Starting phenix.real_space_refine on Fri Jul 3 05:56:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mna_48418/07_2026/9mna_48418.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mna_48418/07_2026/9mna_48418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mna_48418/07_2026/9mna_48418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mna_48418/07_2026/9mna_48418.map" model { file = "/net/cci-nas-00/data/ceres_data/9mna_48418/07_2026/9mna_48418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mna_48418/07_2026/9mna_48418.cif" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 72 5.49 5 Mg 1 5.21 5 S 58 5.16 5 C 7501 2.51 5 N 2132 2.21 5 O 2312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12076 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1617 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1518 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 192} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'ASP:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "E" Number of atoms: 7479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7479 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 65, 'TRANS': 917} Chain breaks: 2 Unresolved non-hydrogen bonds: 375 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 10, 'HIS:plan': 3, 'ARG:plan': 17, 'PHE:plan': 2, 'GLU:plan': 14, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 264 Chain: "N" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 619 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "T" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 611 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "R" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 200 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 8} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.75, per 1000 atoms: 0.23 Number of scatterers: 12076 At special positions: 0 Unit cell: (95.6824, 127.09, 119.055, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 72 15.00 Mg 1 11.99 O 2312 8.00 N 2132 7.00 C 7501 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 501.8 milliseconds 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2646 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 11 sheets defined 57.8% alpha, 6.4% beta 21 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 149 through 155 Processing helix chain 'A' and resid 160 through 166 removed outlier: 3.846A pdb=" N LEU A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 243 through 260 Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'A' and resid 278 through 285 removed outlier: 4.115A pdb=" N PHE A 285 " --> pdb=" O VAL A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 321 through 335 removed outlier: 3.791A pdb=" N SER A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 removed outlier: 3.582A pdb=" N ASP A 342 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 345 " --> pdb=" O TYR A 341 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 354 " --> pdb=" O PHE A 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 166 Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.526A pdb=" N TYR B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 261 Processing helix chain 'B' and resid 278 through 286 removed outlier: 3.550A pdb=" N LYS B 283 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 304 Processing helix chain 'B' and resid 318 through 332 removed outlier: 4.260A pdb=" N VAL B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N HIS B 324 " --> pdb=" O ASP B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 341 removed outlier: 4.458A pdb=" N LEU B 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.563A pdb=" N ALA B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 236 removed outlier: 4.123A pdb=" N LEU E 234 " --> pdb=" O PHE E 230 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU E 235 " --> pdb=" O LYS E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 252 removed outlier: 3.627A pdb=" N HIS E 244 " --> pdb=" O PRO E 240 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU E 245 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN E 252 " --> pdb=" O VAL E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.582A pdb=" N LYS E 257 " --> pdb=" O ARG E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 274 removed outlier: 3.564A pdb=" N GLN E 274 " --> pdb=" O GLY E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 291 removed outlier: 4.190A pdb=" N TYR E 282 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 307 Processing helix chain 'E' and resid 315 through 325 Processing helix chain 'E' and resid 326 through 328 No H-bonds generated for 'chain 'E' and resid 326 through 328' Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 340 through 355 Processing helix chain 'E' and resid 392 through 409 removed outlier: 3.659A pdb=" N ALA E 409 " --> pdb=" O HIS E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 462 removed outlier: 4.012A pdb=" N TYR E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 472 Processing helix chain 'E' and resid 475 through 489 removed outlier: 3.517A pdb=" N VAL E 479 " --> pdb=" O ASP E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 521 removed outlier: 4.449A pdb=" N GLN E 517 " --> pdb=" O