Starting phenix.real_space_refine on Thu Aug 6 07:13:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j8g_36069/08_2026/8j8g_36069.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j8g_36069/08_2026/8j8g_36069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j8g_36069/08_2026/8j8g_36069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j8g_36069/08_2026/8j8g_36069.map" model { file = "/net/cci-nas-00/data/ceres_data/8j8g_36069/08_2026/8j8g_36069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j8g_36069/08_2026/8j8g_36069.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 39 5.49 5 S 71 5.16 5 C 8956 2.51 5 N 2340 2.21 5 O 2748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14157 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 8212 Classifications: {'peptide': 1005} Link IDs: {'PTRANS': 37, 'TRANS': 967} Chain: "B" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1762 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 13, 'TRANS': 204} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3418 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 10, 'TRANS': 408} Chain breaks: 1 Chain: "P" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 291 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 445 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' CA': 3, 'TXJ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.15, per 1000 atoms: 0.15 Number of scatterers: 14157 At special positions: 0 Unit cell: (102.48, 125.16, 144.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 71 16.00 P 39 15.00 O 2748 8.00 N 2340 7.00 C 8956 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: 0.75 Conformation dependent library (CDL) restraints added in 365.5 milliseconds 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3140 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 20 sheets defined 40.0% alpha, 18.1% beta 12 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 44 through 48 removed outlier: 3.601A pdb=" N GLN A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 44 through 48' Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 448 through 473 removed outlier: 3.629A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.892A pdb=" N VAL A 493 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.675A pdb=" N ILE A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 514 Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 576 through 591 removed outlier: 3.882A pdb=" N GLN A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 643 removed outlier: 3.613A pdb=" N ARG A 625 " --> pdb=" O GLY A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 672 removed outlier: 3.612A pdb=" N TYR A 668 " --> pdb=" O ALA A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 Processing helix chain 'A' and resid 763 through 781 removed outlier: 3.575A pdb=" N ASN A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER A 780 " --> pdb=" O ARG A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 857 removed outlier: 3.787A pdb=" N ASN A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET A 842 " --> pdb=" O PHE A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 883 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.597A pdb=" N MET A 891 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 917 Processing helix chain 'A' and resid 947 through 949 No H-bonds generated for 'chain 'A' and resid 947 through 949' Processing helix chain 'A' and resid 967 through 983 removed outlier: 4.453A pdb=" N TYR A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 983 " --> pdb=" O ILE A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 997 Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 19 through 38 removed outlier: 3.938A pdb=" N MET B 23 " --> pdb=" O TRP B 19 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER B 35 " --> pdb=" O ASN B 31 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N TRP B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 101 removed outlier: 3.603A pdb=" N SER B 95 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B 96 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 133 through 152 removed outlier: 3.674A pdb=" N TRP B 137 " --> pdb=" O HIS B 133 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LYS B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS B 151 " --> pdb=" O HIS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 212 through 216 removed outlier: 4.090A pdb=" N GLY B 215 " --> pdb=" O TRP B 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 24 through 43 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 108 through 119 Processing helix chain 'C' and resid 147 through 159 removed outlier: 4.002A pdb=" N ILE C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 188 Processing helix chain 'C' and resid 249 through 257 removed