Starting phenix.real_space_refine on Fri Jul 25 03:59:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sxa_10337/07_2025/6sxa_10337.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sxa_10337/07_2025/6sxa_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6sxa_10337/07_2025/6sxa_10337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sxa_10337/07_2025/6sxa_10337.map" model { file = "/net/cci-nas-00/data/ceres_data/6sxa_10337/07_2025/6sxa_10337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sxa_10337/07_2025/6sxa_10337.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 27, 'ARG:plan': 6} 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: {'GLN:plan1': 5, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 98 Time building chain proxies: 4.44, per 1000 atoms: 0.63 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: 1.80 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.88 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: 1.90 Time building geometry restraints manager: 2.14 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: 0.450 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.710 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.430 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.002 TRP G 121 HIS 0.006 0.001 HIS G 149 PHE 0.016 0.002 PHE F 761 TYR 0.016 0.002 TYR G 130 ARG 0.006 0.000 ARG F 754 Details of bonding type rmsd hydrogen bonds : bond 0.24863 ( 253) hydrogen bonds : angle 8.74452 ( 744) covalent geometry : bond 0.00982 ( 7157) covalent geometry : angle 1.37043 ( 9772) *********************** 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 : 0.802 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: 0.1996 time to fit residues: 39.0818 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 : 0.823 ------------------------------------------------------------------------------- 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 78 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.063776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.056348 restraints weight = 60178.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.057334 restraints weight = 27284.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.058075 restraints weight = 15326.913| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7157 Z= 0.184 Angle : 0.765 10.897 9772 Z= 0.379 Chirality : 0.044 0.154 1178 Planarity : 0.005 0.064 1249 Dihedral : 6.881 62.616 1036 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.32 % Favored : 93.57 % Rotamer: Outliers : 4.48 % Allowed : 19.51 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.25), residues: 933 helix: -0.93 (0.23), residues: 447 sheet: -1.90 (0.46), residues: 126 loop : -3.02 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 121 HIS 0.005 0.001 HIS F 137 PHE 0.019 0.002 PHE G 140 TYR 0.017 0.002 TYR G 130 ARG 0.007 0.001 ARG F 340 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 253) hydrogen bonds : angle 5.39362 ( 744) covalent geometry : bond 0.00378 ( 7157) covalent geometry : angle 0.76515 ( 9772) *********************** 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: 31 poor density : 77 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 182 MET cc_start: 0.9273 (tpp) cc_final: 0.9065 (tpp) REVERT: F 291 LEU cc_start: 0.9672 (tp) cc_final: 0.9331 (tt) REVERT: F 616 GLU cc_start: 0.9254 (tt0) cc_final: 0.8740 (pt0) REVERT: F 791 LEU cc_start: 0.9759 (tt) cc_final: 0.9495 (pp) REVERT: F 849 GLN cc_start: 0.9690 (OUTLIER) cc_final: 0.9325 (mp10) REVERT: F 867 MET cc_start: 0.8869 (tpt) cc_final: 0.8252 (ptm) REVERT: G 157 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9146 (mt) REVERT: G 184 GLU cc_start: 0.9636 (tp30) cc_final: 0.9153 (tm-30) outliers start: 31 outliers final: 12 residues processed: 101 average time/residue: 0.1372 time to fit residues: 20.8459 Evaluate side-chains 75 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 231 ASP 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 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 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 67 optimal weight: 7.9990 chunk 68 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 60 optimal weight: 0.0030 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 86 optimal weight: 0.9980 overall best weight: 0.4190 ------------------------------------------------------------------------------- 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 F 286 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.038957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.029386 restraints weight = 53849.