Starting phenix.real_space_refine on Thu Aug 6 12:25:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mn4_48412/08_2026/9mn4_48412.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mn4_48412/08_2026/9mn4_48412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mn4_48412/08_2026/9mn4_48412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mn4_48412/08_2026/9mn4_48412.map" model { file = "/net/cci-nas-00/data/ceres_data/9mn4_48412/08_2026/9mn4_48412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mn4_48412/08_2026/9mn4_48412.cif" } resolution = 3.05 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 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 101 5.49 5 S 74 5.16 5 C 9112 2.51 5 N 2668 2.21 5 O 2880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14835 Number of models: 1 Model: "" Number of chains: 6 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: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2632 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 21, 'TRANS': 302} Chain: "E" Number of atoms: 8480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8480 Classifications: {'peptide': 1062} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 66, 'TRANS': 995} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 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: "R" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 2} 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: 2.98, per 1000 atoms: 0.20 Number of scatterers: 14835 At special positions: 0 Unit cell: (101.385, 136.682, 144.192, 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 101 15.00 O 2880 8.00 N 2668 7.00 C 9112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 174 " - pdb=" SG CYS E 178 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 478.3 milliseconds 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: 73 helices and 11 sheets defined 60.3% alpha, 4.4% beta 43 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 55 through 72 Proline residue: A 66 - end of helix Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 92 through 121 removed outlier: 3.554A pdb=" N LYS A 96 " --> pdb=" O PRO A 92 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 102 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 103 " --> pdb=" O TYR A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 152 Processing helix chain 'A' and resid 160 through 170 Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 193 through 225 removed outlier: 4.510A pdb=" N LEU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 90 removed outlier: 3.725A pdb=" N GLY B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 129 through 136 removed outlier: 4.028A pdb=" N LEU B 133 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU B 134 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 175 removed outlier: 4.164A pdb=" N LEU B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 214 removed outlier: 3.530A pdb=" N CYS B 214 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 220 removed outlier: 3.848A pdb=" N LYS B 219 " --> pdb=" O SER B 216 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE B 220 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 238 removed outlier: 3.951A pdb=" N LYS B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 257 removed outlier: 3.549A pdb=" N VAL B 252 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 291 Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.929A pdb=" N PHE B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.729A pdb=" N HIS B 338 " --> pdb=" O THR B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 355 removed outlier: 3.793A pdb=" N ILE B 350 " --> pdb=" O ASP B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 removed outlier: 3.881A pdb=" N MET B 365 " --> pdb=" O VAL B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 379 removed outlier: 3.714A pdb=" N PHE B 370 " --> pdb=" O HIS B 366 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU B 378 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG B 379 " --> pdb=" O GLU B 375 " (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 157 Processing helix chain 'E' and resid 168 through 181 Processing helix chain 'E' and resid 186 through 197 removed outlier: 3.741A pdb=" N LEU E 191 " --> pdb=" O TRP E 187 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA E 192 " --> pdb=" O GLU E 188 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU E 195 " --> pdb=" O LEU E 191 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN E 196 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 236 removed outlier: 3.680A pdb=" N LEU E 235 " --> pdb=" O LYS E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 252 removed outlier: 3.945A pdb=" N ALA E 242 " --> pdb=" O GLN E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.905A pdb=" N LYS E 257 " --> pdb=" O ARG E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 273 removed outlier: 3.538A pdb=" N TYR E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL E 267 " --> pdb=" O MET E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 290 removed outlier: 3.645A pdb=" N LEU E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 319 through 327 removed outlier: 3.664A pdb=" N MET E 323 " --> pdb=" O CYS E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 335 removed outlier: 4.003A pdb=" N PHE E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) removed outlier: 3.730A 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 352 Processing helix chain 'E' and resid 392 through 410 Processing helix