outlier: 3.579A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 298 removed outlier: 3.633A pdb=" N LYS C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE C 294 " --> pdb=" O ILE C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 323 Processing helix chain 'C' and resid 330 through 340 Processing helix chain 'C' and resid 341 through 350 removed outlier: 3.922A pdb=" N LYS C 345 " --> pdb=" O SER C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 362 Processing helix chain 'C' and resid 365 through 374 Processing helix chain 'C' and resid 393 through 396 Processing helix chain 'C' and resid 397 through 405 Processing helix chain 'C' and resid 406 through 425 removed outlier: 3.575A pdb=" N PHE C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 134 removed outlier: 8.341A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N CYS A 142 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ARG A 33 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN A 7 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ARG A 23 " --> pdb=" O CYS A 5 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N CYS A 5 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS A 124 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 6.149A pdb=" N SER A 84 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG A 64 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA A 86 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS A 62 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N MET A 88 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ILE A 516 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ARG A 64 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL A 518 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE A 66 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.202A pdb=" N LEU A 568 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP A 616 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 574 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 610 " --> pdb=" O SER A 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 removed outlier: 6.146A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL A 237 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR A 201 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N CYS A 239 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE A 203 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 259 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 305 Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 359 Processing sheet with id=AA8, first strand: chain 'A' and resid 368 through 369 removed outlier: 3.599A pdb=" N ARG A 407 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 533 through 534 removed outlier: 4.312A pdb=" N GLY A 750 " --> pdb=" O PHE A 534 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE A 756 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY A 750 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER A 754 " --> pdb=" O GLY A 750 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 545 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL A 794 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ILE A 547 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU A 798 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR A 807 " --> pdb=" O LEU A 798 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 732 through 734 Processing sheet with id=AB2, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB3, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB4, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AB5, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.543A pdb=" N ILE B 117 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N CYS B 63 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU B 158 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N CYS B 65 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU B 155 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLY B 179 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N CYS B 157 " --> pdb=" O GLY B 179 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 69 through 71 Processing sheet with id=AB7, first strand: chain 'C' and resid 80 through 82 Processing sheet with id=AB8, first strand: chain 'C' and resid 103 through 104 removed outlier: 4.319A pdb=" N MET C 95 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 130 " --> pdb=" O ILE C 137 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 214 through 219 removed outlier: 4.321A pdb=" N SER C 273 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU C 275 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE C 245 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL C 237 " --> pdb=" O ILE C 245 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 302 through 304 