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.030289 restraints weight = 34586.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.030940 restraints weight = 25203.774| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7157 Z= 0.106 Angle : 0.719 13.624 9772 Z= 0.329 Chirality : 0.043 0.143 1178 Planarity : 0.004 0.057 1249 Dihedral : 5.768 59.565 1023 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.86 % Favored : 93.03 % Rotamer: Outliers : 4.19 % Allowed : 21.39 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.27), residues: 933 helix: -0.29 (0.24), residues: 460 sheet: -1.33 (0.50), residues: 124 loop : -2.71 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 326 HIS 0.005 0.001 HIS G 146 PHE 0.013 0.001 PHE G 140 TYR 0.009 0.001 TYR F 71 ARG 0.005 0.000 ARG G 106 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 253) hydrogen bonds : angle 4.77107 ( 744) covalent geometry : bond 0.00224 ( 7157) covalent geometry : angle 0.71910 ( 9772) *********************** 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 101 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 153 ARG cc_start: 0.9396 (OUTLIER) cc_final: 0.9096 (tpp-160) REVERT: F 182 MET cc_start: 0.8937 (tpp) cc_final: 0.8611 (tpp) REVERT: F 291 LEU cc_start: 0.9598 (tp) cc_final: 0.9236 (tp) REVERT: F 798 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9101 (mm) REVERT: F 849 GLN cc_start: 0.9641 (OUTLIER) cc_final: 0.9241 (mp10) REVERT: F 867 MET cc_start: 0.8678 (tpt) cc_final: 0.8001 (ptm) REVERT: G 126 VAL cc_start: 0.7932 (OUTLIER) cc_final: 0.7581 (p) REVERT: G 184 GLU cc_start: 0.9556 (tp30) cc_final: 0.9040 (tm-30) REVERT: G 203 GLU cc_start: 0.9469 (tp30) cc_final: 0.9086 (tp30) outliers start: 29 outliers final: 12 residues processed: 98 average time/residue: 0.1457 time to fit residues: 20.9290 Evaluate side-chains 82 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 581 TYR Chi-restraints excluded: chain F residue 630 PHE 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 849 GLN Chi-restraints excluded: chain G residue 126 VAL 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 58 optimal weight: 0.0980 chunk 48 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.037498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.028585 restraints weight = 65644.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.029461 restraints weight = 41955.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.030092 restraints weight = 30346.031| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7157 Z= 0.136 Angle : 0.673 13.386 9772 Z= 0.317 Chirality : 0.042 0.156 1178 Planarity : 0.004 0.053 1249 Dihedral : 5.460 58.368 1023 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.00 % Favored : 93.89 % Rotamer: Outliers : 4.19 % Allowed : 22.69 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.27), residues: 933 helix: 0.28 (0.24), residues: 462 sheet: -1.65 (0.49), residues: 121 loop : -2.33 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 326 HIS 0.003 0.001 HIS F 555 PHE 0.016 0.001 PHE F 152 TYR 0.014 0.002 TYR F 564 ARG 0.005 0.000 ARG G 106 Details of bonding type rmsd hydrogen bonds : bond 0.03223 ( 253) hydrogen bonds : angle 4.69238 ( 744) covalent geometry : bond 0.00286 ( 7157) covalent geometry : angle 0.67304 ( 9772) *********************** 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 95 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 10 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8091 (pt) REVERT: F 153 ARG cc_start: 0.9488 (OUTLIER) cc_final: 0.9093 (mmm160) REVERT: F 182 MET cc_start: 0.9055 (tpp) cc_final: 0.8852 (tpp) REVERT: F 291 LEU cc_start: 0.9746 (tp) cc_final: 0.9501 (tt) REVERT: F 737 ASN cc_start: 0.9520 (m-40) cc_final: 0.9124 (m110) REVERT: F 798 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9248 (mm) REVERT: F 849 GLN cc_start: 0.9596 (OUTLIER) cc_final: 0.9274 (mp10) REVERT: F 867 MET cc_start: 0.8719 (tpt) cc_final: 0.8020 (ptm) REVERT: G 184 GLU cc_start: 0.9636 (tp30) cc_final: 0.9132 (tm-30) REVERT: G 189 CYS cc_start: 0.9366 (t) cc_final: 0.9008 (p) outliers start: 29 outliers final: 15 residues processed: 87 average