VAL E 513 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG E 518 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL E 519 " --> pdb=" O GLN E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 534 removed outlier: 3.853A pdb=" N ALA E 525 " --> pdb=" O GLY E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 537 No H-bonds generated for 'chain 'E' and resid 535 through 537' Processing helix chain 'E' and resid 548 through 555 removed outlier: 3.759A pdb=" N TRP E 553 " --> pdb=" O PRO E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 568 through 587 Processing helix chain 'E' and resid 624 through 634 Processing helix chain 'E' and resid 678 through 687 removed outlier: 3.721A pdb=" N LEU E 684 " --> pdb=" O HIS E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 692 through 704 Processing helix chain 'E' and resid 711 through 723 removed outlier: 3.663A pdb=" N ALA E 723 " --> pdb=" O GLN E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 726 through 730 removed outlier: 3.599A pdb=" N LEU E 729 " --> pdb=" O CYS E 726 " (cutoff:3.500A) Processing helix chain 'E' and resid 751 through 789 removed outlier: 3.540A pdb=" N GLU E 778 " --> pdb=" O SER E 774 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU E 785 " --> pdb=" O TYR E 781 " (cutoff:3.500A) Processing helix chain 'E' and resid 818 through 824 Processing helix chain 'E' and resid 837 through 850 removed outlier: 3.656A 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 877 Processing helix chain 'E' and resid 890 through 906 Processing helix chain 'E' and resid 925 through 934 Processing helix chain 'E' and resid 954 through 974 removed outlier: 3.561A pdb=" N GLY E 958 " --> pdb=" O ASP E 954 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN E 969 " --> pdb=" O VAL E 965 " (cutoff:3.500A) Processing helix chain 'E' and resid 975 through 982 removed outlier: 4.043A pdb=" N GLN E 979 " --> pdb=" O MET E 975 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL E 980 " --> pdb=" O ARG E 976 " (cutoff:3.500A) Processing helix chain 'E' and resid 986 through 998 removed outlier: 3.666A pdb=" N VAL E 990 " --> pdb=" O THR E 986 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLN E 992 " --> pdb=" O LYS E 988 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N THR E 993 " --> pdb=" O VAL E 989 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL E 998 " --> pdb=" O VAL E 994 " (cutoff:3.500A) Processing helix chain 'E' and resid 1002 through 1017 removed outlier: 3.573A pdb=" N GLN E1009 " --> pdb=" O GLY E1005 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU E1011 " --> pdb=" O ARG E1007 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS E1012 " --> pdb=" O LEU E1008 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG E1013 " --> pdb=" O GLN E1009 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU E1014 " --> pdb=" O ILE E1010 " (cutoff:3.500A) Processing helix chain 'E' and resid 1025 through 1033 Processing helix chain 'E' and resid 1035 through 1044 removed outlier: 4.317A pdb=" N SER E1039 " --> pdb=" O GLN E1035 " (cutoff:3.500A) Processing helix chain 'E' and resid 1046 through 1065 Processing helix chain 'E' and resid 1112 through 1117 removed outlier: 3.604A pdb=" N ASN E1117 " --> pdb=" O ARG E1113 " (cutoff:3.500A) Processing helix chain 'E' and resid 1119 through 1141 removed outlier: 5.553A pdb=" N HIS E1125 " --> pdb=" O PRO E1121 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER E1126 " --> pdb=" O ASN E1122 " (cutoff:3.500A) Processing helix chain 'E' and resid 1159 through 1177 removed outlier: 3.894A pdb=" N GLU E1177 " --> pdb=" O ARG E1173 " (cutoff:3.500A) Processing helix chain 'E' and resid 1178 through 1192 Processing helix chain 'E' and resid 1197 through 1209 removed outlier: 3.625A pdb=" N LEU E1204 " --> pdb=" O GLU E1200 " (cutoff:3.500A) Processing helix chain 'E' and resid 1218 through 1225 removed outlier: 3.550A pdb=" N GLN E1221 " --> pdb=" O ASP E1218 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS E1223 " --> pdb=" O GLU E1220 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 197 removed outlier: 6.472A pdb=" N HIS A 184 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TRP A 194 " --> pdb=" O TRP A 182 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N TRP A 182 " --> pdb=" O TRP A 194 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLN A 196 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE A 180 " --> pdb=" O GLN A 196 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 181 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 170 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE A 171 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N GLU A 232 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N ILE A 173 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N TYR A 229 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N MET A 276 " --> pdb=" O TYR A 229 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU A 231 " --> pdb=" O MET A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 289 Processing sheet with id=AA3, first strand: chain 'B' and resid 191 through 196 removed outlier: 3.818A pdb=" N ASP B 193 