Starting phenix.real_space_refine on Sun Aug 24 01:43:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mn5_48413/08_2025/9mn5_48413_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mn5_48413/08_2025/9mn5_48413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mn5_48413/08_2025/9mn5_48413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mn5_48413/08_2025/9mn5_48413.map" model { file = "/net/cci-nas-00/data/ceres_data/9mn5_48413/08_2025/9mn5_48413_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mn5_48413/08_2025/9mn5_48413_neut.cif" } resolution = 3.04 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= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 978 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 98 5.49 5 S 74 5.16 5 C 9080 2.51 5 N 2648 2.21 5 O 2859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14759 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1615 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 9, 'TRANS': 182} Chain: "B" Number of atoms: 2635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2635 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 21, 'TRANS': 302} Chain: "E" Number of atoms: 8469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8469 Classifications: {'peptide': 1062} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 67, 'TRANS': 994} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "N" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1035 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain: "T" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1005 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Time building chain proxies: 3.22, per 1000 atoms: 0.22 Number of scatterers: 14759 At special positions: 0 Unit cell: (100.634, 136.682, 144.943, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 98 15.00 O 2859 8.00 N 2648 7.00 C 9080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 672.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3010 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 11 sheets defined 59.9% alpha, 5.4% beta 39 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 54 through 71 removed outlier: 3.813A pdb=" N LEU A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.652A pdb=" N LEU A 79 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 120 removed outlier: 4.217A pdb=" N LYS A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 151 Processing helix chain 'A' and resid 159 through 169 Processing helix chain 'A' and resid 176 through 191 Processing helix chain 'A' and resid 192 through 225 removed outlier: 4.638A pdb=" N LEU A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 89 removed outlier: 3.672A pdb=" N LEU B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 117 removed outlier: 3.667A pdb=" N GLY B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 129 through 136 removed outlier: 3.562A pdb=" N LEU B 136 " --> pdb=" O HIS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 199 through 213 Processing helix chain 'B' and resid 215 through 220 removed outlier: 3.726A pdb=" N LYS B 219 " --> pdb=" O SER B 216 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 220 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 237 Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 283 through 293 removed outlier: 3.715A pdb=" N GLU B 287 " --> pdb=" O PRO B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 329 removed outlier: 3.691A pdb=" N PHE B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.610A pdb=" N HIS B 338 " --> pdb=" O THR B 334 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 355 removed outlier: 3.538A pdb=" N ILE B 350 " --> pdb=" O ASP B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 380 removed outlier: 3.911A pdb=" N SER B 380 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'E' and resid 123 through 146 Processing helix chain 'E' and resid 150 through 155 Processing helix chain 'E' and resid 170 through 174 removed outlier: 4.252A pdb=" N CYS E 174 " --> pdb=" O MET E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 195 removed outlier: 3.540A pdb=" N LEU E 195 " --> pdb=" O ALA E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 236 removed outlier: 3.875A pdb=" N ARG E 225 " --> pdb=" O GLY E 221 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU E 235 " --> pdb=" O LYS E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 252 removed outlier: 3.606A pdb=" N GLN E 252 " --> pdb=" O VAL E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 257 removed outlier: 4.305A pdb=" N LYS E 257 " --> pdb=" O ARG E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 271 removed outlier: 3.534A pdb=" N TYR E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL E 267 " --> pdb=" O MET E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 291 removed outlier: 3.513A pdb=" N LEU E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 310 removed outlier: 3.516A pdb=" N TYR E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 322 removed outlier: 3.523A pdb=" N ILE E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 335 removed outlier: 4.196A pdb=" N PHE E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR E 335 " --> pdb=" O GLN E 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 330 through 335' Processing helix chain 'E' and resid 340 through 355 