Processing sheet with id=AC2, first strand: chain 'C' and resid 375 through 380 removed outlier: 3.620A pdb=" N ASN C 386 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU C 380 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N VAL C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 0.98 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: 2368 1.32 - 1.45: 4012 1.45 - 1.57: 7968 1.57 - 1.69: 74 1.69 - 1.81: 109 Bond restraints: 14531 Sorted by residual: bond pdb=" O1B TXJ A1101 " pdb=" PG TXJ A1101 " ideal model delta sigma weight residual 1.741 1.603 0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C4 TXJ A1101 " pdb=" N3 TXJ A1101 " ideal model delta sigma weight residual 1.319 1.397 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C3' DT P 22 " pdb=" C2' DT P 22 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" N HIS B 8 " pdb=" CA HIS B 8 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.25e-02 6.40e+03 9.63e+00 bond pdb=" C2 TXJ A1101 " pdb=" N1 TXJ A1101 " ideal model delta sigma weight residual 1.403 1.341 0.062 2.00e-02 2.50e+03 9.62e+00 ... (remaining 14526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 19483 2.03 - 4.05: 278 4.05 - 6.08: 30 6.08 - 8.10: 1 8.10 - 10.13: 2 Bond angle restraints: 19794 Sorted by residual: angle pdb=" N3 DT P 12 " pdb=" C4 DT P 12 " pdb=" O4 DT P 12 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT T 2 " pdb=" C4 DT T 2 " pdb=" O4 DT T 2 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT T -3 " pdb=" C4 DT T -3 " pdb=" O4 DT T -3 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT P 23 " pdb=" C4 DT P 23 " pdb=" O4 DT P 23 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT T -4 " pdb=" C4 DT T -4 " pdb=" O4 DT T -4 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 19789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 7739 17.73 - 35.47: 744 35.47 - 53.20: 181 53.20 - 70.94: 28 70.94 - 88.67: 9 Dihedral angle restraints: 8701 sinusoidal: 3830 harmonic: 4871 Sorted by residual: dihedral pdb=" CA SER B 43 " pdb=" C SER B 43 " pdb=" N PRO B 44 " pdb=" CA PRO B 44 " ideal model delta harmonic sigma weight residual 180.00 137.66 42.34 0 5.00e+00 4.00e-02 7.17e+01 dihedral pdb=" CA PRO A 593 " pdb=" C PRO A 593 " pdb=" N PRO A 594 " pdb=" CA PRO A 594 " ideal model delta harmonic sigma weight residual 180.00 147.92 32.08 0 5.00e+00 4.00e-02 4.12e+01 dihedral pdb=" CA ASN B 83 " pdb=" C ASN B 83 " pdb=" N PHE B 84 " pdb=" CA PHE B 84 " ideal model delta harmonic sigma weight residual -180.00 -161.04 -18.96 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 8698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1606 0.040 - 0.080: 412 0.080 - 0.121: 150 0.121 - 0.161: 18 0.161 - 0.201: 3 Chirality restraints: 2189 Sorted by residual: chirality pdb=" CA ALA B 9 " pdb=" N ALA B 9 " pdb=" C ALA B 9 " pdb=" CB ALA B 9 " both_signs ideal model delta sigma weight residual False 2.48 2.28 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ASP C 72 " pdb=" N ASP C 72 " pdb=" C ASP C 72 " pdb=" CB ASP C 72 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CB VAL A 3 " pdb=" CA VAL A 3 " pdb=" CG1 VAL A 3 " pdb=" CG2 VAL A 3 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.66e-01 ... (remaining 2186 not shown) Planarity restraints: 2390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 6 " 0.021 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C ILE B 6 " -0.072 2.00e-02 2.50e+03 pdb=" O ILE B 6 " 0.027 2.00e-02 2.50e+03 pdb=" N SER B 7 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 43 " -0.060 5.00e-02 4.00e+02 9.10e-02 1.33e+01 pdb=" N PRO B 44 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 593 " -0.056 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO A 594 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 594 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 594 " -0.048 5.00e-02 4.00e+02 ... (remaining 2387 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 23 2.39 - 3.02: 7670 3.02 - 3.64: 21069 3.64 - 4.27: 31661 4.27 - 4.90: 53212 Nonbonded interactions: 113635 Sorted by model distance: nonbonded pdb=" O TYR A 550 " pdb="CA CA A1104 " model vdw 1.761 2.510 nonbonded pdb=" OH TYR A 749 " pdb=" O LYS A 803 " model vdw 2.116 3.040 nonbonded pdb=" OD2 ASP A 549 " pdb="CA CA A1104 " model vdw 2.218 2.510 nonbonded pdb=" OD1 ASP A 549 " pdb=" OG SER A 754 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR A 900 " pdb=" OP1 DG P 21 " model vdw 2.264 3.040 ... (remaining 113630 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.160 Find NCS groups from input model: 0.040 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:5.