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 174 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA B 183 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B 171 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL B 230 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N PHE B 175 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 274 " --> pdb=" O TYR B 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 412 through 415 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 606 through 609 Processing sheet with id=AA7, first strand: chain 'E' and resid 707 through 709 Processing sheet with id=AA8, first strand: chain 'E' and resid 798 through 800 Processing sheet with id=AA9, first strand: chain 'E' and resid 831 through 832 removed outlier: 3.726A pdb=" N ARG E 831 " --> pdb=" O SER E 915 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 919 through 922 removed outlier: 3.641A pdb=" N VAL E1147 " --> pdb=" O TRP E1154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 1069 through 1071 539 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.29 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: 2664 1.33 - 1.45: 2991 1.45 - 1.57: 6614 1.57 - 1.69: 139 1.69 - 1.82: 93 Bond restraints: 12501 Sorted by residual: bond pdb=" C3' DA N 45 " pdb=" O3' DA N 45 " ideal model delta sigma weight residual 1.435 1.505 -0.070 1.30e-02 5.92e+03 2.88e+01 bond pdb=" C1' DT T 11 " pdb=" N1 DT T 11 " ideal model delta sigma weight residual 1.468 1.526 -0.058 1.40e-02 5.10e+03 1.72e+01 bond pdb=" C3' DA N 43 " pdb=" O3' DA N 43 " ideal model delta sigma weight residual 1.435 1.487 -0.052 1.30e-02 5.92e+03 1.63e+01 bond pdb=" C3' DA N 37 " pdb=" C2' DA N 37 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.28e+01 bond pdb=" C1' DT T 10 " pdb=" N1 DT T 10 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.24e+01 ... (remaining 12496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 16923 2.68 - 5.36: 339 5.36 - 8.05: 41 8.05 - 10.73: 9 10.73 - 13.41: 2 Bond angle restraints: 17314 Sorted by residual: angle pdb=" N ASP E1151 " pdb=" CA ASP E1151 " pdb=" C ASP E1151 " ideal model delta sigma weight residual 113.23 106.58 6.65 1.22e+00 6.72e-01 2.97e+01 angle pdb=" O4' DA N 40 " pdb=" C4' DA N 40 " pdb=" C3' DA N 40 " ideal model delta sigma weight residual 106.00 102.81 3.19 6.00e-01 2.78e+00 2.82e+01 angle pdb=" C LYS B 222 " pdb=" N MET B 223 " pdb=" CA MET B 223 " ideal model delta sigma weight residual 121.20 127.89 -6.69 1.40e+00 5.10e-01 2.28e+01 angle pdb=" C HIS E1150 " pdb=" N ASP E1151 " pdb=" CA ASP E1151 " ideal model delta sigma weight residual 123.47 130.44 -6.97 1.53e+00 4.27e-01 2.08e+01 angle pdb=" CB MET A 288 " pdb=" CG MET A 288 " pdb=" SD MET A 288 " ideal model delta sigma weight residual 112.70 99.29 13.41 3.00e+00 1.11e-01 2.00e+01 ... (remaining 17309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 6948 35.50 - 71.00: 386 71.00 - 106.50: 8 106.50 - 141.99: 0 141.99 - 177.49: 5 Dihedral angle restraints: 7347 sinusoidal: 3288 harmonic: 4059 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 180.00 152.61 27.39 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA MET A 288 " pdb=" C MET A 288 " pdb=" N ILE A 289 " pdb=" CA ILE A 289 " ideal model delta harmonic sigma weight residual 180.00 153.08 26.92 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA GLU E1023 " pdb=" C GLU E1023 " pdb=" N PHE E1024 " pdb=" CA PHE E1024 " ideal model delta harmonic sigma weight residual 180.00 154.38 25.62 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 7344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1709 0.069 - 0.139: 246 0.139 - 0.208: 30 0.208 - 0.278: 6 0.278 - 0.347: 1 Chirality restraints: 1992 Sorted by residual: chirality pdb=" CG LEU A 185 " pdb=" CB LEU A 185 " pdb=" CD1 LEU A 185 " pdb=" CD2 LEU A 185 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CB VAL E 543 " pdb=" CA VAL E 543 " pdb=" CG1 VAL E 543 " pdb=" CG2 VAL E 543 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CG LEU E 234 " pdb=" CB LEU E 234 " pdb=" CD1 LEU E 234 " pdb=" CD2 LEU E 234 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1989 not shown) Planarity restraints: 1962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 441 " -0.046 2.00e-02 2.50e+03 4.81e-02 5.79e+01 pdb=" CG TRP E 441 " 0.131 2.00e-02 2.50e+03 pdb=" CD1 TRP E 441 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TRP E 441 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 441 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP E 441 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 441 " -0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 441 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 441 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 441 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 731 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO E 732 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 732 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 732 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 646 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO E 647 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 647 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 647 " -0.029 5.00e-02 4.00e+02 ... (remaining 1959 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 116 2.64 - 3.20: 10239 3.20 - 3.77: 19918 3.77 - 4.33: 25263 4.33 - 4.90: 39297 Nonbonded interactions: 94833 Sorted by model distance: nonbonded pdb="MG MG E1301 " pdb=" O2B ATP E1302 " model vdw 2.070 2.170 nonbonded pdb=" ND2 ASN E 926 " pdb=" OD2 ASP E1128 " model vdw 2.235 3.120 nonbonded pdb=" OD1 ASP B 193 " pdb=" OH TYR B 325 " model vdw 2.272 3.040 nonbonded pdb=" O LEU A 185 " pdb=" OH TYR A 351 " model vdw 2.272 3.040 nonbonded pdb=" OH TYR E 530 " pdb=" O PRO E 651 " model vdw 2.274 3.040 ... (remaining 94828 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 151 through 152 or (resid 153 and (name N or name CA or na \ me C or name O or name CB )) or resid 154 through 155 or (resid 156 and (name N \ or name CA or name C or name O or name CB )) or resid 157 through 164 or (resid \ 165 through 166 and (name N or name CA or name C or name O or name CB )) or resi \ d 167 through 178 or (resid 179 and (name N or name CA or name C or name O or na \ me CB )) or resid 180 through 185 or (resid 186 through 188 and (name N or name \ CA or name C or name O or name CB )) or resid 189 through 197 or (resid 198 thro \ ugh 199 and (name N or name CA or name C or name O or name CB )) or resid 200 th \ rough 262 or (resid 263 and (name N or name CA or name C or name O or name CB )) \ or resid 264 through 282 or (resid 283 and (name N or name CA or name C or name \ O or name CB )) or resid 284 through 285 or (resid 286 and (name N or name CA o \ r name C or name O or name CB )) or resid 287 or (resid 288 and (name N or name \ CA or name C or name O or name CB )) or resid 289 through 301 or (resid 302 and \ (name N or name CA or name C or name O or name CB )) or resid 303 through 320 or \ (resid 321 and (name N or name CA or name C or name O or name CB )) or resid 32 \ 2 through 325 or (resid 326 through 327 and (name N or name CA or name C or name \ O or name CB )) or resid 328 or (resid 329 through 330 and (name N or name CA o \ r name C or name O or name CB )) or resid 331 or (resid 332 through 334 and (nam \ e N or name CA or name C or name O or name CB )) or resid 335 through 340 or (re \ sid 341 and (name N or name CA or name C or name O or name CB )) or resid 342 th \ rough 351 or (resid 352 and (name N or name CA or name C or name O or name CB )) \ or resid 353 through 355)) selection = (chain 'B' and (resid 151 through 160 or (resid 161 and (name N or name CA or na \ me C or name O or name CB )) or resid 162 through 221 or (resid 222 and (name N \ or name CA or name C or name O or name CB )) or resid 223 through 224 or (resid \ 225 through 226 and (name N or name CA or name C or name O or name CB )) or resi \ d 227 through 238 or (resid 239 and (name N or name CA or name C or name O or na \ me CB )) or resid 240 through 303 or (resid 304 and (name N or name CA or name C \ or name O or name CB )) or resid 305 or (resid 313 and (name N or name CA or na \ me C or name O or name CB )) or resid 314 through 332 or (resid 333 through 334 \ and (name N or name CA or name C or name O or name CB )) or resid 335 through 35 \ 5)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.390 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5310 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 0.070 12501 Z= 0.322 Angle : 0.900 13.409 17314 Z= 0.550 Chirality : 0.052 0.347 1992 Planarity : 0.007 0.073 1962 Dihedral : 19.047 177.492 4701 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.20), residues: 1369 helix: -0.53 (0.17), residues: 718 sheet: -1.05 (0.51), residues: 92 loop : -1.47 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 790 TYR 0.023 0.002 TYR A 229 PHE 0.028 0.003 PHE E1024 TRP 0.131 0.003 TRP E 441 HIS 0.012 0.002 HIS E 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.32 (12501) covalent geometry : angle 0.90022 / 0.55 (17314) hydrogen bonds : bond 0.13411 / 9.06 ( 590) hydrogen bonds : angle 6.00264 / 4.21 ( 1686) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LEU cc_start: 0.8095 (tt) cc_final: 0.7412 (tt) REVERT: A 276 MET cc_start: 0.3010 (mmt) cc_final: 0.2806 (mmt) REVERT: B 253 MET cc_start: 0.7909 (tpp) cc_final: 0.7458 (tpp) REVERT: B 258 TYR cc_start: 0.7327 (t80) cc_final: 0.6583 (t80) REVERT: E 306 MET cc_start: 0.8139 (mmp) cc_final: 0.7832 (mmp) REVERT: E 465 PHE cc_start: 0.6230 (t80) cc_final: 0.5888 (t80) REVERT: E 771 GLU cc_start: 0.6965 (tt0) cc_final: 0.6738 (tt0) REVERT: E 853 LYS cc_start: 0.7641 (tptt) cc_final: 0.7114 (tptt) REVERT: E 892 TRP cc_start: 0.7175 (m100) cc_final: 0.6779 (m100) REVERT: E 995 MET cc_start: 0.6181 (tmm) cc_final: 0.5849 (tmm) REVERT: E 1009 GLN cc_start: 0.6599 (mt0) cc_final: 0.6398 (mt0) REVERT: E 1010 ILE cc_start: 0.7779 (tp) cc_final: 0.7527 (tp) REVERT: E 1017 LEU cc_start: 0.6607 (mp) cc_final: 0.6404 (mp) REVERT: E 1131 HIS cc_start: 0.6615 (t70) cc_final: 0.6393 (t-90) REVERT: E 1135 THR cc_start: 0.6702 (m) cc_final: 0.6454 (m) REVERT: E 1163 MET cc_start: 0.7107 (ttp) cc_final: 0.6864 (ttp) REVERT: E 1224 ARG cc_start: 0.6917 (mtm110) cc_final: 0.6638 (mtm110) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1006 time to fit residues: 32.1261 Evaluate side-chains 204 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.0050 chunk 55 optimal weight: 0.8980 overall best weight: 0.9876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN A 335 GLN B 271 HIS E 250 HIS E 429 HIS E 799 ASN E 916 HIS E 926 ASN E1115 GLN E1117 ASN E1125 HIS E1196 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.187739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.153644 restraints weight = 18878.