chain 'E' and resid 424 through 432 Processing helix chain 'E' and resid 438 through 462 removed outlier: 3.976A pdb=" N LYS E 443 " --> pdb=" O ASP E 439 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA E 444 " --> pdb=" O GLN E 440 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 473 Processing helix chain 'E' and resid 475 through 488 removed outlier: 3.894A pdb=" N LEU E 483 " --> pdb=" O VAL E 479 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN E 488 " --> pdb=" O LEU E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 520 removed outlier: 3.600A pdb=" N ALA E 506 " --> pdb=" O ARG E 502 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG E 511 " --> pdb=" O ARG E 507 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 534 removed outlier: 4.031A pdb=" N ALA E 525 " --> pdb=" O GLY E 521 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS E 532 " --> pdb=" O ASN E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 556 Processing helix chain 'E' and resid 568 through 587 Processing helix chain 'E' and resid 624 through 632 Processing helix chain 'E' and resid 678 through 687 removed outlier: 3.534A pdb=" N CYS E 687 " --> pdb=" O LEU E 683 " (cutoff:3.500A) Processing helix chain 'E' and resid 689 through 691 No H-bonds generated for 'chain 'E' and resid 689 through 691' Processing helix chain 'E' and resid 692 through 704 Processing helix chain 'E' and resid 710 through 723 removed outlier: 4.349A pdb=" N LEU E 716 " --> pdb=" O ARG E 712 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL E 717 " --> pdb=" O VAL E 713 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA E 723 " --> pdb=" O GLN E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 727 through 731 removed outlier: 3.715A pdb=" N GLY E 730 " --> pdb=" O PRO E 727 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL E 731 " --> pdb=" O GLN E 728 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 727 through 731' Processing helix chain 'E' and resid 764 through 789 removed outlier: 3.791A pdb=" N GLU E 778 " --> pdb=" O SER E 774 " (cutoff:3.500A) Processing helix chain 'E' and resid 820 through 823 Processing helix chain 'E' and resid 836 through 850 removed outlier: 4.409A pdb=" N TRP E 840 " --> pdb=" O HIS E 836 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU E 841 " --> pdb=" O GLY E 837 " (cutoff:3.500A) Processing helix chain 'E' and resid 856 through 867 Processing helix chain 'E' and resid 867 through 876 Processing helix chain 'E' and resid 883 through 888 removed outlier: 3.901A pdb=" N MET E 886 " --> pdb=" O LYS E 883 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA E 888 " --> pdb=" O TRP E 885 " (cutoff:3.500A) Processing helix chain 'E' and resid 890 through 906 removed outlier: 3.600A pdb=" N ARG E 906 " --> pdb=" O ALA E 902 " (cutoff:3.500A) Processing helix chain 'E' and resid 909 through 912 Processing helix chain 'E' and resid 925 through 936 Processing helix chain 'E' and resid 939 through 944 removed outlier: 3.924A pdb=" N SER E 943 " --> pdb=" O VAL E 939 " (cutoff:3.500A) Processing helix chain 'E' and resid 954 through 972 removed outlier: 3.612A pdb=" N GLY E 958 " --> pdb=" O ASP E 954 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU E 964 " --> pdb=" O ALA E 960 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL E 965 " --> pdb=" O ALA E 961 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE E 966 " --> pdb=" O GLN E 962 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 981 removed outlier: 3.835A pdb=" N VAL E 980 " --> pdb=" O ARG E 976 " (cutoff:3.500A) Processing helix chain 'E' and resid 990 through 997 removed outlier: 3.697A pdb=" N VAL E 994 " --> pdb=" O VAL E 990 " (cutoff:3.500A) Processing helix chain 'E' and resid 1002 through 1017 removed outlier: 4.026A pdb=" N LEU E1017 " --> pdb=" O ARG E1013 " (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: 3.607A pdb=" N ALA E1028 " --> pdb=" O PHE E1024 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS E1030 " --> pdb=" O TRP E1026 " (cutoff:3.500A) Processing helix chain 'E' and resid 1045 through 1063 removed outlier: 3.630A pdb=" N ALA E1049 " --> pdb=" O SER E1045 " (cutoff:3.500A) Processing helix chain 'E' and resid 1118 through 1142 removed outlier: 3.661A pdb=" N ILE E1124 " --> pdb=" O PRO E1120 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG E1141 " --> pdb=" O LEU E1137 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS E1142 " --> pdb=" O HIS E1138 " (cutoff:3.500A) Processing helix chain 'E' and resid 1156 through 1158 No H-bonds generated for 'chain 'E' and resid 1156 through 1158' Processing helix chain 'E' and resid 1159 through 1177 removed outlier: 4.028A pdb=" N GLU E1177 " --> pdb=" O ARG E1173 " (cutoff:3.500A) Processing helix chain 'E' and resid 1178 through 1190 Processing helix chain 'E' and resid 1197 through 1210 removed outlier: 3.938A pdb=" N ALA E1201 " --> pdb=" O LYS E1197 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS E1205 " --> pdb=" O ALA E1201 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU E1206 " --> pdb=" O SER E1202 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN E1209 " --> pdb=" O LYS E1205 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA E1210 " --> pdb=" O GLU E1206 " (cutoff:3.500A) Processing helix chain 'E' and resid 1218 through 1225 Processing sheet with id=AA1, first strand: chain 'B' and resid 73 through 75 Processing sheet with id=AA2, first strand: chain 'B' and resid 100 through 101 removed outlier: 5.905A pdb=" N LEU B 100 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N