time/residue: 0.1439 time to fit residues: 18.5647 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 : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 ILE 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 719 THR Chi-restraints excluded: chain F residue 748 MET Chi-restraints excluded: chain F residue 798 LEU Chi-restraints excluded: chain F residue 849 GLN Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 153 ILE 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 44 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 262 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 = 0.2929 r_free = 0.2929 target = 0.035541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.027086 restraints weight = 68193.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.027923 restraints weight = 42418.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.028525 restraints weight = 30406.672| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.6116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7157 Z= 0.190 Angle : 0.708 15.041 9772 Z= 0.341 Chirality : 0.043 0.175 1178 Planarity : 0.004 0.049 1249 Dihedral : 5.311 56.209 1023 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.07 % Favored : 92.82 % Rotamer: Outliers : 4.91 % Allowed : 21.97 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.27), residues: 933 helix: 0.47 (0.24), residues: 463 sheet: -1.62 (0.48), residues: 116 loop : -2.04 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 326 HIS 0.004 0.001 HIS F 555 PHE 0.011 0.001 PHE F 152 TYR 0.012 0.002 TYR G 212 ARG 0.004 0.001 ARG F 689 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 253) hydrogen bonds : angle 4.67587 ( 744) covalent geometry : bond 0.00386 ( 7157) covalent geometry : angle 0.70758 ( 9772) *********************** 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 100 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 66 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 182 MET cc_start: 0.8881 (tpp) cc_final: 0.8486 (tpp) REVERT: F 291 LEU cc_start: 0.9798 (tp) cc_final: 0.9557 (tt) REVERT: F 737 ASN cc_start: 0.9546 (m-40) cc_final: 0.9218 (m110) REVERT: F 798 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9246 (mm) REVERT: F 849 GLN cc_start: 0.9599 (OUTLIER) cc_final: 0.9304 (mp10) REVERT: F 867 MET cc_start: 0.8733 (tpt) cc_final: 0.8076 (ptm) REVERT: G 126 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8126 (p) REVERT: G 184 GLU cc_start: 0.9699 (tp30) cc_final: 0.9319 (tm-30) REVERT: G 189 CYS cc_start: 0.9474 (t) cc_final: 0.9153 (p) REVERT: G 212 TYR cc_start: 0.9412 (OUTLIER) cc_final: 0.9079 (m-80) outliers start: 34 outliers final: 18 residues processed: 90 average time/residue: 0.1386 time to fit residues: 18.8287 Evaluate side-chains 85 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 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 849 GLN Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 153 ILE 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 212 TYR 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 82 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 45 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 0.0170 chunk 78 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- 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 571 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.059215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.051911 restraints weight = 63397.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.052885 restraints weight = 28270.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.053572 restraints weight = 15782.303| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.6349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7157 Z= 0.099 Angle : 0.662 11.166 9772 Z= 0.303 Chirality : 0.043 0.266 1178 Planarity : 0.004 0.045 1249 Dihedral : 5.014 57.082 1023 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.68 % Favored : 94.21 % Rotamer: Outliers : 4.05 % Allowed : 23.70 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.28), residues: 933 helix: 0.68 (0.25), residues: 465 sheet: -1.31 (0.49), residues: 116 loop : -1.93 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 326 HIS 0.003 0.000 HIS F 52 PHE 0.018 0.001 PHE G 115 TYR 0.017 0.001 TYR F 564 ARG 0.003 0.000 ARG F 342 Details of bonding type rmsd hydrogen bonds : bond 0.02915 ( 253) hydrogen bonds : angle 4.46865 ( 744) covalent geometry : bond 0.00218 ( 7157) covalent geometry : angle 0.66208 ( 9772) *********************** 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: 28 poor density : 70 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 153 ARG cc_start: 0.9413 (OUTLIER) cc_final: 0.9074 (mmm160) REVERT: F 182 MET cc_start: 0.9021 (tpp) cc_final: 0.8652 (tpp) REVERT: F 291 LEU cc_start: 0.9833 (tp) cc_final: 0.9620 (tp) REVERT: F 737 ASN cc_start: 0.9490 (m-40) cc_final: 0.9159 (m110) REVERT: F 798 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9284 (mm) REVERT: F 849 GLN cc_start: 0.9557 (OUTLIER) cc_final: 0.9200 (mp10) REVERT: F 867 MET cc_start: 0.8794 (tpt) cc_final: 0.8149 (ptm) REVERT: G 126 VAL cc_start: 0.7807 (OUTLIER) cc_final: 0.7556 (p) REVERT: G 184 GLU cc_start: 0.9840 (tp30) cc_final: 0.9483 (tm-30) REVERT: G 212 TYR cc_start: 0.9722 (OUTLIER) cc_final: 0.9374 (m-80) outliers start: 28 outliers final: 16 residues processed: 90 average time/residue: 0.1551 time to fit residues: 19.9950 Evaluate side-chains 85 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 62 LEU 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 285 VAL Chi-restraints excluded: chain F residue 581 TYR 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 849 GLN Chi-restraints excluded: chain G residue 126 VAL 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 212 TYR 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 20 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 47 optimal weight: 0.0970 chunk 39 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 849 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.059315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.051987 restraints weight = 62428.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.052948 restraints weight = 27955.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.053636 restraints weight = 15777.739| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.6568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7157 Z= 0.097 Angle : 0.679 13.693 9772 Z= 0.305 Chirality : 0.042 0.237 1178 Planarity : 0.004 0.057 1249 Dihedral : 4.785 56.907 1022 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.68 % Favored : 94.21 % Rotamer: Outliers : 3.90 % Allowed : 23.84 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.28), residues: 933 helix: 0.71 (0.25), residues: 473 sheet: -0.95 (0.49), residues: 121 loop : -1.96 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP F 326 HIS 0.003 0.000 HIS F 555 PHE 0.020 0.001 PHE G 115 TYR 0.019 0.001 TYR F 564 ARG 0.007 0.000 ARG F 689 Details of bonding type rmsd hydrogen bonds : bond 0.02649 ( 253) hydrogen bonds : angle 4.41539 ( 744) covalent geometry : bond 0.00219 ( 7157) covalent geometry : angle 0.67858 ( 9772) *********************** 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 94 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 153 ARG cc_start: 0.9417 (OUTLIER) cc_final: 0.9008 (mmm160) REVERT: F 182 MET cc_start: 0.9016 (tpp) cc_final: 0.8611 (tpp) REVERT: F 291 LEU cc_start: 0.9840 (tp) cc_final: 0.9630 (tp) REVERT: F 737 ASN cc_start: 0.9469 (m-40) cc_final: 0.9132 (m110) REVERT: F 798 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9236 (mm) REVERT: G 126 VAL cc_start: 0.7718 (OUTLIER) cc_final: 0.7403 (p) REVERT: G 151 ASP cc_start: 0.9685 (m-30) cc_final: 0.9335 (p0) REVERT: G 184 GLU cc_start: 0.9848 (tp30) cc_final: 0.9497 (tm-30) REVERT: G 212 TYR cc_start: 0.9729 (OUTLIER) cc_final: 0.9369 (m-80) outliers start: 27 outliers final: 13 residues processed: 89 average time/residue: 0.1520 time to fit residues: 19.8725 Evaluate side-chains 82 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 60 LEU 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 581 TYR 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 858 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 212 TYR 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 58 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 0.0270 chunk 32 optimal weight: 0.8980 chunk 57 optimal weight: 0.0270 chunk 6 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 84 optimal weight: 0.0980 overall best weight: 0.3496 ------------------------------------------------------------------------------- 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 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.036269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.027107 restraints weight = 54648.