Processing helix chain 'E' and resid 375 through 379 removed outlier: 3.517A pdb=" N ALA E 379 " --> pdb=" O ASP E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 409 removed outlier: 3.575A pdb=" N PHE E 400 " --> pdb=" O LEU E 396 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU E 401 " --> pdb=" O GLN E 397 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA E 409 " --> pdb=" O HIS E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 461 removed outlier: 4.212A pdb=" N ALA E 430 " --> pdb=" O GLU E 426 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU E 442 " --> pdb=" O ARG E 438 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG E 458 " --> pdb=" O ASN E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 472 Processing helix chain 'E' and resid 475 through 489 Processing helix chain 'E' and resid 497 through 520 removed outlier: 3.756A pdb=" N GLN E 517 " --> pdb=" O VAL E 513 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG E 518 " --> pdb=" O VAL E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 534 removed outlier: 3.694A pdb=" N ALA E 525 " --> pdb=" O GLY E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 556 Processing helix chain 'E' and resid 568 through 587 removed outlier: 3.525A pdb=" N THR E 587 " --> pdb=" O LEU E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 624 through 634 Processing helix chain 'E' and resid 676 through 687 removed outlier: 3.705A pdb=" N HIS E 680 " --> pdb=" O GLY E 676 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN E 681 " --> pdb=" O ALA E 677 " (cutoff:3.500A) Processing helix chain 'E' and resid 692 through 704 Processing helix chain 'E' and resid 710 through 723 removed outlier: 3.684A pdb=" N LEU E 716 " --> pdb=" O ARG E 712 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA E 723 " --> pdb=" O GLN E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 789 removed outlier: 3.617A pdb=" N ALA E 769 " --> pdb=" O CYS E 765 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET E 772 " --> pdb=" O VAL E 768 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA E 777 " --> pdb=" O HIS E 773 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU E 778 " --> pdb=" O SER E 774 " (cutoff:3.500A) Processing helix chain 'E' and resid 818 through 824 removed outlier: 3.763A pdb=" N LEU E 824 " --> pdb=" O VAL E 820 " (cutoff:3.500A) Processing helix chain 'E' and resid 836 through 850 removed outlier: 3.551A pdb=" N TRP E 840 " --> pdb=" O HIS E 836 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY E 850 " --> pdb=" O VAL E 846 " (cutoff:3.500A) Processing helix chain 'E' and resid 856 through 867 Processing helix chain 'E' and resid 867 through 877 Processing helix chain 'E' and resid 890 through 906 Processing helix chain 'E' and resid 925 through 936 Processing helix chain 'E' and resid 937 through 944 Processing helix chain 'E' and resid 954 through 972 removed outlier: 3.971A pdb=" N GLY E 958 " --> pdb=" O ASP E 954 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN E 972 " --> pdb=" O ARG E 968 " (cutoff:3.500A) Processing helix chain 'E' and resid 975 through 981 removed outlier: 3.700A pdb=" N LEU E 981 " --> pdb=" O VAL E 977 " (cutoff:3.500A) Processing helix chain 'E' and resid 986 through 999 Processing helix chain 'E' and resid 1006 through 1017 removed outlier: 3.501A pdb=" N ARG E1013 " --> pdb=" O GLN E1009 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU E1014 " --> pdb=" O ILE E1010 " (cutoff:3.500A) Processing helix chain 'E' and resid 1021 through 1023 No H-bonds generated for 'chain 'E' and resid 1021 through 1023' Processing helix chain 'E' and resid 1024 through 1044 removed outlier: 3.952A pdb=" N HIS E1030 " --> pdb=" O TRP E1026 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG E1034 " --> pdb=" O HIS E1030 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE E1044 " --> pdb=" O LEU E1040 " (cutoff:3.500A) Processing helix chain 'E' and resid 1045 through 1064 removed outlier: 3.803A pdb=" N ALA E1049 " --> pdb=" O SER E1045 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET E1064 " --> pdb=" O LEU E1060 " (cutoff:3.500A) Processing helix chain 'E' and resid 1111 through 1117 removed outlier: 3.610A pdb=" N ASN E1117 " --> pdb=" O ARG E1113 " (cutoff:3.500A) Processing helix chain 'E' and resid 1118 through 1141 removed outlier: 3.598A pdb=" N ILE E1124 " --> pdb=" O PRO E1120 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG E1141 " --> pdb=" O LEU E1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 1159 through 1175 removed outlier: 3.669A pdb=" N ARG E1168 " --> pdb=" O ASN E1164 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE E1171 " --> pdb=" O CYS E1167 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS E1175 " --> pdb=" O PHE E1171 " (cutoff:3.500A) Processing helix chain 'E' and resid 1178 through 1191 removed outlier: 3.900A pdb=" N VAL E1188 " --> pdb=" O SER E1184 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS E1189 " --> pdb=" O ARG E1185 " (cutoff:3.500A) Processing helix chain 'E' and resid 1197 through 1209 removed outlier: 3.838A pdb=" N ALA E1201 " --> pdb=" O LYS E1197 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN E1203 " --> pdb=" O LEU E1199 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU E1206 " --> pdb=" O SER E1202 