MET B 194 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N PHE B 228 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N GLY B 193 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU B 296 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N MET B 265 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU B 298 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 412 through 413 Processing sheet with id=AA4, first strand: chain 'E' and resid 495 through 496 removed outlier: 3.838A 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 Processing sheet with id=AA9, first strand: chain 'E' and resid 919 through 922 removed outlier: 3.844A pdb=" N THR E1155 " --> pdb=" O VAL E 919 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 1070 through 1071 Processing sheet with id=AB2, first strand: chain 'E' and resid 1089 through 1091 removed outlier: 3.616A pdb=" N ILE E1098 " --> pdb=" O ILE E1091 " (cutoff:3.500A) 629 hydrogen bonds defined for protein. 1824 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 109 hydrogen bonds 218 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 3.74 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4607 1.35 - 1.48: 4119 1.48 - 1.61: 6523 1.61 - 1.74: 17 1.74 - 1.87: 116 Bond restraints: 15382 Sorted by residual: bond pdb=" O3' DC T 3 " pdb=" P DC T 4 " ideal model delta sigma weight residual 1.607 1.487 0.120 1.20e-02 6.94e+03 1.00e+02 bond pdb=" O3' DT T 5 " pdb=" P DA T 6 " ideal model delta sigma weight residual 1.607 1.532 0.075 1.20e-02 6.94e+03 3.92e+01 bond pdb=" C3' DG N 36 " pdb=" O3' DG N 36 " ideal model delta sigma weight residual 1.435 1.368 0.067 1.30e-02 5.92e+03 2.69e+01 bond pdb=" C1' DC N 37 " pdb=" N1 DC N 37 " ideal model delta sigma weight residual 1.468 1.534 -0.066 1.40e-02 5.10e+03 2.23e+01 bond pdb=" C3' DA N 41 " pdb=" O3' DA N 41 " ideal model delta sigma weight residual 1.435 1.492 -0.057 1.30e-02 5.92e+03 1.90e+01 ... (remaining 15377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 21103 4.18 - 8.36: 126 8.36 - 12.54: 8 12.54 - 16.72: 5 16.72 - 20.90: 3 Bond angle restraints: 21245 Sorted by residual: angle pdb=" C3' DC T 3 " pdb=" O3' DC T 3 " pdb=" P DC T 4 " ideal model delta sigma weight residual 119.70 100.82 18.88 1.20e+00 6.94e-01 2.47e+02 angle pdb=" O4' DG N 36 " pdb=" C4' DG N 36 " pdb=" C3' DG N 36 " ideal model delta sigma weight residual 106.00 100.19 5.81 6.00e-01 2.78e+00 9.37e+01 angle pdb=" O3' DC T 4 " pdb=" P DT T 5 " pdb=" O5' DT T 5 " ideal model delta sigma weight residual 104.00 120.91 -16.91 1.90e+00 2.77e-01 7.92e+01 angle pdb=" N ASP E 819 " pdb=" CA ASP E 819 " pdb=" C ASP E 819 " ideal model delta sigma weight residual 114.04 105.12 8.92 1.24e+00 6.50e-01 5.17e+01 angle pdb=" O3' DC T 3 " pdb=" P DC T 4 " pdb=" OP1 DC T 4 " ideal model delta sigma weight residual 108.00 87.10 20.90 3.00e+00 1.11e-01 4.85e+01 ... (remaining 21240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 8535 35.94 - 71.88: 609 71.88 - 107.81: 11 107.81 - 143.75: 0 143.75 - 179.69: 4 Dihedral angle restraints: 9159 sinusoidal: 4532 harmonic: 4627 Sorted by residual: dihedral pdb=" CA SER E1148 " pdb=" C SER E1148 " pdb=" N VAL E1149 " pdb=" CA VAL E1149 " ideal model delta harmonic sigma weight residual 180.00 145.95 34.05 0 5.00e+00 4.00e-02 4.64e+01 dihedral pdb=" CA CYS E 178 " pdb=" C CYS E 178 " pdb=" N THR E 179 " pdb=" CA THR E 179 " ideal model delta harmonic sigma weight residual 180.00 148.15 31.85 0 5.00e+00 4.00e-02 4.06e+01 dihedral pdb=" CA PHE E 984 " pdb=" C PHE E 984 " pdb=" N ILE E 985 " pdb=" CA ILE E 985 " ideal model delta harmonic sigma weight residual 180.00 156.25 23.75 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 9156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.235: 2330 0.235 - 0.469: 10 0.469 - 0.704: 4 0.704 - 0.939: 0 0.939 - 1.173: 1 Chirality restraints: 2345 Sorted by residual: chirality pdb=" P DC T 4 " pdb=" OP1 DC T 4 " pdb=" OP2 DC T 4 " pdb=" O5' DC T 4 " both_signs ideal model delta sigma weight residual True 2.34 -1.16 1.17 2.00e-01 2.50e+01 3.44e+01 chirality pdb=" P G R 1 " pdb=" OP1 G R 1 " pdb=" OP2 G R 1 " pdb=" O5' G R 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" P DT T 9 " pdb=" OP1 DT T 9 " pdb=" OP2 DT T 9 " pdb=" O5' DT T 9 " both_signs ideal model delta sigma weight residual True 2.34 -2.84 -0.51 2.00e-01 2.50e+01 6.40e+00 ... (remaining 2342 not shown) Planarity restraints: 2367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 163 " -0.062 5.00e-02 4.00e+02 9.49e-02 1.44e+01 pdb=" N PRO B 164 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 175 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C LEU E 175 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU E 175 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU E 176 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 400 " 0.017 2.00e-02 2.50e+03 2.32e-02 9.41e+00 pdb=" CG PHE E 400 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE E 400 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE E 400 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE E 400 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE E 400 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE E 400 " 0.000 2.00e-02 2.50e+03 ... (remaining 2364 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 536 2.71 - 3.26: 13418 3.26 - 3.81: 23792 3.81 - 4.35: 29102 4.35 - 4.90: 47136 Nonbonded interactions: 113984 Sorted by model distance: nonbonded pdb=" O LEU E 175 " pdb=" OG1 THR E 179 " model vdw 2.166 3.040 nonbonded pdb=" OG SER E 505 " pdb=" O GLN E 572 " model vdw 2.231 3.040 nonbonded pdb=" OD1 ASP E 870 " pdb=" NH2 ARG E 882 " model vdw 2.246 3.120 nonbonded pdb=" OH TYR E 530 " pdb=" O PRO E 651 " model vdw 2.262 3.040 nonbonded pdb=" OG SER E1062 " pdb=" OE1 GLN E1115 " model vdw 2.262 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: 4.