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.027955 restraints weight = 35086.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.028584 restraints weight = 25643.765| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.6784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7157 Z= 0.092 Angle : 0.670 10.198 9772 Z= 0.298 Chirality : 0.042 0.217 1178 Planarity : 0.004 0.046 1249 Dihedral : 4.311 56.202 1019 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.47 % Favored : 94.43 % Rotamer: Outliers : 3.03 % Allowed : 23.84 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.28), residues: 933 helix: 0.80 (0.25), residues: 467 sheet: -1.15 (0.49), residues: 117 loop : -1.70 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 326 HIS 0.002 0.000 HIS F 555 PHE 0.011 0.001 PHE F 431 TYR 0.013 0.001 TYR G 130 ARG 0.010 0.000 ARG F 689 Details of bonding type rmsd hydrogen bonds : bond 0.02565 ( 253) hydrogen bonds : angle 4.25980 ( 744) covalent geometry : bond 0.00207 ( 7157) covalent geometry : angle 0.67031 ( 9772) *********************** 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 88 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 153 ARG cc_start: 0.9404 (OUTLIER) cc_final: 0.9037 (mmm160) REVERT: F 182 MET cc_start: 0.8939 (tpp) cc_final: 0.8503 (tpp) REVERT: F 291 LEU cc_start: 0.9827 (tp) cc_final: 0.9614 (tp) REVERT: F 737 ASN cc_start: 0.9477 (m-40) cc_final: 0.9086 (m110) REVERT: F 798 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9065 (mm) REVERT: G 126 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8292 (p) REVERT: G 151 ASP cc_start: 0.9391 (m-30) cc_final: 0.9092 (p0) REVERT: G 184 GLU cc_start: 0.9705 (tp30) cc_final: 0.9362 (tm-30) REVERT: G 212 TYR cc_start: 0.9414 (OUTLIER) cc_final: 0.9048 (m-80) outliers start: 21 outliers final: 11 residues processed: 84 average time/residue: 0.1511 time to fit residues: 19.0010 Evaluate side-chains 78 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 60 LEU 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 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 858 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 212 TYR 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 65 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 52 optimal weight: 0.1980 chunk 50 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.035502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.026633 restraints weight = 57893.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.027451 restraints weight = 36613.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.028028 restraints weight = 26615.347| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.7036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7157 Z= 0.109 Angle : 0.668 9.671 9772 Z= 0.308 Chirality : 0.043 0.215 1178 Planarity : 0.004 0.045 1249 Dihedral : 3.916 16.924 1017 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.14 % Favored : 94.75 % Rotamer: Outliers : 3.18 % Allowed : 24.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.28), residues: 933 helix: 0.70 (0.25), residues: 479 sheet: -1.22 (0.48), residues: 117 loop : -1.58 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 326 HIS 0.003 0.001 HIS F 555 PHE 0.022 0.001 PHE G 115 TYR 0.036 0.001 TYR F 564 ARG 0.008 0.000 ARG F 689 Details of bonding type rmsd hydrogen bonds : bond 0.02855 ( 253) hydrogen bonds : angle 4.29262 ( 744) covalent geometry : bond 0.00240 ( 7157) covalent geometry : angle 0.66794 ( 9772) *********************** 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 83 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 153 ARG cc_start: 0.9435 (OUTLIER) cc_final: 0.9069 (mmm160) REVERT: F 182 MET cc_start: 0.8919 (tpp) cc_final: 0.8458 (tpp) REVERT: F 291 LEU cc_start: 0.9836 (tp) cc_final: 0.9613 (tp) REVERT: F 737 ASN cc_start: 0.9521 (m-40) cc_final: 0.9180 (m110) REVERT: F 798 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9128 (mm) REVERT: G 126 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8311 (p) REVERT: G 151 ASP cc_start: 0.9383 (m-30) cc_final: 0.9123 (p0) REVERT: G 184 GLU cc_start: 0.9717 (tp30) cc_final: 0.9376 (tm-30) REVERT: G 189 CYS cc_start: 0.9476 (t) cc_final: 0.9233 (p) outliers start: 22 outliers final: 17 residues