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR E1207 " --> pdb=" O GLN E1203 " (cutoff:3.500A) Processing helix chain 'E' and resid 1218 through 1225 removed outlier: 3.533A pdb=" N GLN E1221 " --> pdb=" O ASP E1218 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 146 through 148 removed outlier: 5.822A pdb=" N ALA B 122 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL B 191 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 228 through 230 removed outlier: 4.002A pdb=" N HIS B 264 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN B 300 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL B 262 " --> pdb=" O GLN B 300 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE B 302 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE B 260 " --> pdb=" O ILE B 302 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 411 through 415 Processing sheet with id=AA4, first strand: chain 'E' and resid 495 through 496 removed outlier: 3.734A pdb=" N GLU E 495 " --> pdb=" O LEU E 621 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 588 through 590 Processing sheet with id=AA6, first strand: chain 'E' and resid 707 through 709 Processing sheet with id=AA7, first strand: chain 'E' and resid 798 through 800 Processing sheet with id=AA8, first strand: chain 'E' and resid 831 through 832 removed outlier: 3.784A pdb=" N ARG E 831 " --> pdb=" O SER E 915 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 918 through 921 Processing sheet with id=AB1, first strand: chain 'E' and resid 1069 through 1071 Processing sheet with id=AB2, first strand: chain 'E' and resid 1088 through 1091 641 hydrogen bonds defined for protein. 1875 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 99 hydrogen bonds 198 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 4.49 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3531 1.33 - 1.45: 3386 1.45 - 1.57: 8071 1.57 - 1.69: 196 1.69 - 1.81: 116 Bond restraints: 15300 Sorted by residual: bond pdb=" N SER E 505 " pdb=" CA SER E 505 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.20e-02 6.94e+03 5.99e+00 bond pdb=" N LEU E 504 " pdb=" CA LEU E 504 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.70e+00 bond pdb=" N GLU E 503 " pdb=" CA GLU E 503 " ideal model delta sigma weight residual 1.458 1.488 -0.029 1.23e-02 6.61e+03 5.68e+00 bond pdb=" N LEU E 500 " pdb=" CA LEU E 500 " ideal model delta sigma weight residual 1.459 1.486 -0.028 1.16e-02 7.43e+03 5.63e+00 bond pdb=" N ARG E 502 " pdb=" CA ARG E 502 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.16e-02 7.43e+03 5.50e+00 ... (remaining 15295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 20641 2.91 - 5.82: 381 5.82 - 8.73: 84 8.73 - 11.63: 14 11.63 - 14.54: 3 Bond angle restraints: 21123 Sorted by residual: angle pdb=" O3' DC T 45 " pdb=" P DT T 46 " pdb=" O5' DT T 46 " ideal model delta sigma weight residual 104.00 89.46 14.54 1.50e+00 4.44e-01 9.40e+01 angle pdb=" O3' DA T 23 " pdb=" P DC T 24 " pdb=" O5' DC T 24 " ideal model delta sigma weight residual 104.00 93.04 10.96 1.50e+00 4.44e-01 5.34e+01 angle pdb=" O3' DT T 46 " pdb=" P DA T 47 " pdb=" O5' DA T 47 " ideal model delta sigma weight residual 104.00 93.56 10.44 1.50e+00 4.44e-01 4.85e+01 angle pdb=" O3' DT T 27 " pdb=" P DT T 28 " pdb=" O5' DT T 28 " ideal model delta sigma weight residual 104.00 94.75 9.25 1.50e+00 4.44e-01 3.80e+01 angle pdb=" O3' DG T 33 " pdb=" P DT T 34 " pdb=" O5' DT T 34 " ideal model delta sigma weight residual 104.00 112.89 -8.89 1.50e+00 4.44e-01 3.51e+01 ... (remaining 21118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 8430 34.74 - 69.49: 642 69.49 - 104.23: 21 104.23 - 138.97: 2 138.97 - 173.72: 8 Dihedral angle restraints: 9103 sinusoidal: 4476 harmonic: 4627 Sorted by residual: dihedral pdb=" CA GLY B 242 " pdb=" C GLY B 242 " pdb=" N ASN B 243 " pdb=" CA ASN B 243 " ideal model delta harmonic sigma weight residual -180.00 -149.64 -30.36 0 5.00e+00 4.00e-02 3.69e+01 dihedral pdb=" CA GLY E 661 " pdb=" C GLY E 661 " pdb=" N ALA E 662 " pdb=" CA ALA E 662 " ideal model delta harmonic sigma weight residual -180.00 -153.67 -26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA PHE B 328 " pdb=" C PHE B 328 " pdb=" N GLY B 329 " pdb=" CA GLY B 329 " ideal model delta harmonic sigma weight residual 180.00 155.55 24.45 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 9100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 2248 0.149 - 0.299: 31 0.299 - 0.448: 12 0.448 - 0.597: 34 0.597 - 0.746: 4 Chirality restraints: 2329 Sorted by residual: chirality pdb=" P DG N 9 " pdb=" OP1 DG N 9 " pdb=" OP2 DG N 9 " pdb=" O5' DG N 9 " both_signs ideal model delta sigma weight residual True 2.35 -3.09 -0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" P DT T 34 " pdb=" OP1 DT T 34 " pdb=" OP2 DT T 34 " pdb=" O5' DT T 34 " both_signs ideal model delta sigma weight residual True 2.35 -3.00 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" P DG N 11 " pdb=" OP1 DG N 11 " pdb=" OP2 DG N 11 " pdb=" O5' DG N 11 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 2326 not shown) Planarity restraints: 2364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 502 " -0.661 9.50e-02 1.11e+02 2.96e-01 5.36e+01 pdb=" NE ARG E 502 " 0.039 2.00e-02 2.50e+03 pdb=" CZ ARG E 502 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG E 502 