Starting phenix.real_space_refine on Tue Mar 3 16:24:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sxa_10337/03_2026/6sxa_10337.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sxa_10337/03_2026/6sxa_10337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6sxa_10337/03_2026/6sxa_10337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sxa_10337/03_2026/6sxa_10337.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sxa_10337/03_2026/6sxa_10337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sxa_10337/03_2026/6sxa_10337.map" } resolution = 3.6 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= 0.002 sd= 0.050 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 4499 2.51 5 N 1219 2.21 5 O 1271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7014 Number of models: 1 Model: "" Number of chains: 2 Chain: "F" Number of atoms: 5620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5620 Classifications: {'peptide': 747} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 104} Link IDs: {'PTRANS': 34, 'TRANS': 712} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 389 Unresolved non-hydrogen angles: 468 Unresolved non-hydrogen dihedrals: 321 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 27, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 6, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 225 Chain: "G" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1394 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 11, 'TRANS': 184} Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 8, 'GLN:plan1': 5, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 98 Time building chain proxies: 1.69, per 1000 atoms: 0.24 Number of scatterers: 7014 At special positions: 0 Unit cell: (84.18, 111.78, 128.34, 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 1271 8.00 N 1219 7.00 C 4499 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 273.4 milliseconds 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1808 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 7 sheets defined 52.6% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'F' and resid 16 through 29 removed outlier: 4.034A pdb=" N LEU F 22 " --> pdb=" O TYR F 18 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU F 24 " --> pdb=" O ARG F 20 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP F 28 " --> pdb=" O LEU F 24 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 53 removed outlier: 3.544A pdb=" N LEU F 44 " --> pdb=" O GLY F 40 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR F 46 " --> pdb=" O ASP F 42 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS F 47 " --> pdb=" O ARG F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 80 removed outlier: 3.875A pdb=" N GLU F 69 " --> pdb=" O GLN F 65 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU F 79 " --> pdb=" O GLN F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 98 removed outlier: 4.214A pdb=" N ARG F 97 " --> pdb=" O THR F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 104 Processing helix chain 'F' and resid 110 through 121 removed outlier: 3.797A pdb=" N LEU F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL F 115 " --> pdb=" O SER F 111 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL F 116 " --> pdb=" O ARG F 112 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP F 117 " --> pdb=" O ILE F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 141 removed outlier: 3.544A pdb=" N GLU F 141 " --> pdb=" O ARG F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 153 removed outlier: 4.022A pdb=" N PHE F 147 " --> pdb=" O CYS F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 185 Processing helix chain 'F' and resid 197 through 202 removed outlier: 4.015A pdb=" N SER F 202 " --> pdb=" O VAL F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 207 removed outlier: 4.057A pdb=" N GLN F 206 " --> pdb=" O SER F 202 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS F 207 " --> pdb=" O PHE F 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 202 through 207' Processing helix chain 'F' and resid 222 through 243 removed outlier: 4.281A pdb=" N ALA F 228 " --> pdb=" O ALA F 224 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP F 231 " --> pdb=" O THR F 227 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS F 238 " --> pdb=" O ASN F 234 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS F 243 " --> pdb=" O GLU F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 259 removed outlier: 3.701A pdb=" N ILE F 258 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY F 259 " --> pdb=" O GLU F 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 254 through 259' Processing helix chain 'F' and resid 262 through 270 removed outlier: 3.563A pdb=" N ILE F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 301 removed outlier: 4.270A pdb=" N GLN F 286 " --> pdb=" O LYS F 282 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN F 296 " --> pdb=" O ARG F 292 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER F 299 " --> pdb=" O LEU F 295 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN F 300 " --> pdb=" O GLN F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 313 Processing helix chain 'F' and resid 333 through 344 removed outlier: 3.890A pdb=" N ARG F 342 " --> pdb=" O ASN F 338 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 397 removed outlier: 3.911A pdb=" N THR F 385 " --> pdb=" O TRP F 381 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU F 386 " --> pdb=" O GLU F 382 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL F 387 " --> pdb=" O ALA F 383 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS F 389 " --> pdb=" O THR F 385 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU F 392 " --> pdb=" O LEU F 388 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA F 393 " --> pdb=" O LYS