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 14531 Z= 0.230 Angle : 0.543 10.128 19794 Z= 0.353 Chirality : 0.042 0.201 2189 Planarity : 0.004 0.091 2390 Dihedral : 14.905 88.674 5561 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.47 % Favored : 95.10 % Rotamer: Outliers : 0.07 % Allowed : 0.26 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.21), residues: 1634 helix: 1.46 (0.22), residues: 577 sheet: -0.24 (0.28), residues: 359 loop : -0.95 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 234 TYR 0.019 0.001 TYR B 11 PHE 0.016 0.001 PHE A 756 TRP 0.006 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.23 (14531) covalent geometry : angle 0.54284 / 0.35 (19794) hydrogen bonds : bond 0.15736 / 10.80 ( 592) hydrogen bonds : angle 6.04517 / 4.21 ( 1660) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 248 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7458 (pt0) cc_final: 0.7224 (pt0) REVERT: A 211 GLN cc_start: 0.7190 (mp10) cc_final: 0.6941 (mp10) REVERT: A 313 MET cc_start: 0.4659 (mmt) cc_final: 0.4359 (mmt) REVERT: A 362 ASN cc_start: 0.8120 (m110) cc_final: 0.7880 (m-40) REVERT: A 383 ASP cc_start: 0.7380 (m-30) cc_final: 0.7139 (m-30) REVERT: A 539 LYS cc_start: 0.7616 (mtpp) cc_final: 0.7348 (mtpp) REVERT: A 674 ARG cc_start: 0.7058 (ttp80) cc_final: 0.6683 (ttp80) REVERT: A 681 TYR cc_start: 0.7695 (t80) cc_final: 0.7458 (t80) REVERT: A 711 MET cc_start: 0.5101 (mmp) cc_final: 0.4766 (mmp) REVERT: A 734 LYS cc_start: 0.7552 (tppt) cc_final: 0.6963 (pmtt) REVERT: C 147 SER cc_start: 0.5686 (p) cc_final: 0.5433 (m) REVERT: C 335 VAL cc_start: 0.6918 (p) cc_final: 0.6621 (p) REVERT: C 384 VAL cc_start: 0.5996 (t) cc_final: 0.4184 (m) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.4561 time to fit residues: 124.7236 Evaluate side-chains 168 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.218842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.162610 restraints weight = 15696.521| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.75 r_work: 0.3658 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14531 Z= 0.215 Angle : 0.657 10.841 19794 Z= 0.352 Chirality : 0.046 0.170 2189 Planarity : 0.005 0.096 2390 Dihedral : 14.038 89.807 2236 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.51 % Favored : 94.12 % Rotamer: Outliers : 1.98 % Allowed : 10.95 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.34 (0.21), residues: 1634 helix: 0.96 (0.21), residues: 598 sheet: -0.35 (0.28), residues: 366 loop : -1.18 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 744 TYR 0.032 0.002 TYR C 158 PHE 0.017 0.002 PHE A 630 TRP 0.010 0.002 TRP B 19 HIS 0.005 0.001 HIS A 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 (14531) covalent geometry : angle 0.65724 / 0.35 (19794) hydrogen bonds : bond 0.05946 / 4.20 ( 592) hydrogen bonds : angle 5.05398 / 3.53 ( 1660) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.7527 (mp10) cc_final: 0.7248 (mp10) REVERT: A 277 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: A 313 MET cc_start: 0.5057 (mmt) cc_final: 0.4782 (mmt) REVERT: A 383 ASP cc_start: 0.7643 (m-30) cc_final: 0.7429 (m-30) REVERT: A 711 MET cc_start: 0.5443 (mmp) cc_final: 0.5123 (mmp) REVERT: A 734 LYS cc_start: 0.7781 (tppt) cc_final: 0.7177 (pmtt) REVERT: B 195 PHE cc_start: 0.5185 (m-80) cc_final: 0.4411 (t80) REVERT: C 97 GLU cc_start: 0.7317 (tp30) cc_final: 0.7085 (tp30) REVERT: C 147 SER cc_start: 0.5830 (p) cc_final: 0.5609 (m) REVERT: C 186 ARG cc_start: 0.7360 (ttm110) cc_final: 0.7089 (mmp-170) outliers start: 30 outliers final: 20 residues processed: 199 average time/residue: 0.3908 time to fit residues: 86.9654 Evaluate side-chains 182 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 395 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 1 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 154 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 ASN A 862 ASN A 897 HIS A 985 ASN B 31 ASN B 109 ASN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.219331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.163409 restraints weight = 15732.019| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.77 r_work: 0.3659 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14531 Z= 0.163 Angle : 0.580 9.990 19794 Z= 0.313 Chirality : 0.043 0.150 2189 Planarity : 0.005 0.090 2390 Dihedral : 14.242 89.443 2236 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.90 % Favored : 94.80 % Rotamer: Outliers : 2.31 % Allowed : 13.65 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.34 (0.21), residues: 1634 helix: 0.98 (0.21), residues: 599 sheet: -0.37 (0.29), residues: 354 loop : -1.19 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 742 TYR 0.018 0.002 TYR B 180 PHE 0.011 0.002 PHE A 630 TRP 0.011 0.001 TRP B 212 HIS 0.004 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (14531) covalent geometry : angle 0.58020 / 0.31 (19794) hydrogen bonds : bond 0.05236 / 3.67 ( 592) hydrogen bonds : angle 4.84608 / 3.39 ( 1660) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.7506 (mp10) cc_final: 0.7250 (mp10) REVERT: A 227 LEU cc_start: 0.7568 (tp) cc_final: 0.7361 (mp) REVERT: A 277 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: A 313 MET cc_start: 0.5055 (mmt) cc_final: 0.4773 (mmt) REVERT: A 383 ASP cc_start: 0.7616 (m-30) cc_final: 0.7404 (m-30) REVERT: A 539 LYS cc_start: 0.8128 (mtpp) cc_final: 0.7457 (mttp) REVERT: A 711 MET cc_start: 0.5488 (mmp) cc_final: 0.5151 (mmp) REVERT: A 734 LYS cc_start: 0.7949 (tppt) cc_final: 0.7242 (pmtt) REVERT: C 97 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7041 (tp30) REVERT: C 147 SER cc_start: 0.5943 (p) cc_final: 0.5733 (m) outliers start: 35 outliers final: 17 residues processed: 192 average time/residue: 0.4105 time to fit residues: 88.6065 Evaluate side-chains 178 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 395 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 67 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 86 optimal weight: 0.4980 chunk 82 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN A 303 ASN A 897 HIS B 31 ASN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.220018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.163841 restraints weight = 15633.495| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 1.65 r_work: 0.3676 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14531 Z= 0.133 Angle : 0.551 9.891 19794 Z= 0.298 Chirality : 0.042 0.148 2189 Planarity : 0.005 0.090 2390 Dihedral : 14.262 88.527 2236 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.96 % Favored : 94.74 % Rotamer: Outliers : 2.11 % Allowed : 15.70 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.21), residues: 1634 helix: 1.09 (0.21), residues: 593 sheet: -0.37 (0.28), residues: 354 loop : -1.16 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 744 TYR 0.017 0.001 TYR C 181 PHE 0.012 0.001 PHE B 195 TRP 0.007 0.001 TRP B 19 HIS 0.006 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (14531) covalent geometry : angle 0.55140 / 0.30 (19794) hydrogen bonds : bond 0.04668 / 3.28 ( 592) hydrogen bonds : angle 4.72281 / 3.29 ( 1660) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.7477 (mp10) cc_final: 0.7211 (mp10) REVERT: A 277 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: A 313 MET cc_start: 0.5034 (mmt) cc_final: 0.4804 (mmt) REVERT: A 383 ASP cc_start: 0.7597 (m-30) cc_final: 0.7383 (m-30) REVERT: A 539 LYS cc_start: 0.8138 (mtpp) cc_final: 0.7478 (mttp) REVERT: A 674 ARG cc_start: 0.7476 (ttp80) cc_final: 0.7258 (ttp80) REVERT: A 711 MET cc_start: 0.5517 (mmp) cc_final: 0.5224 (mmp) REVERT: A 734 LYS cc_start: 0.8015 (tppt) cc_final: 0.7309 (pmtt) REVERT: C 97 GLU cc_start: 0.7205 (tp30) cc_final: 0.6973 (tp30) outliers start: 32 outliers final: 16 residues processed: 197 average time/residue: 0.4288 time to fit residues: 95.0644 Evaluate side-chains 178 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 395 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 41 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 HIS A 100 GLN A 303 ASN A 801 GLN A 897 HIS B 31 ASN B 109 ASN C 208 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.216083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.158844 restraints weight = 15602.422| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.73 r_work: 0.3615 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14531 Z= 0.233 Angle : 0.664 11.979 19794 Z= 0.353 Chirality : 0.046 0.165 2189 Planarity : 0.006 0.098 2390 Dihedral : 14.452 88.947 2236 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.06 % Favored : 93.70 % Rotamer: Outliers : 3.10 % Allowed : 17.28 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.21), residues: 1634 helix: 0.62 (0.21), residues: 600 sheet: -0.53 (0.29), residues: 354 loop : -1.35 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 744 TYR 0.022 0.002 TYR A 190 PHE 0.017 0.002 PHE A 630 TRP 0.009 0.002 TRP B 19 HIS 0.007 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.23 (14531) covalent geometry : angle 0.66425 / 0.35 (19794) hydrogen bonds : bond 0.05792 / 4.08 ( 592) hydrogen bonds : angle 4.97169 / 3.46 ( 1660) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.7712 (mp10) cc_final: 0.7440 (mp10) REVERT: A 227 LEU cc_start: 0.7628 (tp) cc_final: 0.7391 (mp) REVERT: A 277 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: A 313 MET cc_start: 0.5183 (mmt) cc_final: 0.4961 (mmt) REVERT: A 383 ASP cc_start: 0.7610 (m-30) cc_final: 0.7389 (m-30) REVERT: A 399 GLU cc_start: 0.7123 (mp0) cc_final: 0.6726 (tt0) REVERT: A 495 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7792 (mm-30) REVERT: A 539 LYS cc_start: 0.8229 (mtpp) cc_final: 0.7520 (mttp) REVERT: A 656 MET cc_start: 0.7569 (mtm) cc_final: 