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.740 Find NCS groups from input model: 0.070 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5301 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 0.120 15383 Z= 0.380 Angle : 0.942 20.897 21247 Z= 0.590 Chirality : 0.063 1.173 2345 Planarity : 0.007 0.095 2367 Dihedral : 20.230 179.691 6146 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.02 % Favored : 95.91 % Rotamer: Outliers : 0.86 % Allowed : 12.64 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.19), residues: 1566 helix: -0.11 (0.16), residues: 863 sheet: -1.43 (0.60), residues: 66 loop : -1.61 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 304 TYR 0.019 0.002 TYR B 297 PHE 0.053 0.003 PHE E 400 TRP 0.026 0.002 TRP E 707 HIS 0.009 0.001 HIS E 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.38 (15382) covalent geometry : angle 0.94133 / 0.59 (21245) SS BOND : bond 0.01775 / 0.93 ( 1) SS BOND : angle 4.14988 / 2.24 ( 2) hydrogen bonds : bond 0.13285 / 8.93 ( 738) hydrogen bonds : angle 4.94863 / 3.54 ( 2042) *********************** 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 202 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 295 LYS cc_start: 0.7479 (ttmt) cc_final: 0.7226 (ttmt) REVERT: E 237 ASP cc_start: 0.6309 (p0) cc_final: 0.5453 (t0) REVERT: E 653 LEU cc_start: 0.8428 (tp) cc_final: 0.8213 (mp) REVERT: E 819 ASP cc_start: 0.6236 (OUTLIER) cc_final: 0.4707 (t0) outliers start: 12 outliers final: 8 residues processed: 197 average time/residue: 0.1341 time to fit residues: 37.7086 Evaluate side-chains 195 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 186 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 813 PHE Chi-restraints excluded: chain E residue 819 ASP Chi-restraints excluded: chain E residue 1114 LYS Chi-restraints excluded: chain E residue 1163 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 40.0000 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 0.0770 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 HIS E 161 GLN E 244 HIS E 304 GLN E 528 ASN E 916 HIS E 920 HIS E 921 GLN E 926 ASN E 930 HIS E1080 GLN E1090 GLN ** E1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1102 HIS E1115 GLN E1209 GLN E1221 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.214252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.170093 restraints weight = 21829.176| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 2.11 r_work: 0.3981 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15383 Z= 0.148 Angle : 0.617 11.907 21247 Z= 0.333 Chirality : 0.042 0.384 2345 Planarity : 0.005 0.086 2367 Dihedral : 21.993 174.573 2893 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.65 % Allowed : 13.51 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.20), residues: 1566 helix: 0.81 (0.17), residues: 873 sheet: -1.24 (0.60), residues: 66 loop : -1.44 (0.22), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 304 TYR 0.009 0.001 TYR E 264 PHE 0.018 0.002 PHE E 802 TRP 0.019 0.001 TRP E 707 HIS 0.005 0.001 HIS E 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (15382) covalent geometry : angle 0.61584 / 0.33 (21245) SS BOND : bond 0.01832 / 0.96 ( 1) SS BOND : angle 3.31449 / 1.84 ( 2) hydrogen bonds : bond 0.05257 / 3.44 ( 738) hydrogen bonds : angle 3.82796 / 2.78 ( 2042) *********************** 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 209 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 137 MET cc_start: 0.7147 (mmm) cc_final: 0.6919 (mmm) REVERT: E 819 ASP cc_start: 0.6777 (OUTLIER) cc_final: 0.5374 (t0) REVERT: E 1113 ARG cc_start: 0.7976 (ttt180) cc_final: 0.7635 (ttt-90) outliers start: 23 outliers final: 9 residues processed: 197 average time/residue: 0.1434 time to fit residues: 40.3684 Evaluate side-chains 195 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 813 PHE Chi-restraints excluded: chain E residue 819 ASP Chi-restraints excluded: chain E residue 1043 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 126 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 25 optimal weight: 0.0570 chunk 112 optimal weight: 0.6980 chunk 36 optimal weight: 0.0670 chunk 5 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 255 GLN E 222 GLN ** E1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.214536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.170248 restraints weight = 22316.453| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 2.14 r_work: 0.3985 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15383 Z= 0.134 Angle : 0.576 10.747 21247 Z= 0.312 Chirality : 0.040 0.397 2345 Planarity : 0.005 0.081 2367 Dihedral : 21.911 174.680 2879 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.58 % Allowed : 15.16 % Favored : 83.26 % 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 are not related in a simple way. whole: 0.16 (0.21), residues: 1566 helix: 1.20 (0.18), residues: 876 sheet: -1.14 (0.59), residues: 66 loop : -1.35 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 882 TYR 0.010 0.001 TYR E 264 PHE 0.015 0.001 PHE B 220 TRP 0.016 0.001 TRP E 707 HIS 0.004 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (15382) covalent geometry : angle 0.57493 / 0.31 (21245) SS BOND : bond 0.01781 / 0.94 ( 1) SS BOND : angle 3.17175 / 1.74 ( 2) hydrogen bonds : bond 0.04710 / 3.05 ( 738) hydrogen bonds : angle 3.60166 / 2.60 ( 2042) *********************** 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 213 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 227 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.6929 (mpp) REVERT: E 137 MET cc_start: 0.7210 (mmm) cc_final: 0.6909 (mmm) REVERT: E 279 GLU cc_start: 0.7330 (mt-10) cc_final: 0.7002 (mt-10) REVERT: E 308 ARG cc_start: 0.7604 (mtm-85) cc_final: 0.7396 (ttm110) REVERT: E 344 ARG cc_start: 0.6887 (mtt90) cc_final: 0.6655 (mtt90) REVERT: E 795 TRP cc_start: 0.6450 (m-10) cc_final: 0.6217 (m-10) REVERT: E 819 ASP cc_start: 0.6910 (OUTLIER) cc_final: 0.5413 (t0) REVERT: E 1109 LYS cc_start: 0.7832 (mmmm) cc_final: 0.7610 (mmmm) REVERT: E 1113 ARG cc_start: 0.8042 (ttt180) cc_final: 0.7725 (ttt-90) outliers start: 22 outliers final: 13 residues processed: 202 average time/residue: 0.1351 time to fit residues: 39.0146 Evaluate side-chains 200 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 813 PHE Chi-restraints excluded: chain E residue 819 ASP Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 1043 MET Chi-restraints excluded: chain E residue 1144 LEU Chi-restraints excluded: chain E residue 1192 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 112 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 16 optimal weight: 50.0000 chunk 114 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.212926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.168917 restraints weight = 22143.227| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.61 r_work: 0.3936 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15383 Z= 0.158 Angle : 0.585 10.522 21247 Z= 0.316 Chirality : 0.041 0.425 2345 Planarity : 0.005 0.077 2367 Dihedral : 21.865 174.028 2879 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.01 % Allowed : 15.30 % Favored : 82.69 % 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 are not related in a simple way. whole: 0.23 (0.21), residues: 1566 helix: 1.25 (0.18), residues: 878 sheet: -1.17 (0.59), residues: 66 loop : -1.30 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1173 TYR 0.011 0.001 TYR E1227 PHE 0.014 0.002 PHE E 497 TRP 0.018 0.001 TRP E 707 HIS 0.005 0.001 HIS E 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (15382) covalent geometry : angle 0.58460 / 0.32 (21245) SS BOND : bond 0.01753 / 0.92 ( 1) SS BOND : angle 3.10698 / 1.70 ( 2) hydrogen bonds : bond 0.04817 / 3.11 ( 738) hydrogen bonds : angle 3.57490 / 2.58 ( 2042) *********************** 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 229 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.2907 (mmp) cc_final: 0.2678 (mmp) REVERT: B 227 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7102 (mpp) REVERT: B 256 LEU cc_start: 0.8026 (mt) cc_final: 0.7752 (mt) REVERT: B 295 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7557 (ttpp) REVERT: E 137 MET cc_start: 0.7289 (mmm) cc_final: 0.6940 (mmm) REVERT: E 237 ASP cc_start: 0.6297 (p0) cc_final: 0.5806 (t0) REVERT: E 308 ARG cc_start: 0.7654 (mtm-85) cc_final: 0.7383 (ttm110) REVERT: E 344 ARG cc_start: 0.6922 (mtt90) cc_final: 0.6722 (mtt90) REVERT: E 795 TRP cc_start: 0.6648 (OUTLIER) cc_final: 0.6290 (m-10) REVERT: E 1069 GLU cc_start: 0.7380 (tt0) cc_final: 0.7148 (tt0) REVERT: E 1113 ARG cc_start: 0.8123 (ttt180) cc_final: 0.7809 (ttt-90) outliers start: 28 outliers final: 19 residues processed: 214 average time/residue: 0.1385 time to fit residues: 42.5405 Evaluate side-chains 212 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 411 ARG Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 795 TRP Chi-restraints excluded: chain E residue 802 PHE Chi-restraints excluded: chain E residue 813 PHE Chi-restraints excluded: chain E residue 943 SER Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 1043 MET Chi-restraints excluded: chain E residue 1144 LEU Chi-restraints excluded: chain E residue 1161 SER Chi-restraints excluded: chain E residue 1192 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 42 optimal weight: 0.0570 chunk 143 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 50 optimal weight: 0.0040 chunk 30 optimal weight: 0.0370 chunk 99 optimal weight: 0.0770 chunk 125 optimal weight: 0.9980 overall best weight: 0.1746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 311 ASN E 787 GLN ** E1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.215148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.170752 restraints weight = 22339.213| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.20 r_work: 0.3998 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 15383 Z= 0.119 Angle : 0.557 11.914 21247 Z= 0.299 Chirality : 0.039 0.354 2345 Planarity : 0.005 0.077 2367 Dihedral : 21.762 175.759 2877 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.08 % Allowed : 15.52 % Favored : 82.40 % 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 are not related in a simple way. whole: 0.58 (0.21), residues: 1566 helix: 1.53 (0.18), residues: 877 sheet: -0.74 (0.64), residues: 61 loop : -1.16 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1173 TYR 0.010 0.001 TYR E 264 PHE 0.013 0.001 PHE E 802 TRP 0.011 0.001 TRP E 707 HIS 0.005 0.001 HIS E1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.12 (15382) covalent geometry : angle 0.55633 / 0.30 (21245) SS BOND : bond 0.01744 / 0.92 ( 1) SS BOND : angle 3.09718 / 1.70 ( 2) hydrogen bonds : bond 0.04159 / 2.67 ( 738) hydrogen bonds : angle 3.36756 / 2.42 ( 2042) *********************** 