F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 403 removed outlier: 4.033A pdb=" N GLY F 403 " --> pdb=" O GLU F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 426 Processing helix chain 'F' and resid 427 through 440 removed outlier: 3.809A pdb=" N PHE F 431 " --> pdb=" O GLY F 427 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU F 432 " --> pdb=" O ALA F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 573 Processing helix chain 'F' and resid 584 through 595 removed outlier: 3.940A pdb=" N VAL F 588 " --> pdb=" O GLU F 584 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN F 590 " --> pdb=" O THR F 586 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU F 592 " --> pdb=" O VAL F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 613 through 638 removed outlier: 3.786A pdb=" N ALA F 622 " --> pdb=" O ARG F 618 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU F 631 " --> pdb=" O LYS F 627 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU F 633 " --> pdb=" O ALA F 629 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE F 634 " --> pdb=" O PHE F 630 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG F 635 " --> pdb=" O GLU F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 689 through 692 removed outlier: 4.015A pdb=" N ARG F 692 " --> pdb=" O ARG F 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 689 through 692' Processing helix chain 'F' and resid 694 through 700 Processing helix chain 'F' and resid 729 through 738 removed outlier: 3.688A pdb=" N ILE F 733 " --> pdb=" O ILE F 729 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN F 737 " --> pdb=" O ILE F 733 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 752 removed outlier: 3.731A pdb=" N ILE F 746 " --> pdb=" O TYR F 742 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER F 747 " --> pdb=" O SER F 743 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG F 750 " --> pdb=" O ILE F 746 " (cutoff:3.500A) Processing helix chain 'F' and resid 771 through 778 Processing helix chain 'F' and resid 783 through 795 removed outlier: 3.850A pdb=" N HIS F 794 " --> pdb=" O LEU F 790 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE F 795 " --> pdb=" O LEU F 791 " (cutoff:3.500A) Processing helix chain 'F' and resid 805 through 817 removed outlier: 4.326A pdb=" N ALA F 810 " --> pdb=" O PRO F 806 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU F 811 " --> pdb=" O HIS F 807 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU F 814 " --> pdb=" O ALA F 810 " (cutoff:3.500A) Processing helix chain 'F' and resid 827 through 832 removed outlier: 4.449A pdb=" N THR F 832 " --> pdb=" O ALA F 828 " (cutoff:3.500A) Processing helix chain 'F' and resid 847 through 855 removed outlier: 3.958A pdb=" N PHE F 851 " --> pdb=" O GLY F 847 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS F 854 " --> pdb=" O ASP F 850 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET F 855 " --> pdb=" O PHE F 851 " (cutoff:3.500A) Processing helix chain 'F' and resid 859 through 868 Processing helix chain 'F' and resid 880 through 889 Processing helix chain 'F' and resid 891 through 902 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.700A pdb=" N VAL G 116 " --> pdb=" O LEU G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 149 Processing helix chain 'G' and resid 152 through 161 removed outlier: 4.143A pdb=" N GLN G 158 " --> pdb=" O HIS G 154 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER G 159 " --> pdb=" O GLY G 155 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU G 160 " --> pdb=" O ARG G 156 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY G 161 " --> pdb=" O LEU G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 191 removed outlier: 3.944A pdb=" N LYS G 187 " --> pdb=" O LYS G 183 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU G 191 " --> pdb=" O LYS G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 214 removed outlier: 3.905A pdb=" N ARG G 207 " --> pdb=" O GLU G 203 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS G 213 " --> pdb=" O LEU G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 239 Processing helix chain 'G' and resid 240 through 242 No H-bonds generated for 'chain 'G' and resid 240 through 242' Processing helix chain 'G' and resid 246 through 255 removed outlier: 3.585A pdb=" N SER G 250 " --> pdb=" O ASN G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 264 Processing helix chain 'G' and resid 269 through 273 removed outlier: 3.883A pdb=" N LEU G 273 " --> pdb=" O ASP G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 289 Processing sheet with id=AA1, first strand: chain 'F' and resid 86 through 87 removed outlier: 7.163A pdb=" N ARG F 86 " --> pdb=" O PHE F 108 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL F 59 " --> pdb=" O ILE F 107 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU F 58 " --> pdb=" O GLY F 130 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N LEU F 132 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU F 60 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE F 164 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL F 33 " --> pdb=" O THR F 165 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU F 32 " --> pdb=" O TYR F 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 214 through 216 Processing sheet with id=AA3, first strand: chain 'F' and resid 410 through 411 removed outlier: 3.770A pdb=" N ALA F 411 " --> pdb=" O HIS F 555 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 705 through 709 removed outlier: 3.865A pdb=" N GLU F 707 " --> pdb=" O ILE F 684 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL F 685 " --> pdb=" O ILE F 717 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE F 717 " --> pdb=" O VAL F 685 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 723 through 728 removed outlier: 4.001A pdb=" N GLU F 725 " --> pdb=" O