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.157989 restraints weight = 10041.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.161063 restraints weight = 6256.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.162910 restraints weight = 4418.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.164307 restraints weight = 3509.758| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12501 Z= 0.173 Angle : 0.655 8.607 17314 Z= 0.354 Chirality : 0.044 0.301 1992 Planarity : 0.005 0.049 1962 Dihedral : 21.064 178.098 2306 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.37 % Allowed : 9.07 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.22), residues: 1369 helix: 0.46 (0.19), residues: 722 sheet: -1.33 (0.46), residues: 103 loop : -1.24 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 518 TYR 0.017 0.001 TYR E1140 PHE 0.028 0.002 PHE A 150 TRP 0.038 0.002 TRP E 441 HIS 0.010 0.001 HIS E 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (12501) covalent geometry : angle 0.65501 / 0.35 (17314) hydrogen bonds : bond 0.04724 / 3.18 ( 590) hydrogen bonds : angle 4.87767 / 3.44 ( 1686) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 211 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 MET cc_start: 0.7933 (tpp) cc_final: 0.7227 (tpp) REVERT: B 258 TYR cc_start: 0.7289 (t80) cc_final: 0.6500 (t80) REVERT: E 456 LEU cc_start: 0.8291 (mm) cc_final: 0.8045 (mt) REVERT: E 701 GLN cc_start: 0.7526 (tt0) cc_final: 0.7308 (tt0) REVERT: E 995 MET cc_start: 0.7493 (tmm) cc_final: 0.6686 (tmm) REVERT: E 1010 ILE cc_start: 0.8561 (tp) cc_final: 0.8219 (tp) outliers start: 15 outliers final: 9 residues processed: 214 average time/residue: 0.0935 time to fit residues: 28.8393 Evaluate side-chains 214 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 205 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain E residue 406 MET Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 800 MET Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain E residue 1071 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 59 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 56 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 629 GLN E 945 ASN E1009 GLN E1117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.188907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.153766 restraints weight = 19132.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.158586 restraints weight = 9920.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.161814 restraints weight = 6046.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.163597 restraints weight = 4198.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.165062 restraints weight = 3327.396| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12501 Z= 0.143 Angle : 0.610 6.730 17314 Z= 0.329 Chirality : 0.043 0.305 1992 Planarity : 0.005 0.051 1962 Dihedral : 20.952 176.543 2306 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.47 % Allowed : 12.55 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.22), residues: 1369 helix: 0.95 (0.19), residues: 714 sheet: -1.52 (0.46), residues: 103 loop : -1.18 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 790 TYR 0.012 0.001 TYR E1140 PHE 0.024 0.002 PHE A 150 TRP 0.016 0.001 TRP E 441 HIS 0.008 0.001 HIS E 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (12501) covalent geometry : angle 0.60979 / 0.33 (17314) hydrogen bonds : bond 0.04275 / 2.91 ( 590) hydrogen bonds : angle 4.58795 / 3.24 ( 1686) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 207 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 MET cc_start: 0.7926 (tpp) cc_final: 0.7430 (tpp) REVERT: B 258 TYR cc_start: 0.7348 (t80) cc_final: 0.6521 (t80) REVERT: B 346 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6709 (pp30) REVERT: E 230 PHE cc_start: 0.8137 (m-80) cc_final: 0.7812 (m-80) REVERT: E 263 MET cc_start: 0.7105 (mtm) cc_final: 0.6735 (mtt) REVERT: E 407 GLU cc_start: 0.7567 (tp30) cc_final: 0.7278 (tp30) REVERT: E 456 LEU cc_start: 0.8303 (mm) cc_final: 0.8004 (mt) REVERT: E 485 GLN cc_start: 0.6942 (tm-30) cc_final: 0.6632 (tm-30) REVERT: E 701 GLN cc_start: 0.7563 (tt0) cc_final: 0.7316 (tt0) REVERT: E 831 ARG cc_start: 0.8014 (tpp-160) cc_final: 0.7743 (mmt-90) REVERT: E 892 TRP cc_start: 0.7850 (m100) cc_final: 0.7501 (m100) REVERT: E 1043 MET cc_start: 0.1846 (OUTLIER) cc_final: 0.0344 (pmm) REVERT: E 1151 ASP cc_start: 0.5078 (t0) cc_final: 0.4753 (t0) outliers start: 16 outliers final: 10 residues processed: 211 average time/residue: 0.0963 time to fit residues: 29.2740 Evaluate side-chains 219 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 207 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 825 LEU Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain E residue 1043 MET Chi-restraints excluded: chain E residue 1071 VAL Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 103 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 704 ASN E 815 HIS ** E 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1009 GLN E1117 ASN E1156 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.184753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.150366 restraints weight = 18910.