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 225 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 256 LEU cc_start: 0.7949 (mt) cc_final: 0.7655 (mt) REVERT: E 137 MET cc_start: 0.7282 (mmm) cc_final: 0.6913 (mmm) REVERT: E 308 ARG cc_start: 0.7609 (mtm-85) cc_final: 0.7330 (ttm110) REVERT: E 582 MET cc_start: 0.6697 (ttp) cc_final: 0.6256 (ttp) REVERT: E 795 TRP cc_start: 0.6687 (OUTLIER) cc_final: 0.6170 (m-10) REVERT: E 1069 GLU cc_start: 0.7299 (tt0) cc_final: 0.7054 (tt0) REVERT: E 1109 LYS cc_start: 0.7832 (mmmm) cc_final: 0.7623 (mmmm) REVERT: E 1113 ARG cc_start: 0.8078 (ttt180) cc_final: 0.7780 (ttt-90) outliers start: 29 outliers final: 19 residues processed: 210 average time/residue: 0.1425 time to fit residues: 42.7378 Evaluate side-chains 213 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain E residue 795 TRP Chi-restraints excluded: chain E residue 813 PHE Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 1043 MET Chi-restraints excluded: chain E residue 1085 ASP Chi-restraints excluded: chain E residue 1144 LEU Chi-restraints excluded: chain E residue 1161 SER Chi-restraints excluded: chain E residue 1192 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 6 optimal weight: 10.0000 chunk 39 optimal weight: 0.2980 chunk 53 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 71 optimal weight: 0.4980 chunk 136 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 311 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.212798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.169160 restraints weight = 22145.936| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.58 r_work: 0.3948 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15383 Z= 0.149 Angle : 0.574 9.720 21247 Z= 0.309 Chirality : 0.041 0.395 2345 Planarity : 0.005 0.078 2367 Dihedral : 21.720 175.978 2875 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.51 % Allowed : 15.73 % Favored : 81.75 % 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 are not related in a simple way. whole: 0.53 (0.21), residues: 1566 helix: 1.48 (0.18), residues: 878 sheet: -0.95 (0.60), residues: 66 loop : -1.16 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1173 TYR 0.010 0.001 TYR B 247 PHE 0.016 0.002 PHE B 220 TRP 0.017 0.001 TRP E 707 HIS 0.005 0.001 HIS E 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (15382) covalent geometry : angle 0.57319 / 0.31 (21245) SS BOND : bond 0.01720 / 0.91 ( 1) SS BOND : angle 3.05921 / 1.67 ( 2) hydrogen bonds : bond 0.04597 / 2.97 ( 738) hydrogen bonds : angle 3.43268 / 2.47 ( 2042) *********************** 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 236 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: B 256 LEU cc_start: 0.8162 (mt) cc_final: 0.7882 (mt) REVERT: E 137 MET cc_start: 0.7312 (mmm) cc_final: 0.6903 (mmm) REVERT: E 237 ASP cc_start: 0.6343 (p0) cc_final: 0.5696 (t0) REVERT: E 308 ARG cc_start: 0.7655 (mtm-85) cc_final: 0.7415 (ttm110) REVERT: E 795 TRP cc_start: 0.6839 (OUTLIER) cc_final: 0.6258 (m-10) REVERT: E 800 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7666 (ptp) REVERT: E 1109 LYS cc_start: 0.7861 (mmmm) cc_final: 0.7646 (mmmm) REVERT: E 1113 ARG cc_start: 0.8118 (ttt180) cc_final: 0.7813 (ttt-90) REVERT: E 1150 HIS cc_start: 0.6103 (OUTLIER) cc_final: 0.5342 (m-70) outliers start: 35 outliers final: 22 residues processed: 217 average time/residue: 0.1401 time to fit residues: 43.6202 Evaluate side-chains 219 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 795 TRP Chi-restraints excluded: chain E residue 800 MET Chi-restraints excluded: chain E residue 802 PHE Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain E residue 943 SER Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 992 GLN Chi-restraints excluded: chain E residue 1043 MET Chi-restraints excluded: chain E residue 1144 LEU Chi-restraints excluded: chain E residue 1150 HIS Chi-restraints excluded: chain E residue 1192 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 21 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 24 optimal weight: 0.0370 chunk 0 optimal weight: 20.0000 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 311 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.212862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.169288 restraints weight = 22074.801| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.65 r_work: 0.3941 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15383 Z= 0.143 Angle : 0.576 10.735 21247 Z= 0.309 Chirality : 0.041 0.374 2345 Planarity : 0.005 0.081 2367 Dihedral : 21.668 175.980 2873 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.37 % Allowed : 16.24 % Favored : 81.39 % 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 are not related in a simple way. whole: 0.56 (0.21), residues: 1566 helix: 1.52 (0.18), residues: 877 sheet: -0.96 (0.61), residues: 66 loop : -1.16 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1173 TYR 0.010 0.001 TYR E1227 PHE 0.013 0.001 PHE B 151 TRP 0.016 0.001 TRP E 707 HIS 0.004 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (15382) covalent geometry : angle 0.57527 / 0.31 (21245) SS BOND : bond 0.01717 / 0.90 ( 1) SS BOND : angle 3.04409 / 1.66 ( 2) hydrogen bonds : bond 0.04481 / 2.88 ( 738) hydrogen bonds : angle 3.41702 / 2.46 ( 2042) *********************** 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 228 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: B 194 MET cc_start: 0.2866 (mmp) cc_final: 0.2594 (mmp) REVERT: B 256 LEU cc_start: 0.8187 (mt) cc_final: 0.7938 (mt) REVERT: E 137 