processed: 78 average time/residue: 0.1391 time to fit residues: 16.2073 Evaluate side-chains 81 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 123 ILE 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 298 LEU Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 634 ILE 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 160 LEU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 173 VAL 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 31 optimal weight: 6.9990 chunk 71 optimal weight: 0.2980 chunk 35 optimal weight: 0.0060 chunk 72 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.035780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.026814 restraints weight = 58066.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.027652 restraints weight = 36291.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.028181 restraints weight = 26202.499| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.7156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7157 Z= 0.100 Angle : 0.709 19.327 9772 Z= 0.312 Chirality : 0.043 0.202 1178 Planarity : 0.004 0.045 1249 Dihedral : 3.814 17.498 1017 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.04 % Favored : 94.86 % Rotamer: Outliers : 3.03 % Allowed : 25.00 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.28), residues: 933 helix: 0.72 (0.25), residues: 480 sheet: -0.91 (0.48), residues: 123 loop : -1.70 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 326 HIS 0.003 0.001 HIS F 555 PHE 0.015 0.001 PHE G 115 TYR 0.029 0.001 TYR F 564 ARG 0.009 0.000 ARG F 689 Details of bonding type rmsd hydrogen bonds : bond 0.02770 ( 253) hydrogen bonds : angle 4.29295 ( 744) covalent geometry : bond 0.00225 ( 7157) covalent geometry : angle 0.70862 ( 9772) ********************** 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 82 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 153 ARG cc_start: 0.9458 (OUTLIER) cc_final: 0.9067 (mmm160) REVERT: F 182 MET cc_start: 0.8928 (tpp) cc_final: 0.8464 (tpp) REVERT: F 291 LEU cc_start: 0.9832 (tp) cc_final: 0.9467 (tp) REVERT: F 748 MET cc_start: 0.9468 (mtp) cc_final: 0.9264 (tpt) REVERT: F 798 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9119 (mm) REVERT: G 126 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8319 (p) REVERT: G 130 TYR cc_start: 0.8414 (m-10) cc_final: 0.8184 (m-10) REVERT: G 184 GLU cc_start: 0.9749 (tp30) cc_final: 0.9377 (tm-30) REVERT: G 189 CYS cc_start: 0.9474 (t) cc_final: 0.9252 (p) REVERT: G 212 TYR cc_start: 0.9508 (OUTLIER) cc_final: 0.9062 (m-80) outliers start: 21 outliers final: 17 residues processed: 78 average time/residue: 0.1474 time to fit residues: 17.4230 Evaluate side-chains 80 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 123 ILE 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 298 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 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 212 TYR 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 41 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.035624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.026730 restraints weight = 56332.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.027539 restraints weight = 35646.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.028127 restraints weight = 26021.616| |-----------------------------------------------------------------------------| r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.7366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7157 Z= 0.099 Angle : 0.702 15.789 9772 Z= 0.310 Chirality : 0.043 0.194 1178 Planarity : 0.004 0.046 1249 Dihedral : 3.769 16.670 1017 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.14 % Favored : 94.75 % Rotamer: Outliers : 3.18 % Allowed : 25.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.29), residues: 933 helix: 0.71 (0.25), residues: 482 sheet: -0.82 (0.48), residues: 123 loop : -1.72 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 326 HIS 0.003 0.001 HIS F 555 PHE 0.014 0.001 PHE G 115 TYR 0.026 0.001 TYR F 564 ARG 0.008 0.000 ARG F 689 Details of bonding type rmsd hydrogen bonds : bond 0.02758 ( 253) hydrogen bonds : angle 4.29011 ( 744) covalent geometry : bond 0.00225 ( 7157) covalent geometry : angle 0.70237 ( 9772) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2320.87 seconds wall clock time: 40 minutes 55.54 seconds (2455.54 seconds total)