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.154669 restraints weight = 10109.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.157655 restraints weight = 6310.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.159466 restraints weight = 4476.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.160672 restraints weight = 3556.277| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 12501 Z= 0.221 Angle : 0.661 10.153 17314 Z= 0.356 Chirality : 0.045 0.296 1992 Planarity : 0.005 0.052 1962 Dihedral : 20.923 177.436 2306 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.75 % Allowed : 14.74 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.22), residues: 1369 helix: 1.03 (0.19), residues: 707 sheet: -1.82 (0.45), residues: 97 loop : -1.31 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 776 TYR 0.019 0.002 TYR E1140 PHE 0.033 0.002 PHE E 465 TRP 0.016 0.002 TRP E 885 HIS 0.013 0.001 HIS E 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.22 (12501) covalent geometry : angle 0.66080 / 0.36 (17314) hydrogen bonds : bond 0.04768 / 3.25 ( 590) hydrogen bonds : angle 4.68013 / 3.31 ( 1686) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 MET cc_start: 0.7050 (tpp) cc_final: 0.6706 (tpp) REVERT: B 253 MET cc_start: 0.7921 (tpp) cc_final: 0.7404 (tpp) REVERT: B 258 TYR cc_start: 0.7262 (t80) cc_final: 0.6557 (t80) REVERT: B 346 GLN cc_start: 0.7070 (OUTLIER) cc_final: 0.6545 (pp30) REVERT: E 230 PHE cc_start: 0.8282 (m-80) cc_final: 0.7868 (m-80) REVERT: E 263 MET cc_start: 0.7118 (mtm) cc_final: 0.6626 (mtt) REVERT: E 295 ASP cc_start: 0.8486 (t0) cc_final: 0.8259 (t0) REVERT: E 407 GLU cc_start: 0.7514 (tp30) cc_final: 0.7277 (tp30) REVERT: E 701 GLN cc_start: 0.7699 (tt0) cc_final: 0.7383 (tt0) REVERT: E 825 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7726 (mt) REVERT: E 831 ARG cc_start: 0.7999 (tpp-160) cc_final: 0.7730 (mmt-90) REVERT: E 892 TRP cc_start: 0.7900 (m100) cc_final: 0.7623 (m100) REVERT: E 898 CYS cc_start: 0.7072 (t) cc_final: 0.6777 (t) REVERT: E 987 ARG cc_start: 0.8640 (mtm180) cc_final: 0.8372 (ttp80) REVERT: E 995 MET cc_start: 0.7516 (tmm) cc_final: 0.7221 (tmm) REVERT: E 1043 MET cc_start: 0.2115 (OUTLIER) cc_final: 0.1691 (pmm) REVERT: E 1111 ASN cc_start: 0.8375 (t0) cc_final: 0.8016 (t0) REVERT: E 1133 MET cc_start: 0.6628 (mtm) cc_final: 0.6374 (mtt) REVERT: E 1151 ASP cc_start: 0.5164 (t0) cc_final: 0.4797 (t0) REVERT: E 1227 TYR cc_start: 0.6665 (m-10) cc_final: 0.6144 (m-10) outliers start: 30 outliers final: 18 residues processed: 227 average time/residue: 0.1152 time to fit residues: 37.7072 Evaluate side-chains 235 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 624 HIS Chi-restraints excluded: chain E residue 629 GLN Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 648 MET Chi-restraints excluded: chain E residue 704 ASN Chi-restraints excluded: chain E residue 815 HIS Chi-restraints excluded: chain E residue 825 LEU Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 1043 MET Chi-restraints excluded: chain E residue 1071 VAL Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 76 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 138 optimal weight: 20.0000 chunk 104 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 251 HIS E 814 ASN E1009 GLN E1117 ASN E1156 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.186744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.151664 restraints weight = 18957.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.156231 restraints weight = 9895.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.159334 restraints weight = 6073.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.161373 restraints weight = 4249.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.162537 restraints weight = 3357.151| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12501 Z= 0.148 Angle : 0.615 9.071 17314 Z= 0.328 Chirality : 0.042 0.307 1992 Planarity : 0.005 0.052 1962 Dihedral : 20.883 176.524 2306 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.75 % Allowed : 15.84 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.22), residues: 1369 helix: 1.26 (0.19), residues: 709 sheet: -1.77 (0.45), residues: 97 loop : -1.22 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 518 TYR 0.019 0.001 TYR E 627 PHE 0.023 0.002 PHE E 465 TRP 0.012 0.001 TRP E 885 HIS 0.009 0.001 HIS E 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (12501) covalent geometry : angle 0.61488 / 0.33 (17314) hydrogen bonds : bond 0.04188 / 2.87 ( 590) hydrogen bonds : angle 4.49384 / 3.17 ( 1686) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 MET cc_start: 0.7080 (tpp) cc_final: 0.6690 (tpp) REVERT: A 288 MET cc_start: 0.5880 (OUTLIER) cc_final: 0.5640 (mtm) REVERT: B 253 MET cc_start: 0.7887 (tpp) cc_final: 0.7359 (tpp) REVERT: B 258 TYR cc_start: 0.7292 (t80) cc_final: 0.6550 (t80) REVERT: B 346 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.6558 (pp30) REVERT: E 235 LEU cc_start: 0.7723 (mt) cc_final: 0.7511 (mp) REVERT: E 295 ASP cc_start: 0.8444 (t0) cc_final: 0.8209 (t0) REVERT: E 407 GLU cc_start: 0.7516 (tp30) cc_final: 0.7304 (tp30) REVERT: E 485 GLN cc_start: 0.7026 (tm-30) cc_final: 0.6730 (tm-30) REVERT: E 571 VAL cc_start: 0.7215 (t) cc_final: 0.7007 (t) REVERT: E 701 GLN cc_start: 0.7647 (tt0) cc_final: 0.7334 (tt0) REVERT: E 705 CYS cc_start: 0.7333 (t) cc_final: 0.6931 (p) REVERT: E 800 MET cc_start: 0.5657 (tpp) cc_final: 0.5316 (mmm) REVERT: E 822 ARG cc_start: 0.8029 (ttm-80) cc_final: 0.7788 (ttm-80) REVERT: E 825 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7663 (mt) REVERT: E 831 ARG cc_start: 0.7999 (tpp-160) cc_final: 0.7710 (mmt-90) REVERT: E 892 TRP cc_start: 0.7927 (m100) cc_final: 0.7437 (m100) REVERT: E 987 ARG cc_start: 0.8626 (mtm180) cc_final: 0.8314 (ttp80) REVERT: E 995 MET cc_start: 0.7501 (tmm) cc_final: 0.6591 (tmm) REVERT: E 1043 MET cc_start: 0.1884 (OUTLIER) cc_final: 0.0665 (pmm) REVERT: E 1133 MET cc_start: 0.6515 (mtm) cc_final: 0.6315 (mtm) REVERT: E 1151 ASP cc_start: 0.5066 (t0) cc_final: 0.4720 (t0) outliers start: 30 outliers final: 13 residues processed: 225 average time/residue: 0.1012 time to fit residues: 32.7367 Evaluate side-chains 230 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 213 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain E residue 405 HIS Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 814 ASN Chi-restraints excluded: chain E residue 825 LEU Chi-restraints excluded: chain E residue 1043 MET Chi-restraints excluded: chain E residue 1071 VAL Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 118 optimal weight: 0.5980 chunk 55 optimal weight: 0.0570 chunk 10 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 20 optimal weight: 0.0570 chunk 31 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 251 HIS ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 773 HIS E1009 GLN E1117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.188417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.153416 restraints weight = 19044.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.158079 restraints weight = 9866.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.161196 restraints weight = 6045.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.163220 restraints weight = 4237.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.164602 restraints weight = 3328.410| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12501 Z= 0.128 Angle : 0.605 8.670 17314 Z= 0.321 Chirality : 0.042 0.308 1992 Planarity : 0.005 0.051 1962 Dihedral : 20.827 176.242 2306 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.38 % Allowed : 16.30 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.23), residues: 1369 helix: 1.40 (0.20), residues: 710 sheet: -1.66 (0.44), residues: 103 loop : -1.15 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 518 TYR 0.018 0.001 TYR E 627 PHE 0.031 0.002 PHE E 465 TRP 0.012 0.001 TRP E 885 HIS 0.013 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (12501) covalent geometry : angle 0.60530 / 0.32 (17314) hydrogen bonds : bond 0.03864 / 2.65 ( 590) hydrogen bonds : angle 4.38569 / 3.10 ( 1686) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 MET cc_start: 0.7140 (tpp) cc_final: 0.6715 (tpp) REVERT: B 234 THR cc_start: 0.8729 (m) cc_final: 0.8470 (t) REVERT: B 253 MET cc_start: 0.7811 (tpp) cc_final: 0.7267 (tpp) REVERT: B 258 TYR cc_start: 0.7389 (t80) cc_final: 0.6628 (t80) REVERT: B 346 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.6606 (pp30) REVERT: E 235 LEU cc_start: 0.7613 (mt) cc_final: 0.7384 (mp) REVERT: E 295 ASP cc_start: 0.8462 (t0) cc_final: 0.8216 (t0) REVERT: E 485 GLN cc_start: 0.7015 (tm-30) cc_final: 0.6721 (tm-30) REVERT: E 571 VAL cc_start: 0.7049 (t) cc_final: 0.6845 (t) REVERT: E 704 ASN cc_start: 0.7171 (t0) cc_final: 0.6935 (m-40) REVERT: E 800 MET cc_start: 0.5654 (OUTLIER) cc_final: 0.5333 (mmm) REVERT: E 825 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7661 (mt) REVERT: E 831 ARG cc_start: 0.8018 (tpp-160) cc_final: 0.7734 (mmt-90) REVERT: E 892 TRP cc_start: 0.7870 (m100) cc_final: 0.7393 (m100) REVERT: E 987 ARG cc_start: 0.8593 (mtm180) cc_final: 0.8285 (ttp80) REVERT: E 1043 MET cc_start: 0.1451 (OUTLIER) cc_final: 0.0564 (pmm) REVERT: E 1133 MET cc_start: 0.6410 (mtm) cc_final: 0.6161 (mtm) REVERT: E 1151 ASP cc_start: 0.5024 (t0) cc_final: 0.4630 (t0) outliers start: 26 outliers final: 14 residues processed: 220 average time/residue: 0.0971 time to fit residues: 30.6724 Evaluate side-chains 221 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 405 HIS Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 800 MET Chi-restraints excluded: chain E residue 825 LEU Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 1043 MET Chi-restraints excluded: chain E residue 1071 VAL Chi-restraints excluded: chain E residue 1150 HIS Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 88 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 83 optimal weight: 0.0970 chunk 135 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 815 HIS E1009 GLN E1117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.185343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.149161 restraints weight = 19346.