MET cc_start: 0.7351 (mmm) cc_final: 0.6935 (mmm) REVERT: E 237 ASP cc_start: 0.6326 (p0) cc_final: 0.5717 (t0) REVERT: E 308 ARG cc_start: 0.7668 (mtm-85) cc_final: 0.7423 (ttm110) REVERT: E 531 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.6042 (mpt90) REVERT: E 795 TRP cc_start: 0.6903 (OUTLIER) cc_final: 0.6252 (m-10) REVERT: E 819 ASP cc_start: 0.6920 (OUTLIER) cc_final: 0.5838 (t0) REVERT: E 1109 LYS cc_start: 0.7858 (mmmm) cc_final: 0.7636 (mmmm) REVERT: E 1113 ARG cc_start: 0.8111 (ttt180) cc_final: 0.7816 (ttt-90) REVERT: E 1150 HIS cc_start: 0.6073 (OUTLIER) cc_final: 0.5344 (m-70) outliers start: 33 outliers final: 21 residues processed: 211 average time/residue: 0.1434 time to fit residues: 43.0523 Evaluate side-chains 218 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 531 ARG Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain E residue 795 TRP Chi-restraints excluded: chain E residue 802 PHE Chi-restraints excluded: chain E residue 819 ASP Chi-restraints excluded: chain E residue 826 GLU Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 1043 MET Chi-restraints excluded: chain E residue 1144 LEU Chi-restraints excluded: chain E residue 1150 HIS Chi-restraints excluded: chain E residue 1192 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 165 optimal weight: 50.0000 chunk 44 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 30 optimal weight: 0.0270 chunk 142 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 131 optimal weight: 0.0770 chunk 108 optimal weight: 2.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.212987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.169353 restraints weight = 22164.379| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.64 r_work: 0.3940 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15383 Z= 0.138 Angle : 0.567 11.919 21247 Z= 0.305 Chirality : 0.040 0.358 2345 Planarity : 0.005 0.085 2367 Dihedral : 21.635 176.521 2873 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.23 % Allowed : 16.52 % Favored : 81.25 % 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 are not related in a simple way. whole: 0.63 (0.21), residues: 1566 helix: 1.58 (0.18), residues: 876 sheet: -0.76 (0.61), residues: 68 loop : -1.17 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1173 TYR 0.009 0.001 TYR E1227 PHE 0.015 0.002 PHE E 802 TRP 0.016 0.001 TRP E 707 HIS 0.004 0.001 HIS E 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (15382) covalent geometry : angle 0.56612 / 0.30 (21245) SS BOND : bond 0.01710 / 0.90 ( 1) SS BOND : angle 3.03600 / 1.66 ( 2) hydrogen bonds : bond 0.04410 / 2.84 ( 738) hydrogen bonds : angle 3.38591 / 2.43 ( 2042) *********************** 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 223 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: E 137 MET cc_start: 0.7369 (mmm) cc_final: 0.6961 (mmm) REVERT: E 308 ARG cc_start: 0.7683 (mtm-85) cc_final: 0.7421 (ttm110) REVERT: E 531 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.6054 (mpt90) REVERT: E 795 TRP cc_start: 0.6897 (OUTLIER) cc_final: 0.6100 (m-10) REVERT: E 819 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.5850 (t0) REVERT: E 1109 LYS cc_start: 0.7867 (mmmm) cc_final: 0.7653 (mmmm) REVERT: E 1113 ARG cc_start: 0.8114 (ttt180) cc_final: 0.7822 (ttt-90) REVERT: E 1150 HIS cc_start: 0.6069 (OUTLIER) cc_final: 0.5267 (m-70) outliers start: 31 outliers final: 22 residues processed: 209 average time/residue: 0.1450 time to fit residues: 43.5102 Evaluate side-chains 217 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 531 ARG Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain E residue 795 TRP Chi-restraints excluded: chain E residue 802 PHE Chi-restraints excluded: chain E residue 819 ASP Chi-restraints excluded: chain E residue 826 GLU Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 1043 MET Chi-restraints excluded: chain E residue 1144 LEU Chi-restraints excluded: chain E residue 1150 HIS Chi-restraints excluded: chain E residue 1163 MET Chi-restraints excluded: chain E residue 1192 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 91 optimal weight: 0.5980 chunk 165 optimal weight: 50.0000 chunk 27 optimal weight: 1.9990 chunk 138 optimal weight: 0.3980 chunk 111 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 123 optimal weight: 0.0870 chunk 33 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.213554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.169943 restraints weight = 22180.308| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 2.57 r_work: 0.3953 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15383 Z= 0.130 Angle : 0.557 10.422 21247 Z= 0.301 Chirality : 0.040 0.324 2345 Planarity : 0.005 0.075 2367 Dihedral : 21.643 177.392 2873 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.37 % Allowed : 16.88 % Favored : 80.75 % 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 are not related in a simple way. whole: 0.68 (0.21), residues: 1566 helix: 1.63 (0.18), residues: 877 sheet: -0.69 (0.60), residues: 68 loop : -1.16 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 344 TYR 0.012 0.001 TYR B 88 PHE 0.017 0.001 PHE B 220 TRP 0.015 0.001 TRP E 707 HIS 0.004 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (15382) covalent geometry : angle 0.55635 / 0.30 (21245) SS BOND : bond 0.01704 / 0.90 ( 1) SS BOND : angle 3.04214 / 1.66 ( 2) hydrogen bonds : bond 0.04279 / 2.75 ( 738) hydrogen bonds : angle 3.34380 / 2.40 ( 2042) *********************** 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 224 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 