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 502 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 299 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.25e+00 pdb=" C ILE B 299 " 0.043 2.00e-02 2.50e+03 pdb=" O ILE B 299 " -0.016 2.00e-02 2.50e+03 pdb=" N GLN B 300 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E1034 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.22e+00 pdb=" C ARG E1034 " -0.043 2.00e-02 2.50e+03 pdb=" O ARG E1034 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN E1035 " 0.014 2.00e-02 2.50e+03 ... (remaining 2361 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 27 2.41 - 3.03: 7842 3.03 - 3.65: 22303 3.65 - 4.28: 31934 4.28 - 4.90: 51878 Nonbonded interactions: 113984 Sorted by model distance: nonbonded pdb=" OE1 GLU B 394 " pdb=" N4 DC N 38 " model vdw 1.785 3.120 nonbonded pdb=" CE2 TYR A 56 " pdb=" OP1 DA N 23 " model vdw 1.943 3.340 nonbonded pdb=" O3' DC N 37 " pdb=" O3' DC N 38 " model vdw 2.010 3.040 nonbonded pdb=" OH TYR E 530 " pdb=" O PRO E 651 " model vdw 2.216 3.040 nonbonded pdb=" O THR E 370 " pdb=" OG1 THR E 370 " model vdw 2.245 3.040 ... (remaining 113979 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: 5.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.210 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2758 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15300 Z= 0.258 Angle : 0.995 14.542 21123 Z= 0.511 Chirality : 0.088 0.746 2329 Planarity : 0.009 0.296 2364 Dihedral : 21.112 173.715 6093 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.86 % Allowed : 12.66 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -0.33 (0.20), residues: 1566 helix: 0.54 (0.17), residues: 841 sheet: -0.68 (0.49), residues: 108 loop : -1.10 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 516 TYR 0.032 0.002 TYR A 56 PHE 0.014 0.002 PHE B 271 TRP 0.018 0.002 TRP E1070 HIS 0.011 0.001 HIS E 693 Details of bonding type rmsd covalent geometry : bond 0.00540 (15300) covalent geometry : angle 0.99549 (21123) hydrogen bonds : bond 0.15700 ( 740) hydrogen bonds : angle 6.51888 ( 2073) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 249 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 178 ILE cc_start: 0.5559 (OUTLIER) cc_final: 0.4997 (pt) REVERT: E 516 ARG cc_start: 0.5100 (OUTLIER) cc_final: 0.4827 (ttm170) outliers start: 12 outliers final: 6 residues processed: 253 average time/residue: 0.1674 time to fit residues: 58.1508 Evaluate side-chains 245 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 237 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain E residue 516 ARG Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 638 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 132 HIS B 305 GLN B 366 HIS E 244 HIS ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 GLN E 331 GLN E 397 GLN E 485 GLN E 517 GLN E 585 GLN E 588 GLN E 608 HIS E 616 GLN E 680 HIS E 722 GLN E 916 HIS E 920 HIS E 945 ASN E1096 GLN E1170 GLN E1209 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.190908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.137421 restraints weight = 20627.557| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.02 r_work: 0.3503 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15300 Z= 0.181 Angle : 0.646 8.399 21123 Z= 0.341 Chirality : 0.041 0.193 2329 Planarity : 0.006 0.052 2364 Dihedral : 23.077 176.235 2846 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.30 % Allowed : 12.81 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.21), residues: 1566 helix: 1.18 (0.17), residues: 868 sheet: -0.89 (0.48), residues: 113 loop : -1.11 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 464 TYR 0.028 0.002 TYR B 247 PHE 0.015 0.001 PHE B 328 TRP 0.018 0.002 TRP E 707 HIS 0.009 0.001 HIS E 693 Details of bonding type rmsd covalent geometry : bond 0.00415 (15300) covalent geometry : angle 0.64599 (21123) hydrogen bonds : bond 0.05764 ( 740) hydrogen bonds : angle 3.84643 ( 2073) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 255 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 LEU cc_start: 0.8098 (tp) cc_final: 0.7811 (tt) REVERT: B 178 ILE cc_start: 0.8558 (tp) cc_final: 0.8338 (mm) REVERT: B 356 LYS cc_start: 0.8460 (mtpp) cc_final: 0.8260 (mttp) REVERT: E 271 TRP cc_start: 0.7799 (OUTLIER) cc_final: 0.6936 (m100) REVERT: E 987 ARG cc_start: 0.7764 (ttt90) cc_final: 0.7515 (ttt90) REVERT: E 1129 SER cc_start: 0.8533 (p) cc_final: 0.8321 (t) outliers start: 32 outliers final: 19 residues processed: 269 average time/residue: 0.1557 time to fit residues: 58.5553 Evaluate side-chains 266 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 246 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 791 ASP Chi-restraints excluded: chain E residue 869 ASP Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1147 VAL Chi-restraints excluded: chain E residue 1213 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 126 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 37 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 142 optimal weight: 0.0020 chunk 156 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 254 GLN ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 485 GLN E 585 GLN E 588 GLN E 680 HIS E 916 HIS E1096 GLN E1150 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.190706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.137465 