VAL F 756 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU F 758 " --> pdb=" O GLU F 725 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU F 760 " --> pdb=" O LYS F 727 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LEU F 801 " --> pdb=" O PRO F 755 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU F 757 " --> pdb=" O LEU F 801 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N CYS F 803 " --> pdb=" O LEU F 757 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE F 759 " --> pdb=" O CYS F 803 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 121 through 123 removed outlier: 3.770A pdb=" N TYR G 130 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR G 136 " --> pdb=" O LEU G 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 140 through 142 removed outlier: 6.705A pdb=" N LEU G 141 " --> pdb=" O GLN G 172 " (cutoff:3.500A) 253 hydrogen bonds defined for protein. 744 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: 1.13 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1238 1.32 - 1.44: 1766 1.44 - 1.57: 4121 1.57 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 7157 Sorted by residual: bond pdb=" C SER G 104 " pdb=" N PRO G 105 " ideal model delta sigma weight residual 1.337 1.378 -0.041 9.80e-03 1.04e+04 1.76e+01 bond pdb=" C LEU F 84 " pdb=" N PRO F 85 " ideal model delta sigma weight residual 1.331 1.379 -0.048 1.20e-02 6.94e+03 1.61e+01 bond pdb=" C ASP F 271 " pdb=" N PRO F 272 " ideal model delta sigma weight residual 1.333 1.372 -0.039 1.01e-02 9.80e+03 1.46e+01 bond pdb=" N GLN F 65 " pdb=" CA GLN F 65 " ideal model delta sigma weight residual 1.453 1.487 -0.034 9.20e-03 1.18e+04 1.37e+01 bond pdb=" N VAL F 709 " pdb=" CA VAL F 709 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.07e-02 8.73e+03 1.21e+01 ... (remaining 7152 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 8477 1.99 - 3.98: 1151 3.98 - 5.97: 108 5.97 - 7.95: 28 7.95 - 9.94: 8 Bond angle restraints: 9772 Sorted by residual: angle pdb=" N GLU F 68 " pdb=" CA GLU F 68 " pdb=" C GLU F 68 " ideal model delta sigma weight residual 111.28 103.47 7.81 1.09e+00 8.42e-01 5.14e+01 angle pdb=" N PRO F 14 " pdb=" CA PRO F 14 " pdb=" CB PRO F 14 " ideal model delta sigma weight residual 103.36 109.47 -6.11 8.80e-01 1.29e+00 4.82e+01 angle pdb=" N GLN F 206 " pdb=" CA GLN F 206 " pdb=" C GLN F 206 " ideal model delta sigma weight residual 111.28 104.43 6.85 1.09e+00 8.42e-01 3.95e+01 angle pdb=" C PRO F 66 " pdb=" CA PRO F 66 " pdb=" CB PRO F 66 " ideal model delta sigma weight residual 113.06 103.18 9.88 1.59e+00 3.96e-01 3.86e+01 angle pdb=" N PRO F 347 " pdb=" CA PRO F 347 " pdb=" CB PRO F 347 " ideal model delta sigma weight residual 103.38 109.80 -6.42 1.05e+00 9.07e-01 3.74e+01 ... (remaining 9767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 3835 17.85 - 35.69: 352 35.69 - 53.54: 88 53.54 - 71.39: 15 71.39 - 89.23: 4 Dihedral angle restraints: 4294 sinusoidal: 1517 harmonic: 2777 Sorted by residual: dihedral pdb=" CA GLU F 394 " pdb=" C GLU F 394 " pdb=" N ASN F 395 " pdb=" CA ASN F 395 " ideal model delta harmonic sigma weight residual 180.00 154.17 25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA CYS F 143 " pdb=" C CYS F 143 " pdb=" N GLN F 144 " pdb=" CA GLN F 144 " ideal model delta harmonic sigma weight residual -180.00 -154.47 -25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA VAL F 61 " pdb=" C VAL F 61 " pdb=" N LEU F 62 " pdb=" CA LEU F 62 " ideal model delta harmonic sigma weight residual -180.00 -155.11 -24.89 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 4291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 792 0.075 - 0.149: 271 0.149 - 0.224: 90 0.224 - 0.299: 17 0.299 - 0.373: 8 Chirality restraints: 1178 Sorted by residual: chirality pdb=" CA GLU F 836 " pdb=" N GLU F 836 " pdb=" C GLU F 836 " pdb=" CB GLU F 836 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA GLU F 69 " pdb=" N GLU F 69 " pdb=" C GLU F 69 " pdb=" CB GLU F 69 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CA GLN F 206 " pdb=" N GLN F 206 " pdb=" C GLN F 206 " pdb=" CB GLN F 206 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 1175 not shown) Planarity restraints: 1249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 719 " 0.055 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO F 720 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO F 720 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 720 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 35 " 0.013 2.00e-02 2.50e+03 2.73e-02 7.47e+00 pdb=" C CYS F 35 " -0.047 2.00e-02 2.50e+03 pdb=" O CYS F 35 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA F 36 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 160 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C PHE F 160 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE F 160 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE F 161 " -0.014 2.00e-02 2.50e+03 ... (remaining 1246 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1479 2.78 - 3.31: 6795 3.31 - 3.84: 10235 3.84 - 4.37: 11496 4.37 - 4.90: 18828 Nonbonded interactions: 48833 Sorted by model distance: nonbonded pdb=" O LEU F 149 " pdb=" N PHE F 152 " model vdw 2.245 3.120 nonbonded pdb=" N ASP F 850 " pdb=" OD1 ASP F 850 " model vdw 2.257 3.120 nonbonded pdb=" N GLU F 179 " pdb=" OE1 GLU F 179 " model vdw 2.297 3.120 nonbonded pdb=" O ARG G 207 " pdb=" OG1 THR G 211 " model vdw 2.322 3.040 nonbonded pdb=" O SER F 332 " pdb=" OG SER F 332 " model vdw 2.337 3.040 ... (remaining 48828 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.930 Find NCS groups from input model: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 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 : 0.010 0.061 7157 Z= 0.661 Angle : 1.370 9.943 9772 Z= 0.985 Chirality : 0.088 0.373 1178 Planarity : 0.007 0.083 1249 Dihedral : 15.201 