0.7341 (mtm) REVERT: A 711 MET cc_start: 0.5608 (mmp) cc_final: 0.5294 (mmp) REVERT: A 734 LYS cc_start: 0.8126 (tppt) cc_final: 0.7415 (pmtt) REVERT: C 97 GLU cc_start: 0.7278 (tp30) cc_final: 0.6994 (tp30) outliers start: 47 outliers final: 27 residues processed: 210 average time/residue: 0.4032 time to fit residues: 95.0679 Evaluate side-chains 188 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 395 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 ASN A 100 GLN A 303 ASN A 897 HIS C 102 ASN C 409 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.218310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.161929 restraints weight = 15573.368| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.64 r_work: 0.3659 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14531 Z= 0.136 Angle : 0.580 9.901 19794 Z= 0.311 Chirality : 0.042 0.177 2189 Planarity : 0.005 0.090 2390 Dihedral : 14.501 88.170 2236 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.90 % Favored : 94.86 % Rotamer: Outliers : 2.51 % Allowed : 18.73 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.54 (0.21), residues: 1634 helix: 0.83 (0.21), residues: 599 sheet: -0.50 (0.28), residues: 362 loop : -1.30 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 744 TYR 0.019 0.001 TYR A 811 PHE 0.011 0.001 PHE B 84 TRP 0.008 0.001 TRP B 19 HIS 0.005 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (14531) covalent geometry : angle 0.58008 / 0.31 (19794) hydrogen bonds : bond 0.04699 / 3.30 ( 592) hydrogen bonds : angle 4.78784 / 3.33 ( 1660) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.7563 (mp10) cc_final: 0.7292 (mp10) REVERT: A 277 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: A 313 MET cc_start: 0.5084 (mmt) cc_final: 0.4870 (mmt) REVERT: A 383 ASP cc_start: 0.7535 (m-30) cc_final: 0.7329 (m-30) REVERT: A 402 ILE cc_start: 0.7546 (mt) cc_final: 0.7298 (mt) REVERT: A 539 LYS cc_start: 0.8275 (mtpp) cc_final: 0.7562 (mttp) REVERT: A 656 MET cc_start: 0.7371 (mtm) cc_final: 0.7117 (mtm) REVERT: A 674 ARG cc_start: 0.7466 (ttp80) cc_final: 0.7263 (ttp80) REVERT: A 711 MET cc_start: 0.5625 (mmp) cc_final: 0.5304 (mmp) REVERT: A 734 LYS cc_start: 0.8069 (tppt) cc_final: 0.7346 (pmtt) REVERT: A 976 THR cc_start: 0.8115 (m) cc_final: 0.7907 (p) REVERT: B 64 VAL cc_start: 0.7349 (p) cc_final: 0.6946 (m) REVERT: B 195 PHE cc_start: 0.5201 (m-80) cc_final: 0.4353 (t80) REVERT: C 97 GLU cc_start: 0.7283 (tp30) cc_final: 0.7016 (tp30) outliers start: 38 outliers final: 23 residues processed: 198 average time/residue: 0.4133 time to fit residues: 92.2610 Evaluate side-chains 182 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 395 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 79 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 59 optimal weight: 0.0030 chunk 1 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 ASN A 897 HIS B 111 ASN C 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.218697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.160444 restraints weight = 15630.664| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.95 r_work: 0.3669 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14531 Z= 0.134 Angle : 0.575 10.350 19794 Z= 0.308 Chirality : 0.042 0.157 2189 Planarity : 0.005 0.093 2390 Dihedral : 14.496 88.143 2236 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.96 % Favored : 94.80 % Rotamer: Outliers : 2.64 % Allowed : 18.93 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.21), residues: 1634 helix: 0.92 (0.21), residues: 598 sheet: -0.51 (0.28), residues: 362 loop : -1.29 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 742 TYR 0.017 0.001 TYR A 811 PHE 0.011 0.001 PHE B 84 TRP 0.008 0.001 TRP B 212 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (14531) covalent geometry : angle 0.57539 / 0.31 (19794) hydrogen bonds : bond 0.04473 / 3.14 ( 592) hydrogen bonds : angle 4.70315 / 3.27 ( 1660) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.7535 (mp10) cc_final: 0.7224 (mp10) REVERT: A 277 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: A 313 MET cc_start: 0.5118 (mmt) cc_final: 0.4918 (mmt) REVERT: A 383 ASP cc_start: 0.7518 (m-30) cc_final: 0.7295 (m-30) REVERT: A 402 ILE cc_start: 0.7510 (mt) cc_final: 0.7272 (mt) REVERT: A 495 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7756 (mm-30) REVERT: A 539 LYS cc_start: 0.8283 (mtpp) cc_final: 0.7544 (mttp) REVERT: A 674 ARG cc_start: 0.7398 (ttp80) cc_final: 0.7192 (ttp80) REVERT: A 711 MET cc_start: 0.5608 (mmp) cc_final: 0.5275 (mmp) REVERT: A 734 LYS cc_start: 0.8092 (tppt) cc_final: 0.7310 (pmtt) REVERT: A 774 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6767 (mp) REVERT: B 64 VAL cc_start: 0.7320 (p) cc_final: 0.6910 (m) REVERT: B 111 ASN cc_start: 0.5076 (t0) cc_final: 0.4694 (p0) REVERT: B 195 PHE cc_start: 0.5045 (m-80) cc_final: 0.4359 (t80) REVERT: C 97 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6924 (tp30) outliers start: 40 outliers final: 22 residues processed: 193 average time/residue: 0.4263 time to fit residues: 92.5437 Evaluate side-chains 185 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 392 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 90 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 59 optimal weight: 0.0670 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 897 HIS B 109 ASN C 102 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.218999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.162534 restraints weight = 15581.698| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.69 r_work: 0.3674 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14531 Z= 0.134 Angle : 0.583 10.391 19794 Z= 0.312 Chirality : 0.042 0.167 2189 Planarity : 0.005 0.091 2390 Dihedral : 14.503 88.143 2236 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.96 % Favored : 94.80 % Rotamer: Outliers : 2.37 % Allowed : 19.53 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.46 (0.21), residues: 1634 helix: 0.96 (0.21), residues: 598 sheet: -0.54 (0.28), residues: 362 loop : -1.28 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 742 TYR 0.042 0.001 TYR C 158 PHE 0.011 0.001 PHE B 84 TRP 0.008 0.001 TRP B 212 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (14531) covalent geometry : angle 0.58276 / 0.31 (19794) hydrogen bonds : bond 0.04424 / 3.10 ( 592) hydrogen bonds : angle 4.70500 / 3.27 ( 1660) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.7522 (mp10) cc_final: 0.7213 (mp10) REVERT: A 277 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: A 362 ASN cc_start: 0.8143 (m110) cc_final: 0.7618 (m-40) REVERT: A 383 ASP cc_start: 0.7511 (m-30) cc_final: 0.7298 (m-30) REVERT: A 402 ILE cc_start: 0.7505 (mt) cc_final: 0.7261 (mt) REVERT: A 495 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7768 (mm-30) REVERT: A 497 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7268 (mpp80) REVERT: A 539 LYS cc_start: 0.8304 (mtpp) cc_final: 0.7572 (mttp) REVERT: A 711 MET cc_start: 0.5622 (mmp) cc_final: 0.5287 (mmp) REVERT: A 734 LYS cc_start: 0.8074 (tppt) cc_final: 0.7314 (pmtt) REVERT: A 742 ARG cc_start: 0.6902 (ttm110) cc_final: 0.6638 (ttp80) REVERT: B 64 VAL cc_start: 0.7325 (p) cc_final: 0.6905 (m) REVERT: B 109 ASN cc_start: 0.5813 (OUTLIER) cc_final: 0.5578 (t0) REVERT: B 111 ASN cc_start: 0.5008 (t0) cc_final: 0.4610 (p0) REVERT: B 195 PHE cc_start: 0.5048 (m-80) cc_final: 0.4387 (t80) REVERT: C 97 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6951 (tp30) outliers start: 36 outliers final: 24 residues processed: 189 average time/residue: 0.4597 time to fit residues: 97.4502 Evaluate side-chains 186 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 392 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 60 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN A 897 HIS B 165 ASN C 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.216826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.160431 restraints weight = 15535.438| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.75 r_work: 0.3627 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14531 Z= 0.199 Angle : 0.629 11.406 19794 Z= 0.336 Chirality : 0.045 0.166 2189 Planarity : 0.005 0.096 2390 Dihedral : 14.559 88.241 2236 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.57 % Favored : 94.19 % Rotamer: Outliers : 2.51 % Allowed : 19.66 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.66 (0.21), residues: 1634 helix: 0.75 (0.21), residues: 604 sheet: -0.63 (0.28), residues: 363 loop : -1.37 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 423 TYR 0.019 0.002 TYR A 190 PHE 0.013 0.002 PHE A 630 TRP 0.010 0.001 TRP B 212 HIS 0.006 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (14531) covalent geometry : angle 0.62943 / 0.34 (19794) hydrogen bonds : bond 0.05095 / 3.57 ( 592) hydrogen bonds : angle 4.80915 / 3.34 ( 1660) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.7621 (mp10) cc_final: 0.7303 (mp10) REVERT: A 277 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: A 362 ASN cc_start: 0.8179 (m110) cc_final: 0.7675 (m-40) REVERT: A 383 ASP cc_start: 0.7578 (m-30) cc_final: 0.7363 (m-30) REVERT: A 399 GLU cc_start: 0.7106 (mp0) cc_final: 0.6716 (tt0) REVERT: A 402 ILE cc_start: 0.7608 (mt) cc_final: 0.7351 (mt) REVERT: A 495 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7791 (mm-30) REVERT: A 497 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7318 (mpp80) REVERT: A 539 LYS cc_start: 0.8362 (mtpp) cc_final: 0.7622 (mttp) REVERT: A 566 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7120 (pm20) REVERT: A 656 MET cc_start: 0.6932 (mtm) cc_final: 0.6701 (mtp) REVERT: A 711 MET cc_start: 0.5702 (mmp) cc_final: 0.5367 (mmp) REVERT: A 734 LYS cc_start: 0.8075 (tppt) cc_final: 0.7379 (pmtt) REVERT: B 111 ASN cc_start: 0.5102 (t0) cc_final: 0.4698 (p0) REVERT: B 195 PHE cc_start: 0.5027 (m-80) cc_final: 0.4359 (t80) REVERT: C 97 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6999 (tp30) REVERT: C 186 ARG cc_start: 0.7325 (tpp80) cc_final: 0.6933 (ptt180) outliers start: 38 outliers final: 27 residues processed: 186 average time/residue: 0.4330 time to fit residues: 90.7310 Evaluate side-chains 186 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 392 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 61 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 159 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 59 optimal weight: 0.0020 chunk 160 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN A 897 HIS B 165 ASN C 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.218985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.162972 restraints weight = 15607.415| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.00 r_work: 0.3669 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14531 Z= 0.127 Angle : 0.583 10.356 19794 Z= 0.311 Chirality : 0.042 0.160 2189 Planarity : 0.005 0.089 2390 Dihedral : 14.590 87.823 2236 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.65 % Favored : 95.10 % Rotamer: Outliers : 2.11 % Allowed : 19.99 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.50 (0.21), residues: 1634 helix: 0.95 (0.21), residues: 599 sheet: -0.70 (0.28), residues: 374 loop : -1.23 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 742 TYR 0.015 0.001 TYR A 190 PHE 0.010 0.001 PHE B 84 TRP 0.008 0.001 TRP A 470 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (14531) covalent geometry : angle 0.58294 / 0.31 (19794) hydrogen bonds : bond 0.04298 / 3.00 ( 592) hydrogen bonds : angle 4.69913 / 3.26 ( 1660) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6497 (tmt90) cc_final: 0.6189 (ttp80) REVERT: A 34 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.8115 (m-80) REVERT: A 211 GLN cc_start: 0.7502 (mp10) cc_final: 0.7179 (mp10) REVERT: A 277 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: A 362 ASN cc_start: 0.8139 (m110) cc_final: 0.7645 (m-40) REVERT: A 383 ASP cc_start: 0.7522 (m-30) cc_final: 0.7296 (m-30) REVERT: A 402 ILE cc_start: 0.7428 (mt) cc_final: 0.7186 (mt) REVERT: A 495 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7771 (mm-30) REVERT: A 497 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7268 (mpp80) REVERT: A 539 LYS cc_start: 0.8294 (mtpp) cc_final: 0.7611 (mttp) REVERT: A 711 MET cc_start: 0.5624 (mmp) cc_final: 0.5287 (mmp) REVERT: A 734 LYS cc_start: 0.8041 (tppt) cc_final: 0.7354 (pmtt) REVERT: A 742 ARG cc_start: 0.6936 (ttm110) cc_final: 0.6627 (ttp80) REVERT: A 976 THR cc_start: 0.8015 (m) cc_final: 0.7779 (p) REVERT: B 64 VAL cc_start: 0.7315 (p) cc_final: 0.6895 (m) REVERT: B 111 ASN cc_start: 0.4883 (t0) cc_final: 0.4476 (p0) REVERT: B 195 PHE cc_start: 0.4989 (m-80) cc_final: 0.4289 (t80) REVERT: C 97 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6908 (tp30) REVERT: C 186 ARG cc_start: 0.7333 (tpp80) cc_final: 0.6912 (ptt180) outliers start: 32 outliers final: 24 residues processed: 184 average time/residue: 0.4242 time to fit residues: 87.6670 Evaluate side-chains 187 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 392 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 158 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 133 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN A 897 HIS B 165 ASN C 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.217969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.160929 restraints weight = 15492.475| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.70 r_work: 0.3656 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14531 Z= 0.149 Angle : 0.594 10.891 19794 Z= 0.318 Chirality : 0.043 0.160 2189 Planarity : 0.005 0.095 2390 Dihedral : 14.573 87.930 2236 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.32 % Favored : 94.43 % Rotamer: Outliers : 2.04 % Allowed : 19.99 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.55 (0.21), residues: 1634 helix: 0.90 (0.21), residues: 599 sheet: -0.74 (0.28), residues: 374 loop : -1.25 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 742 TYR 0.028 0.001 TYR C 89 PHE 0.012 0.001 PHE B 84 TRP 0.006 0.001 TRP B 19 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (14531) covalent geometry : angle 0.59424 / 0.32 (19794) hydrogen bonds : bond 0.04553 / 3.19 ( 592) hydrogen bonds : angle 4.71765 / 3.28 ( 1660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5358.04 seconds wall clock time: 91 minutes 46.94 seconds (5506.94 seconds total)