restraints weight = 20990.647| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.00 r_work: 0.3513 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15300 Z= 0.153 Angle : 0.582 7.627 21123 Z= 0.310 Chirality : 0.039 0.170 2329 Planarity : 0.005 0.047 2364 Dihedral : 22.827 176.519 2831 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.09 % Allowed : 13.53 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.21), residues: 1566 helix: 1.58 (0.18), residues: 862 sheet: -0.93 (0.48), residues: 113 loop : -1.10 (0.23), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 464 TYR 0.021 0.001 TYR B 247 PHE 0.011 0.001 PHE B 328 TRP 0.016 0.001 TRP E 553 HIS 0.008 0.001 HIS E 693 Details of bonding type rmsd covalent geometry : bond 0.00343 (15300) covalent geometry : angle 0.58192 (21123) hydrogen bonds : bond 0.05073 ( 740) hydrogen bonds : angle 3.61984 ( 2073) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 248 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7262 (mm) REVERT: B 178 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8386 (mm) REVERT: B 231 GLU cc_start: 0.6982 (pm20) cc_final: 0.6724 (pm20) REVERT: B 295 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8215 (mtmt) REVERT: B 373 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8015 (tt) REVERT: E 271 TRP cc_start: 0.7788 (OUTLIER) cc_final: 0.6915 (m100) outliers start: 43 outliers final: 26 residues processed: 264 average time/residue: 0.1572 time to fit residues: 57.6371 Evaluate side-chains 274 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 244 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 542 GLU Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 772 MET Chi-restraints excluded: chain E residue 791 ASP Chi-restraints excluded: chain E residue 869 ASP Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 1042 GLU Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1098 ILE Chi-restraints excluded: chain E residue 1150 HIS Chi-restraints excluded: chain E residue 1213 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 47 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 39 optimal weight: 0.0870 chunk 146 optimal weight: 0.2980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 485 GLN E 680 HIS E 916 HIS E 920 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.191321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.137655 restraints weight = 20907.873| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.10 r_work: 0.3512 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15300 Z= 0.141 Angle : 0.564 7.060 21123 Z= 0.300 Chirality : 0.038 0.148 2329 Planarity : 0.005 0.045 2364 Dihedral : 22.707 176.902 2831 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.45 % Allowed : 13.88 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.21), residues: 1566 helix: 1.77 (0.18), residues: 866 sheet: -0.98 (0.48), residues: 111 loop : -1.03 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 464 TYR 0.018 0.001 TYR B 247 PHE 0.010 0.001 PHE B 328 TRP 0.014 0.001 TRP E 553 HIS 0.011 0.001 HIS E1150 Details of bonding type rmsd covalent geometry : bond 0.00315 (15300) covalent geometry : angle 0.56365 (21123) hydrogen bonds : bond 0.04703 ( 740) hydrogen bonds : angle 3.49486 ( 2073) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 244 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7384 (mm) REVERT: B 178 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8409 (mm) REVERT: B 373 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8081 (tt) REVERT: E 271 TRP cc_start: 0.7812 (OUTLIER) cc_final: 0.6945 (m100) REVERT: E 306 MET cc_start: 0.8298 (mtp) cc_final: 0.7984 (mtm) outliers start: 48 outliers final: 30 residues processed: 265 average time/residue: 0.1615 time to fit residues: 59.5488 Evaluate side-chains 274 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 240 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 405 HIS Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 542 GLU Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 772 MET Chi-restraints excluded: chain E residue 791 ASP Chi-restraints excluded: chain E residue 869 ASP Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 1042 GLU Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1098 ILE Chi-restraints excluded: chain E residue 1147 VAL Chi-restraints excluded: chain E residue 1207 THR Chi-restraints excluded: chain E residue 1213 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 87 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 109 optimal weight: 0.0570 chunk 12 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 143 optimal weight: 0.0060 overall best weight: 0.8116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 485 GLN E 588 GLN E 680 HIS E 916 HIS E 921 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.189576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.135641 restraints weight = 20819.585| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.04 r_work: 0.3481 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15300 Z= 0.174 Angle : 0.598 9.017 21123 Z= 0.315 Chirality : 0.040 0.192 2329 Planarity : 0.005 0.048 2364 Dihedral : 22.623 176.727 2831 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.81 % Allowed : 14.60 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.21), residues: 