.001 TRP B 110 HIS 0.002 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9578) covalent geometry : angle 0.47933 / 0.25 (12989) SS BOND : bond 0.00399 / 0.13 ( 4) SS BOND : angle 0.83165 / 0.47 ( 8) hydrogen bonds : bond 0.03085 / 1.97 ( 190) hydrogen bonds : angle 6.19612 / 4.16 ( 483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3424.83 seconds wall clock time: 59 minutes 12.29 seconds (3552.29 seconds total)