137 MET cc_start: 0.7356 (mmm) cc_final: 0.6938 (mmm) REVERT: E 308 ARG cc_start: 0.7669 (mtm-85) cc_final: 0.7399 (ttm110) REVERT: E 531 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.6064 (mpt90) REVERT: E 795 TRP cc_start: 0.6853 (OUTLIER) cc_final: 0.5988 (m-10) REVERT: E 819 ASP cc_start: 0.6937 (OUTLIER) cc_final: 0.5843 (t0) REVERT: E 1109 LYS cc_start: 0.7861 (mmmm) cc_final: 0.7660 (mmmm) REVERT: E 1113 ARG cc_start: 0.8108 (ttt180) cc_final: 0.7823 (ttt-90) REVERT: E 1150 HIS cc_start: 0.6054 (OUTLIER) cc_final: 0.5257 (m-70) outliers start: 33 outliers final: 25 residues processed: 206 average time/residue: 0.1400 time to fit residues: 41.2675 Evaluate side-chains 219 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 531 ARG Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain E residue 795 TRP Chi-restraints excluded: chain E residue 819 ASP Chi-restraints excluded: chain E residue 826 GLU Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 1043 MET Chi-restraints excluded: chain E residue 1144 LEU Chi-restraints excluded: chain E residue 1147 VAL Chi-restraints excluded: chain E residue 1150 HIS Chi-restraints excluded: chain E residue 1163 MET Chi-restraints excluded: chain E residue 1192 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 128 optimal weight: 0.6980 chunk 165 optimal weight: 50.0000 chunk 64 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 95 optimal weight: 0.0980 chunk 116 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.212403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.168420 restraints weight = 22083.604| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.50 r_work: 0.3944 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15383 Z= 0.147 Angle : 0.586 12.121 21247 Z= 0.311 Chirality : 0.040 0.315 2345 Planarity : 0.005 0.078 2367 Dihedral : 21.652 177.922 2873 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.23 % Allowed : 17.03 % Favored : 80.75 % 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 are not related in a simple way. whole: 0.62 (0.21), residues: 1566 helix: 1.59 (0.18), residues: 876 sheet: -0.75 (0.58), residues: 74 loop : -1.20 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 344 TYR 0.013 0.001 TYR B 88 PHE 0.013 0.002 PHE E 794 TRP 0.016 0.001 TRP E 707 HIS 0.005 0.001 HIS E 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (15382) covalent geometry : angle 0.58523 / 0.31 (21245) SS BOND : bond 0.01703 / 0.90 ( 1) SS BOND : angle 3.02559 / 1.65 ( 2) hydrogen bonds : bond 0.04468 / 2.87 ( 738) hydrogen bonds : angle 3.39232 / 2.43 ( 2042) ********************** 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 224 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.3114 (mmp) cc_final: 0.2847 (mmp) REVERT: E 137 MET cc_start: 0.7339 (mmm) cc_final: 0.6916 (mmm) REVERT: E 308 ARG cc_start: 0.7677 (mtm-85) cc_final: 0.7397 (ttm110) REVERT: E 531 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.6073 (mpt90) REVERT: E 795 TRP cc_start: 0.6893 (OUTLIER) cc_final: 0.5946 (m-10) REVERT: E 819 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.5760 (t0) REVERT: E 1109 LYS cc_start: 0.7861 (mmmm) cc_final: 0.7653 (mmmm) REVERT: E 1113 ARG cc_start: 0.8100 (ttt180) cc_final: 0.7812 (ttt-90) REVERT: E 1150 HIS cc_start: 0.6053 (OUTLIER) cc_final: 0.5246 (m-70) outliers start: 31 outliers final: 23 residues processed: 207 average time/residue: 0.1449 time to fit residues: 43.0612 Evaluate side-chains 218 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 531 ARG Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 795 TRP Chi-restraints excluded: chain E residue 819 ASP Chi-restraints excluded: chain E residue 826 GLU Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 1043 MET Chi-restraints excluded: chain E residue 1144 LEU Chi-restraints excluded: chain E residue 1147 VAL Chi-restraints excluded: chain E residue 1150 HIS Chi-restraints excluded: chain E residue 1192 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 4 optimal weight: 6.9990 chunk 37 optimal weight: 0.0870 chunk 164 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 126 optimal weight: 0.3980 chunk 134 optimal weight: 0.4980 chunk 159 optimal weight: 10.0000 chunk 115 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 812 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.213263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.169647 restraints weight = 22058.660| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 2.56 r_work: 0.3948 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15383 Z= 0.132 Angle : 0.576 10.399 21247 Z= 0.306 Chirality : 0.039 0.290 2345 Planarity : 0.005 0.076 2367 Dihedral : 21.637 178.034 2873 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.30 % Allowed : 16.74 % Favored : 80.96 % 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 are not related in a simple way. whole: 0.68 (0.21), residues: 1566 helix: 1.66 (0.18), residues: 875 sheet: -0.66 (0.58), residues: 74 loop : -1.21 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 344 TYR 0.010 0.001 TYR B 88 PHE 0.017 0.001 PHE B 220 TRP 0.017 0.001 TRP E 795 HIS 0.004 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (15382) covalent geometry : angle 0.57478 / 0.31 (21245) SS BOND : bond 0.01694 / 0.89 ( 1) SS BOND : angle 3.03538 / 1.66 ( 2) hydrogen bonds : bond 0.04269 / 2.74 ( 738) hydrogen bonds : angle 3.33113 / 2.38 ( 2042) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4096.14 seconds wall clock time: 70 minutes 46.13 seconds (4246.13 seconds total)