1566 helix: 1.77 (0.18), residues: 870 sheet: -0.95 (0.49), residues: 111 loop : -1.15 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 464 TYR 0.030 0.001 TYR B 247 PHE 0.011 0.001 PHE E 641 TRP 0.017 0.001 TRP E 707 HIS 0.009 0.001 HIS E 693 Details of bonding type rmsd covalent geometry : bond 0.00404 (15300) covalent geometry : angle 0.59826 (21123) hydrogen bonds : bond 0.05367 ( 740) hydrogen bonds : angle 3.57117 ( 2073) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 247 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7379 (mm) REVERT: B 373 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8054 (tt) REVERT: E 194 LEU cc_start: 0.5766 (OUTLIER) cc_final: 0.5546 (tt) REVERT: E 271 TRP cc_start: 0.7810 (OUTLIER) cc_final: 0.6946 (m100) REVERT: E 306 MET cc_start: 0.8366 (mtp) cc_final: 0.8112 (mtp) REVERT: E 690 THR cc_start: 0.7919 (p) cc_final: 0.7647 (m) REVERT: E 871 ILE cc_start: 0.8135 (pt) cc_final: 0.7903 (mt) REVERT: E 987 ARG cc_start: 0.7800 (ttt90) cc_final: 0.7573 (ttt90) outliers start: 53 outliers final: 31 residues processed: 269 average time/residue: 0.1548 time to fit residues: 58.1919 Evaluate side-chains 277 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 542 GLU Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 772 MET Chi-restraints excluded: chain E residue 869 ASP Chi-restraints excluded: chain E residue 914 VAL Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 1042 GLU Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1098 ILE Chi-restraints excluded: chain E residue 1147 VAL Chi-restraints excluded: chain E residue 1207 THR Chi-restraints excluded: chain E residue 1213 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 119 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 109 optimal weight: 0.0370 chunk 151 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 485 GLN E 588 GLN E 680 HIS E 916 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.190987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.137285 restraints weight = 20570.280| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.02 r_work: 0.3510 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15300 Z= 0.144 Angle : 0.561 8.494 21123 Z= 0.296 Chirality : 0.038 0.154 2329 Planarity : 0.005 0.047 2364 Dihedral : 22.558 176.937 2831 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.02 % Allowed : 15.76 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.21), residues: 1566 helix: 1.91 (0.18), residues: 872 sheet: -1.00 (0.48), residues: 113 loop : -1.09 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 464 TYR 0.027 0.001 TYR A 56 PHE 0.019 0.001 PHE E 465 TRP 0.013 0.001 TRP E 553 HIS 0.006 0.001 HIS E 693 Details of bonding type rmsd covalent geometry : bond 0.00328 (15300) covalent geometry : angle 0.56141 (21123) hydrogen bonds : bond 0.04599 ( 740) hydrogen bonds : angle 3.40756 ( 2073) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 238 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7370 (mm) REVERT: B 373 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8027 (tt) REVERT: E 194 LEU cc_start: 0.5729 (OUTLIER) cc_final: 0.5509 (tt) REVERT: E 271 TRP cc_start: 0.7796 (OUTLIER) cc_final: 0.6944 (m100) REVERT: E 306 MET cc_start: 0.8378 (mtp) cc_final: 0.8115 (mtp) REVERT: E 690 THR cc_start: 0.7889 (p) cc_final: 0.7609 (m) outliers start: 42 outliers final: 28 residues processed: 256 average time/residue: 0.1601 time to fit residues: 56.7207 Evaluate side-chains 267 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 235 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 542 GLU Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 772 MET Chi-restraints excluded: chain E residue 869 ASP Chi-restraints excluded: chain E residue 914 VAL Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 1042 GLU Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1098 ILE Chi-restraints excluded: chain E residue 1147 VAL Chi-restraints excluded: chain E residue 1207 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 158 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 HIS ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN E 254 GLN E 485 GLN E 588 GLN E 680 HIS E 916 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.188299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.133850 restraints weight = 20442.249| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.03 r_work: 0.3463 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15300 Z= 0.211 Angle : 0.615 8.188 21123 Z= 0.324 Chirality : 0.041 0.164 2329 Planarity : 0.005 0.052 2364 Dihedral : 22.608 176.987 2831 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.38 % Allowed : 15.68 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.21), residues: 1566 helix: 1.79 (0.18), residues: 871 sheet: -0.98 (0.49), residues: 111 loop : -1.22 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 464 TYR 0.032 0.002 TYR B 247 PHE 0.017 0.002 PHE E 465 TRP 0.020 0.002 TRP E 707 HIS 0.009 0.001 HIS E 693 Details of bonding type rmsd covalent geometry : bond 0.00499 (15300) covalent geometry : angle 0.61506 (21123) hydrogen bonds : bond 0.05775 ( 740) hydrogen bonds : angle 3.61223 ( 2073) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 243 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7392 (mm) REVERT: B 373 