89.233 2486 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.93 % Favored : 88.85 % Rotamer: Outliers : 3.18 % Allowed : 15.17 % Favored : 81.65 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.66 (0.22), residues: 933 helix: -2.92 (0.19), residues: 421 sheet: -2.74 (0.41), residues: 128 loop : -3.25 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 754 TYR 0.016 0.002 TYR G 130 PHE 0.016 0.002 PHE F 761 TRP 0.009 0.002 TRP G 121 HIS 0.006 0.001 HIS G 149 Details of bonding type rmsd covalent geometry : bond 0.00982 ( 7157) covalent geometry : angle 1.37043 ( 9772) hydrogen bonds : bond 0.24863 ( 253) hydrogen bonds : angle 8.74452 ( 744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 630 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6863 (m-80) outliers start: 22 outliers final: 7 residues processed: 149 average time/residue: 0.0895 time to fit residues: 17.5482 Evaluate side-chains 79 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 564 TYR Chi-restraints excluded: chain F residue 630 PHE Chi-restraints excluded: chain F residue 849 GLN Chi-restraints excluded: chain F residue 850 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.0270 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.0870 overall best weight: 2.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 GLN F 268 HIS F 395 ASN F 738 ASN F 782 ASN F 849 GLN F 859 ASN F 868 HIS G 147 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.063741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.056301 restraints weight = 60998.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.057295 restraints weight = 27585.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.057947 restraints weight = 15475.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.058360 restraints weight = 10126.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.058735 restraints weight = 7538.562| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7157 Z= 0.186 Angle : 0.763 10.864 9772 Z= 0.378 Chirality : 0.044 0.152 1178 Planarity : 0.005 0.064 1249 Dihedral : 6.895 62.833 1036 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.32 % Favored : 93.57 % Rotamer: Outliers : 4.62 % Allowed : 19.80 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.25), residues: 933 helix: -0.95 (0.23), residues: 448 sheet: -1.90 (0.46), residues: 126 loop : -3.02 (0.27), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 106 TYR 0.018 0.002 TYR G 130 PHE 0.019 0.002 PHE G 140 TRP 0.008 0.001 TRP G 121 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 7157) covalent geometry : angle 0.76258 ( 9772) hydrogen bonds : bond 0.04175 ( 253) hydrogen bonds : angle 5.41445 ( 744) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 48 PHE cc_start: 0.9644 (OUTLIER) cc_final: 0.9434 (m-10) REVERT: F 182 MET cc_start: 0.9229 (tpp) cc_final: 0.9005 (tpp) REVERT: F 291 LEU cc_start: 0.9672 (tp) cc_final: 0.9324 (tt) REVERT: F 616 GLU cc_start: 0.9244 (tt0) cc_final: 0.8727 (pt0) REVERT: F 791 LEU cc_start: 0.9732 (tt) cc_final: 0.9449 (pp) REVERT: F 849 GLN cc_start: 0.9682 (OUTLIER) cc_final: 0.9272 (mp10) REVERT: F 867 MET cc_start: 0.8876 (tpt) cc_final: 0.8245 (ptm) REVERT: G 157 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9166 (mt) REVERT: G 184 GLU cc_start: 0.9616 (tp30) cc_final: 0.9124 (tm-30) REVERT: G 189 CYS cc_start: 0.9248 (t) cc_final: 0.8983 (p) outliers start: 32 outliers final: 15 residues processed: 102 average time/residue: 0.0562 time to fit residues: 8.6959 Evaluate side-chains 81 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 564 TYR Chi-restraints excluded: chain F residue 581 TYR Chi-restraints excluded: chain F residue 630 PHE Chi-restraints excluded: chain F residue 798 LEU Chi-restraints excluded: chain F residue 849 GLN Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 147 ASN Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 230 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 79 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.060414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.053006 restraints weight = 61639.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.053983 restraints weight = 27771.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.054669 restraints weight = 15603.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.055061 restraints weight = 10107.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.055348 restraints weight = 7378.538| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7157 Z= 0.165 Angle : 0.728 13.737 9772 Z= 0.348 Chirality : 0.043 0.140 1178 Planarity : 0.004 0.055 1249 Dihedral : 6.137 57.989 1025 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.61 % Favored : 92.28 % Rotamer: Outliers : 5.35 % Allowed : 21.10 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.27), residues: 933 helix: -0.04 (0.24), residues: 457 sheet: -1.70 (0.47), residues: 128 loop : -2.70 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 106 TYR 0.012 0.001 TYR F 46 PHE 0.014 0.001 PHE G 140 TRP 0.011 0.002 TRP F 326 HIS 0.006 0.001 HIS G 146 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7157) covalent geometry : angle 0.72751 ( 9772) hydrogen bonds : bond 0.03733 ( 253) hydrogen bonds : angle 5.03314 ( 744) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 68 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 153 ARG cc_start: 0.9382 (OUTLIER) cc_final: 0.9134 (mmp-170) REVERT: F 291 LEU cc_start: 0.9720 (tp) cc_final: 0.9466 (tt) REVERT: F 686 VAL cc_start: 0.8989 (OUTLIER) cc_final: 0.8736 (p) REVERT: F 737 ASN cc_start: 0.9458 (m-40) cc_final: 0.9058 (m110) REVERT: F 798 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9330 (mm) REVERT: F 849 GLN cc_start: 0.9650 (OUTLIER) cc_final: 0.9290 (mp10) REVERT: F 867 MET cc_start: 0.8839 (tpt) cc_final: 0.8153 (ptm) REVERT: G 126 VAL cc_start: 0.7677 (OUTLIER) cc_final: 0.7459 (p) REVERT: G 157 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9244 (mt) REVERT: G 184 GLU cc_start: 0.9731 (tp30) cc_final: 0.9282 (tm-30) REVERT: G 203 GLU cc_start: 0.9443 (tp30) cc_final: 0.9171 (tp30) REVERT: G 215 TYR cc_start: 0.8512 (m-80) cc_final: 0.8197 (m-80) outliers start: 37 outliers final: 16 residues processed: 99 average time/residue: 0.0615 time to fit residues: 9.0069 Evaluate side-chains 84 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 581 TYR Chi-restraints excluded: chain F residue 630 PHE Chi-restraints excluded: chain F residue 686 VAL Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 745 CYS Chi-restraints excluded: chain F residue 798 LEU Chi-restraints excluded: chain F residue 805 SER Chi-restraints excluded: chain F residue 849 GLN Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 147 ASN Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 230 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 27 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 34 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS G 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.059616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.052268 restraints weight = 62966.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.053274 restraints weight = 27991.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.053881 restraints weight = 15645.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.054340 restraints weight = 10228.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.054577 restraints weight = 7368.417| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7157 Z= 0.134 Angle : 0.690 13.887 9772 Z= 0.322 Chirality : 0.042 0.174 1178 Planarity : 0.004 0.045 1249 Dihedral : 5.558 57.386 1023 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.00 % Favored : 93.89 % Rotamer: Outliers : 4.34 % Allowed : 23.55 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.27), residues: 933 helix: 0.40 (0.24), residues: 465 sheet: -1.60 (0.49), residues: 119 loop : -2.39 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 689 TYR 0.011 0.001 TYR F 564 PHE 0.009 0.001 PHE F 171 TRP 0.011 0.001 TRP F 802 HIS 0.003 0.001 HIS F 555 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7157) covalent geometry : angle 0.69018 ( 9772) hydrogen bonds : bond 0.03140 ( 253) hydrogen bonds : angle 4.72231 ( 744) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 145 GLU cc_start: 0.9544 (OUTLIER) cc_final: 0.9090 (pm20) REVERT: F 291 LEU cc_start: 0.9762 (tp) cc_final: 0.9506 (tp) REVERT: F 564 TYR cc_start: 0.7746 (t80) cc_final: 0.7494 (t80) REVERT: F 737 ASN cc_start: 0.9493 (m-40) cc_final: 0.9133 (m110) REVERT: F 798 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9332 (mm) REVERT: F 849 GLN cc_start: 0.9562 (OUTLIER) cc_final: 0.9269 (mp10) REVERT: F 867 MET cc_start: 0.8852 (tpt) cc_final: 0.8195 (ptm) REVERT: G 157 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9262 (mt) REVERT: G 184 GLU cc_start: 0.9776 (tp30) cc_final: 0.9352 (tm-30) REVERT: G 215 TYR cc_start: 0.8390 (m-80) cc_final: 0.7927 (m-80) outliers start: 30 outliers final: 15 residues processed: 93 average time/residue: 0.0616 time to fit residues: 8.4396 Evaluate side-chains 81 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 581 TYR Chi-restraints excluded: chain F residue 630 PHE Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 798 LEU Chi-restraints excluded: chain F residue 849 GLN Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 230 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 8 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 51 optimal weight: 0.0050 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 47 HIS ** F 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 GLN F 571 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.060651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.053280 restraints weight = 62488.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.054275 restraints weight = 27876.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.054963 restraints weight = 15663.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.055344 restraints weight = 10067.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.055601 restraints weight = 7368.430| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7157 Z= 0.097 Angle : 0.655 12.075 9772 Z= 0.298 Chirality : 0.042 0.148 1178 Planarity : 0.004 0.048 1249 Dihedral : 5.147 57.317 1023 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.32 % Favored : 93.57 % Rotamer: Outliers : 4.48 % Allowed : 23.99 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.28), residues: 933 helix: 0.77 (0.25), residues: 463 sheet: -1.38 (0.49), residues: 119 loop : -2.10 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 106 TYR 0.008 0.001 TYR F 716 PHE 0.008 0.001 PHE F 171 TRP 0.009 0.001 TRP F 381 HIS 0.002 0.000 HIS F 555 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 7157) covalent geometry : angle 0.65518 ( 9772) hydrogen bonds : bond 0.02906 ( 253) hydrogen bonds : angle 4.54233 ( 744) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 73 ILE cc_start: 0.9904 (OUTLIER) cc_final: 0.9661 (tp) REVERT: F 76 LEU cc_start: 0.9887 (tt) cc_final: 0.9685 (pp) REVERT: F 145 GLU cc_start: 0.9550 (OUTLIER) cc_final: 0.9106 (pm20) REVERT: F 153 ARG cc_start: 0.9431 (OUTLIER) cc_final: 0.9052 (mmm160) REVERT: F 291 LEU cc_start: 0.9785 (tp) cc_final: 0.9540 (tp) REVERT: F 737 ASN cc_start: 0.9494 (m-40) cc_final: 0.9160 (m110) REVERT: F 798 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9274 (mm) REVERT: F 849 GLN cc_start: 0.9547 (OUTLIER) cc_final: 0.9270 (mp10) REVERT: F 867 MET cc_start: 0.8801 (tpt) cc_final: 0.8103 (ptm) REVERT: G 126 VAL cc_start: 0.7663 (OUTLIER) cc_final: 0.7406 (p) REVERT: G 157 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9224 (mt) REVERT: G 184 GLU cc_start: 0.9796 (tp30) cc_final: 0.9504 (tm-30) REVERT: G 189 CYS cc_start: 0.9405 (p) cc_final: 0.9155 (t) REVERT: G 215 TYR cc_start: 0.8317 (m-80) cc_final: 0.7855 (m-80) outliers start: 31 outliers final: 15 residues processed: 101 average time/residue: 0.0675 time to fit residues: 9.8308 Evaluate side-chains 89 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 581 TYR Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 630 PHE Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 798 LEU Chi-restraints excluded: chain F residue 849 GLN Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 230 ASP Chi-restraints excluded: chain G residue 239 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 66 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 85 optimal weight: 0.0470 chunk 87 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 ASN ** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.034897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.026203 restraints weight = 58658.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.027012 restraints weight = 36913.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.027554 restraints weight = 26692.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.027998 restraints weight = 21355.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.028344 restraints weight = 17773.639| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.6351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7157 Z= 0.146 Angle : 0.680 10.971 9772 Z= 0.320 Chirality : 0.042 0.149 1178 Planarity : 0.004 0.043 1249 Dihedral : 5.258 56.323 1023 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.32 % Favored : 93.57 % Rotamer: Outliers : 4.77 % Allowed : 23.70 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.28), residues: 933 helix: 0.80 (0.24), residues: 474 sheet: -1.38 (0.48), residues: 119 loop : -1.88 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 689 TYR 0.010 0.002 TYR F 594 PHE 0.020 0.001 PHE G 115 TRP 0.010 0.001 TRP F 802 HIS 0.003 0.001 HIS G 146 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7157) covalent geometry : angle 0.68022 ( 9772) hydrogen bonds : bond 0.03036 ( 253) hydrogen bonds : angle 4.63400 ( 744) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 65 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 153 ARG cc_start: 0.9507 (OUTLIER) cc_final: 0.9167 (mmm160) REVERT: F 161 ILE cc_start: 0.9722 (OUTLIER) cc_final: 0.9303 (mm) REVERT: F 291 LEU cc_start: 0.9820 (tp) cc_final: 0.9563 (tp) REVERT: F 688 MET cc_start: 0.9139 (mmt) cc_final: 0.8879 (mpp) REVERT: F 737 ASN cc_start: 0.9532 (m-40) cc_final: 0.9187 (m110) REVERT: F 798 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9234 (mm) REVERT: F 849 GLN cc_start: 0.9607 (OUTLIER) cc_final: 0.9175 (mp10) REVERT: F 867 MET cc_start: 0.8734 (tpt) cc_final: 0.8089 (ptm) REVERT: G 126 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8232 (p) REVERT: G 157 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9328 (mt) REVERT: G 184 GLU cc_start: 0.9721 (tp30) cc_final: 0.9450 (tm-30) REVERT: G 215 TYR cc_start: 0.8439 (m-80) cc_final: 0.7929 (m-80) outliers start: 33 outliers final: 18 residues processed: 92 average time/residue: 0.0661 time to fit residues: 8.8300 Evaluate side-chains 83 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 581 TYR Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 630 PHE Chi-restraints excluded: chain F residue 709 VAL Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 798 LEU Chi-restraints excluded: chain F residue 849 GLN Chi-restraints excluded: chain F residue 858 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 230 ASP Chi-restraints excluded: chain G residue 239 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 18 optimal weight: 0.0770 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 overall best weight: 0.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 74 ASN ** F 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.059038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.051663 restraints weight = 62993.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.052628 restraints weight = 28122.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.053303 restraints weight = 15765.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.053701 restraints weight = 10198.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.054016 restraints weight = 7410.250| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.6578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7157 Z= 0.094 Angle : 0.672 12.067 9772 Z= 0.300 Chirality : 0.042 0.143 1178 Planarity : 0.004 0.049 1249 Dihedral : 4.939 56.114 1023 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.57 % Favored : 94.32 % Rotamer: Outliers : 4.77 % Allowed : 23.41 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.28), residues: 933 helix: 0.95 (0.25), residues: 470 sheet: -1.25 (0.48), residues: 119 loop : -2.00 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 342 TYR 0.013 0.001 TYR F 564 PHE 0.020 0.001 PHE G 115 TRP 0.010 0.001 TRP F 381 HIS 0.002 0.000 HIS F 555 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 7157) covalent geometry : angle 0.67187 ( 9772) hydrogen bonds : bond 0.02720 ( 253) hydrogen bonds : angle 4.40492 ( 744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 145 GLU cc_start: 0.9550 (OUTLIER) cc_final: 0.9203 (pm20) REVERT: F 153 ARG cc_start: 0.9417 (OUTLIER) cc_final: 0.9053 (mmm160) REVERT: F 161 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.8992 (mm) REVERT: F 291 LEU cc_start: 0.9842 (tp) cc_final: 0.9634 (tp) REVERT: F 737 ASN cc_start: 0.9466 (m-40) cc_final: 0.9126 (m110) REVERT: F 798 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9224 (mm) REVERT: F 849 GLN cc_start: 0.9582 (OUTLIER) cc_final: 0.9166 (mp10) REVERT: F 867 MET cc_start: 0.8759 (tpt) cc_final: 0.8121 (ptm) REVERT: G 126 VAL cc_start: 0.7897 (OUTLIER) cc_final: 0.7553 (p) REVERT: G 151 ASP cc_start: 0.9699 (m-30) cc_final: 0.9403 (p0) REVERT: G 157 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9269 (mt) REVERT: G 184 GLU cc_start: 0.9831 (tp30) cc_final: 0.9562 (tm-30) REVERT: G 215 TYR cc_start: 0.8307 (m-80) cc_final: 0.7868 (m-80) outliers start: 33 outliers final: 20 residues processed: 96 average time/residue: 0.0630 time to fit residues: 8.8441 Evaluate side-chains 92 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 581 TYR Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 630 PHE Chi-restraints excluded: chain F residue 634 ILE Chi-restraints excluded: chain F residue 709 VAL Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 798 LEU Chi-restraints excluded: chain F residue 803 CYS Chi-restraints excluded: chain F residue 849 GLN Chi-restraints excluded: chain F residue 858 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 230 ASP Chi-restraints excluded: chain G residue 239 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 14 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 849 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.035420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.026932 restraints weight = 68400.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.027744 restraints weight = 42573.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.028339 restraints weight = 30691.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.028757 restraints weight = 24092.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.028994 restraints weight = 20183.774| |-----------------------------------------------------------------------------| r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.6919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7157 Z= 0.136 Angle : 0.678 13.746 9772 Z= 0.314 Chirality : 0.042 0.143 1178 Planarity : 0.004 0.050 1249 Dihedral : 4.976 55.613 1023 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.89 % Favored : 94.00 % Rotamer: Outliers : 3.90 % Allowed : 24.57 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.28), residues: 933 helix: 0.96 (0.24), residues: 469 sheet: -1.28 (0.47), residues: 117 loop : -1.89 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 342 TYR 0.014 0.001 TYR G 130 PHE 0.013 0.001 PHE F 431 TRP 0.010 0.001 TRP F 326 HIS 0.003 0.001 HIS F 700 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7157) covalent geometry : angle 0.67815 ( 9772) hydrogen bonds : bond 0.02900 ( 253) hydrogen bonds : angle 4.55239 ( 744) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 10 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8676 (pp) REVERT: F 145 GLU cc_start: 0.9509 (OUTLIER) cc_final: 0.9022 (pm20) REVERT: F 153 ARG cc_start: 0.9511 (OUTLIER) cc_final: 0.9242 (mmm160) REVERT: F 161 ILE cc_start: 0.9711 (OUTLIER) cc_final: 0.9307 (mm) REVERT: F 291 LEU cc_start: 0.9845 (tp) cc_final: 0.9616 (tp) REVERT: F 722 MET cc_start: 0.9328 (mmm) cc_final: 0.8968 (mmm) REVERT: F 737 ASN cc_start: 0.9572 (m-40) cc_final: 0.9271 (m110) REVERT: F 798 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9214 (mm) REVERT: G 126 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8240 (p) REVERT: G 157 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9329 (mt) REVERT: G 184 GLU cc_start: 0.9733 (tp30) cc_final: 0.9481 (tm-30) REVERT: G 215 TYR cc_start: 0.8571 (m-80) cc_final: 0.8109 (m-80) outliers start: 27 outliers final: 17 residues processed: 82 average time/residue: 0.0649 time to fit residues: 7.7612 Evaluate side-chains 82 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 581 TYR Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 630 PHE Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 798 LEU Chi-restraints excluded: chain F residue 803 CYS Chi-restraints excluded: chain F residue 858 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 230 ASP Chi-restraints excluded: chain G residue 239 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 4 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.033918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.025453 restraints weight = 60090.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.026198 restraints weight = 38050.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.026741 restraints weight = 27768.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.027131 restraints weight = 22068.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.027434 restraints weight = 18582.846| |-----------------------------------------------------------------------------| r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.7451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7157 Z= 0.146 Angle : 0.667 11.404 9772 Z= 0.314 Chirality : 0.042 0.199 1178 Planarity : 0.004 0.047 1249 Dihedral : 4.667 54.969 1020 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.32 % Favored : 93.57 % Rotamer: Outliers : 4.91 % Allowed : 23.84 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.28), residues: 933 helix: 0.87 (0.24), residues: 476 sheet: -1.35 (0.47), residues: 113 loop : -1.81 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 689 TYR 0.010 0.001 TYR F 594 PHE 0.024 0.001 PHE G 115 TRP 0.012 0.001 TRP F 381 HIS 0.003 0.001 HIS F 555 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7157) covalent geometry : angle 0.66727 ( 9772) hydrogen bonds : bond 0.02948 ( 253) hydrogen bonds : angle 4.60118 ( 744) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 61 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 145 GLU cc_start: 0.9564 (OUTLIER) cc_final: 0.8874 (pm20) REVERT: F 153 ARG cc_start: 0.9504 (OUTLIER) cc_final: 0.9179 (mmm160) REVERT: F 161 ILE cc_start: 0.9681 (OUTLIER) cc_final: 0.9254 (mm) REVERT: F 291 LEU cc_start: 