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8055 (tt) REVERT: E 176 GLU cc_start: 0.6730 (pt0) cc_final: 0.6409 (pp20) REVERT: E 194 LEU cc_start: 0.5902 (OUTLIER) cc_final: 0.5658 (tt) REVERT: E 271 TRP cc_start: 0.7821 (OUTLIER) cc_final: 0.6975 (m100) REVERT: E 328 LEU cc_start: 0.8746 (mp) cc_final: 0.8533 (mt) REVERT: E 515 GLN cc_start: 0.8500 (tm-30) cc_final: 0.7982 (tm-30) REVERT: E 690 THR cc_start: 0.7948 (p) cc_final: 0.7641 (m) outliers start: 47 outliers final: 37 residues processed: 262 average time/residue: 0.1565 time to fit residues: 56.8256 Evaluate side-chains 280 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 239 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 542 GLU Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 682 GLU Chi-restraints excluded: chain E residue 772 MET Chi-restraints excluded: chain E residue 869 ASP Chi-restraints excluded: chain E residue 914 VAL Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 1017 LEU Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1098 ILE Chi-restraints excluded: chain E residue 1147 VAL Chi-restraints excluded: chain E residue 1159 ASP Chi-restraints excluded: chain E residue 1169 GLU Chi-restraints excluded: chain E residue 1207 THR Chi-restraints excluded: chain E residue 1213 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 29 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 115 optimal weight: 0.4980 chunk 15 optimal weight: 40.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 485 GLN E 588 GLN E 680 HIS E 916 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.189481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.135360 restraints weight = 20735.389| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.08 r_work: 0.3477 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15300 Z= 0.159 Angle : 0.573 8.219 21123 Z= 0.303 Chirality : 0.039 0.163 2329 Planarity : 0.005 0.051 2364 Dihedral : 22.594 176.893 2831 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.24 % Allowed : 16.33 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.21), residues: 1566 helix: 1.90 (0.18), residues: 870 sheet: -1.10 (0.48), residues: 111 loop : -1.19 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 464 TYR 0.021 0.001 TYR B 247 PHE 0.018 0.001 PHE E 465 TRP 0.016 0.001 TRP E 707 HIS 0.007 0.001 HIS E 693 Details of bonding type rmsd covalent geometry : bond 0.00367 (15300) covalent geometry : angle 0.57272 (21123) hydrogen bonds : bond 0.04919 ( 740) hydrogen bonds : angle 3.49397 ( 2073) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 237 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7433 (mm) REVERT: B 130 ILE cc_start: 0.5261 (OUTLIER) cc_final: 0.4941 (mm) REVERT: B 373 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8099 (tt) REVERT: E 194 LEU cc_start: 0.5790 (OUTLIER) cc_final: 0.5552 (tt) REVERT: E 271 TRP cc_start: 0.7853 (OUTLIER) cc_final: 0.7018 (m100) REVERT: E 344 ARG cc_start: 0.7334 (mtm180) cc_final: 0.6822 (mtm180) REVERT: E 690 THR cc_start: 0.7947 (p) cc_final: 0.7645 (m) outliers start: 45 outliers final: 36 residues processed: 256 average time/residue: 0.1576 time to fit residues: 55.9195 Evaluate side-chains 277 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 542 GLU Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 772 MET Chi-restraints excluded: chain E residue 869 ASP Chi-restraints excluded: chain E residue 914 VAL Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 1017 LEU Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1098 ILE Chi-restraints excluded: chain E residue 1147 VAL Chi-restraints excluded: chain E residue 1150 HIS Chi-restraints excluded: chain E residue 1159 ASP Chi-restraints excluded: chain E residue 1207 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 55 optimal weight: 8.9990 chunk 28 optimal weight: 0.3980 chunk 165 optimal weight: 20.0000 chunk 83 optimal weight: 0.0980 chunk 147 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 88 optimal weight: 0.0980 chunk 105 optimal weight: 0.5980 chunk 16 optimal weight: 30.0000 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 485 GLN E 588 GLN E 680 HIS E 916 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.191087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137312 restraints weight = 20895.221| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.08 r_work: 0.3512 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15300 Z= 0.130 Angle : 0.543 8.152 21123 Z= 0.287 Chirality : 0.037 0.160 2329 Planarity : 0.005 0.048 2364 Dihedral : 22.536 178.002 2831 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.24 % Allowed : 16.33 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.21), residues: 1566 helix: 2.06 (0.18), residues: 872 sheet: -1.14 (0.48), residues: 113 loop : -1.06 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 464 TYR 0.019 0.001 TYR A 56 PHE 0.017 0.001 PHE E 465 TRP 0.011 0.001 TRP E 707 HIS 0.005 0.001 HIS E 693 Details of bonding type rmsd covalent geometry : bond 0.00291 (15300) covalent geometry : angle 0.54321 (21123) hydrogen bonds : bond 0.04214 ( 740) hydrogen bonds : angle 3.33511 ( 2073) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 239 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 MET cc_start: 0.4042 (OUTLIER) cc_final: 0.3786 (mmt) REVERT: B 113 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7466 (mm) REVERT: B 373 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8093 (tt) REVERT: E 194 LEU cc_start: 0.5692 (OUTLIER) cc_final: 0.5466 (tt) REVERT: E 271 TRP cc_start: 0.7848 (OUTLIER) cc_final: 0.6993 (m100) REVERT: E 344 ARG cc_start: 0.7283 (mtm180) cc_final: 0.6743 (mtm180) REVERT: E 690 THR cc_start: 0.7882 (p) cc_final: 0.7634 (m) REVERT: E 987 ARG cc_start: 0.7816 (ttt90) cc_final: 0.7605 (ttt90) outliers start: 45 outliers final: 34 residues processed: 256 average time/residue: 0.1551 time to fit residues: 54.9497 Evaluate side-chains 272 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 542 GLU Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 682 GLU Chi-restraints excluded: chain E residue 772 MET Chi-restraints excluded: chain E residue 791 ASP Chi-restraints excluded: chain E residue 869 ASP Chi-restraints excluded: chain E residue 914 VAL Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 1017 LEU Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1098 ILE Chi-restraints excluded: chain E residue 1147 VAL Chi-restraints excluded: chain E residue 1207 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 79 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 157 optimal weight: 30.0000 chunk 152 optimal weight: 0.9990 chunk 90 optimal weight: 0.0030 chunk 27 optimal weight: 0.0040 chunk 48 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 overall best weight: 0.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 485 GLN E 588 GLN E 680 HIS E 916 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.190207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.137531 restraints weight = 20686.985| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.01 r_work: 0.3502 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15300 Z= 0.144 Angle : 0.562 8.202 21123 Z= 0.297 Chirality : 0.038 0.164 2329 Planarity : 0.005 0.049 2364 Dihedral : 22.518 178.180 2831 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.88 % Allowed : 17.05 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.21), residues: 1566 helix: 2.07 (0.18), residues: 874 sheet: -1.16 (0.48), residues: 113 loop : -1.07 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 464 TYR 0.018 0.001 TYR A 56 PHE 0.021 0.001 PHE E 465 TRP 0.014 0.001 TRP E 707 HIS 0.006 0.001 HIS E 693 Details of bonding type rmsd covalent geometry : bond 0.00327 (15300) covalent geometry : angle 0.56151 (21123) hydrogen bonds : bond 0.04596 ( 740) hydrogen bonds : angle 3.36658 ( 2073) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 MET cc_start: 0.4037 (OUTLIER) cc_final: 0.3809 (mmt) REVERT: B 113 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7423 (mm) REVERT: B 373 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8096 (tt) REVERT: E 194 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.5501 (tt) REVERT: E 271 TRP cc_start: 0.7837 (OUTLIER) cc_final: 0.6974 (m100) REVERT: E 306 MET cc_start: 0.8690 (mtp) cc_final: 0.8447 (mtm) REVERT: E 344 ARG cc_start: 0.7308 (mtm180) cc_final: 0.6742 (mtm180) REVERT: E 412 VAL cc_start: 0.8862 (t) cc_final: 0.8576 (p) REVERT: E 690 THR cc_start: 0.7843 (p) cc_final: 0.7619 (m) outliers start: 40 outliers final: 32 residues processed: 251 average time/residue: 0.1429 time to fit residues: 49.7018 Evaluate side-chains 268 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 542 GLU Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 772 MET Chi-restraints excluded: chain E residue 869 ASP Chi-restraints excluded: chain E residue 914 VAL Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 1017 LEU Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1098 ILE Chi-restraints excluded: chain E residue 1147 VAL Chi-restraints excluded: chain E residue 1207 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 11 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 83 optimal weight: 0.1980 chunk 91 optimal weight: 0.6980 chunk 87 optimal weight: 0.0670 chunk 69 optimal weight: 0.6980 chunk 140 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 26 optimal weight: 0.1980 chunk 96 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 HIS E 485 GLN E 680 HIS E 916 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.191753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.139337 restraints weight = 20692.244| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.02 r_work: 0.3528 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15300 Z= 0.127 Angle : 0.544 8.160 21123 Z= 0.288 Chirality : 0.037 0.167 2329 Planarity : 0.005 0.048 2364 Dihedral : 22.467 178.494 2831 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.59 % Allowed : 17.27 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.21), residues: 1566 helix: 2.16 (0.18), residues: 875 sheet: -1.09 (0.48), residues: 113 loop : -0.99 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 464 TYR 0.018 0.001 TYR A 56 PHE 0.021 0.001 PHE E 465 TRP 0.010 0.001 TRP E1070 HIS 0.005 0.001 HIS E 693 Details of bonding type rmsd covalent geometry : bond 0.00283 (15300) covalent geometry : angle 0.54410 (21123) hydrogen bonds : bond 0.04061 ( 740) hydrogen bonds : angle 3.26875 ( 2073) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5678.83 seconds wall clock time: 97 minutes 28.38 seconds (5848.38 seconds total)