0.9880 (tp) cc_final: 0.9656 (tp) REVERT: F 326 TRP cc_start: 0.8739 (m-10) cc_final: 0.8527 (m100) REVERT: F 722 MET cc_start: 0.9475 (mmm) cc_final: 0.9053 (mmm) REVERT: F 798 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9199 (mm) REVERT: G 126 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8446 (p) REVERT: G 140 PHE cc_start: 0.9433 (t80) cc_final: 0.9219 (t80) REVERT: G 184 GLU cc_start: 0.9754 (tp30) cc_final: 0.9491 (tm-30) REVERT: G 215 TYR cc_start: 0.8608 (m-80) cc_final: 0.8145 (m-80) outliers start: 34 outliers final: 24 residues processed: 89 average time/residue: 0.0658 time to fit residues: 8.6515 Evaluate side-chains 85 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 56 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 564 TYR Chi-restraints excluded: chain F residue 581 TYR Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 630 PHE Chi-restraints excluded: chain F residue 634 ILE Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 758 LEU Chi-restraints excluded: chain F residue 798 LEU Chi-restraints excluded: chain F residue 803 CYS Chi-restraints excluded: chain F residue 805 SER Chi-restraints excluded: chain F residue 858 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 230 ASP Chi-restraints excluded: chain G residue 239 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 57 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 30 optimal weight: 0.0570 chunk 26 optimal weight: 0.0370 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.034801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.026070 restraints weight = 56722.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.026836 restraints weight = 36146.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.027415 restraints weight = 26415.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.027832 restraints weight = 20980.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.028151 restraints weight = 17648.278| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.7539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7157 Z= 0.100 Angle : 0.707 17.973 9772 Z= 0.312 Chirality : 0.042 0.185 1178 Planarity : 0.004 0.050 1249 Dihedral : 4.431 55.596 1020 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.93 % Favored : 94.96 % Rotamer: Outliers : 3.47 % Allowed : 25.58 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.28), residues: 933 helix: 1.01 (0.25), residues: 471 sheet: -1.28 (0.47), residues: 115 loop : -1.89 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 342 TYR 0.016 0.001 TYR G 130 PHE 0.010 0.001 PHE G 115 TRP 0.011 0.001 TRP F 381 HIS 0.002 0.000 HIS F 555 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 7157) covalent geometry : angle 0.70668 ( 9772) hydrogen bonds : bond 0.02816 ( 253) hydrogen bonds : angle 4.45081 ( 744) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 145 GLU cc_start: 0.9523 (OUTLIER) cc_final: 0.9029 (pm20) REVERT: F 153 ARG cc_start: 0.9463 (OUTLIER) cc_final: 0.9234 (mmm160) REVERT: F 161 ILE cc_start: 0.9667 (OUTLIER) cc_final: 0.9217 (mm) REVERT: F 291 LEU cc_start: 0.9869 (tp) cc_final: 0.9554 (tp) REVERT: F 616 GLU cc_start: 0.9468 (tt0) cc_final: 0.9125 (pt0) REVERT: F 722 MET cc_start: 0.9354 (mmm) cc_final: 0.8990 (mmm) REVERT: F 798 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9145 (mm) REVERT: G 126 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8418 (p) REVERT: G 184 GLU cc_start: 0.9740 (tp30) cc_final: 0.9480 (tm-30) REVERT: G 215 TYR cc_start: 0.8521 (m-80) cc_final: 0.8041 (m-80) outliers start: 24 outliers final: 16 residues processed: 82 average time/residue: 0.0627 time to fit residues: 7.5759 Evaluate side-chains 79 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 581 TYR Chi-restraints excluded: chain F residue 603 LEU Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 758 LEU Chi-restraints excluded: chain F residue 798 LEU Chi-restraints excluded: chain F residue 803 CYS Chi-restraints excluded: chain F residue 858 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 230 ASP Chi-restraints excluded: chain G residue 239 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 1 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 17 optimal weight: 0.0970 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 27 optimal weight: 0.0870 chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.0158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.034506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.025891 restraints weight = 59698.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.026679 restraints weight = 37414.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.027251 restraints weight = 27156.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.027677 restraints weight = 21338.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.028005 restraints weight = 17808.507| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.7732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7157 Z= 0.106 Angle : 0.715 16.365 9772 Z= 0.318 Chirality : 0.042 0.166 1178 Planarity : 0.004 0.050 1249 Dihedral : 3.982 17.612 1018 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.36 % Favored : 94.53 % Rotamer: Outliers : 3.76 % Allowed : 25.72 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.28), residues: 933 helix: 0.84 (0.25), residues: 485 sheet: -1.21 (0.47), residues: 115 loop : -1.71 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 342 TYR 0.016 0.001 TYR G 130 PHE 0.014 0.001 PHE F 630 TRP 0.035 0.002 TRP F 326 HIS 0.002 0.000 HIS F 555 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 7157) covalent geometry : angle 0.71464 ( 9772) hydrogen bonds : bond 0.02757 ( 253) hydrogen bonds : angle 4.46229 ( 744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1231.50 seconds wall clock time: 21 minutes 54.66 seconds (1314.66 seconds total)