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.153978 restraints weight = 10154.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.157200 restraints weight = 6247.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.159020 restraints weight = 4406.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.160549 restraints weight = 3507.900| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12501 Z= 0.158 Angle : 0.621 9.414 17314 Z= 0.328 Chirality : 0.042 0.302 1992 Planarity : 0.005 0.054 1962 Dihedral : 20.798 176.580 2306 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.56 % Allowed : 16.58 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.22), residues: 1369 helix: 1.38 (0.20), residues: 710 sheet: -1.67 (0.45), residues: 97 loop : -1.21 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 518 TYR 0.016 0.001 TYR E 627 PHE 0.034 0.002 PHE E 465 TRP 0.014 0.001 TRP E 885 HIS 0.020 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (12501) covalent geometry : angle 0.62083 / 0.33 (17314) hydrogen bonds : bond 0.04012 / 2.75 ( 590) hydrogen bonds : angle 4.40704 / 3.11 ( 1686) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 MET cc_start: 0.7194 (tpp) cc_final: 0.6748 (tpp) REVERT: A 288 MET cc_start: 0.5856 (OUTLIER) cc_final: 0.5574 (mtm) REVERT: B 234 THR cc_start: 0.8735 (m) cc_final: 0.8461 (t) REVERT: B 253 MET cc_start: 0.7860 (tpp) cc_final: 0.7335 (tpp) REVERT: B 258 TYR cc_start: 0.7460 (t80) cc_final: 0.6667 (t80) REVERT: B 346 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6707 (pp30) REVERT: E 295 ASP cc_start: 0.8483 (t0) cc_final: 0.8235 (t0) REVERT: E 456 LEU cc_start: 0.8263 (mm) cc_final: 0.7991 (tp) REVERT: E 478 GLU cc_start: 0.7349 (tp30) cc_final: 0.7117 (tp30) REVERT: E 485 GLN cc_start: 0.7027 (tm-30) cc_final: 0.6734 (tm-30) REVERT: E 584 VAL cc_start: 0.5646 (OUTLIER) cc_final: 0.5366 (t) REVERT: E 685 GLU cc_start: 0.7288 (mm-30) cc_final: 0.7087 (mm-30) REVERT: E 800 MET cc_start: 0.5642 (OUTLIER) cc_final: 0.5392 (mmm) REVERT: E 825 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7680 (mt) REVERT: E 831 ARG cc_start: 0.8013 (tpp-160) cc_final: 0.7719 (mmt-90) REVERT: E 892 TRP cc_start: 0.7910 (m100) cc_final: 0.7420 (m100) REVERT: E 987 ARG cc_start: 0.8622 (mtm180) cc_final: 0.8290 (ttp80) REVERT: E 995 MET cc_start: 0.7513 (tmm) cc_final: 0.7284 (tmm) REVERT: E 1043 MET cc_start: 0.1548 (OUTLIER) cc_final: 0.0937 (pmm) REVERT: E 1133 MET cc_start: 0.6527 (mtm) cc_final: 0.6270 (mtm) REVERT: E 1151 ASP cc_start: 0.5090 (t0) cc_final: 0.4707 (t0) REVERT: E 1227 TYR cc_start: 0.6529 (m-10) cc_final: 0.6080 (m-10) outliers start: 28 outliers final: 15 residues processed: 221 average time/residue: 0.0931 time to fit residues: 29.5472 Evaluate side-chains 226 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 405 HIS Chi-restraints excluded: chain E residue 584 VAL Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain E residue 800 MET Chi-restraints excluded: chain E residue 815 HIS Chi-restraints excluded: chain E residue 825 LEU Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 1043 MET Chi-restraints excluded: chain E residue 1071 VAL Chi-restraints excluded: chain E residue 1150 HIS Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 48 optimal weight: 0.0170 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 251 HIS ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 704 ASN E 815 HIS E1009 GLN E1117 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.186411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.150156 restraints weight = 19334.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.154941 restraints weight = 10139.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.158185 restraints weight = 6237.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.160041 restraints weight = 4383.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.161660 restraints weight = 3486.716| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12501 Z= 0.134 Angle : 0.615 9.198 17314 Z= 0.322 Chirality : 0.042 0.306 1992 Planarity : 0.005 0.055 1962 Dihedral : 20.771 176.163 2306 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.38 % Allowed : 17.12 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.22), residues: 1369 helix: 1.45 (0.20), residues: 710 sheet: -1.51 (0.46), residues: 95 loop : -1.17 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 518 TYR 0.016 0.001 TYR E 627 PHE 0.038 0.002 PHE E 465 TRP 0.013 0.001 TRP E 885 HIS 0.028 0.001 HIS E 815 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (12501) covalent geometry : angle 0.61452 / 0.32 (17314) hydrogen bonds : bond 0.03823 / 2.62 ( 590) hydrogen bonds : angle 4.34008 / 3.06 ( 1686) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 MET cc_start: 0.7199 (tpp) cc_final: 0.6747 (tpp) REVERT: B 234 THR cc_start: 0.8718 (m) cc_final: 0.8440 (t) REVERT: B 253 MET cc_start: 0.7880 (tpp) cc_final: 0.7351 (tpp) REVERT: B 258 TYR cc_start: 0.7443 (t80) cc_final: 0.6681 (t80) REVERT: B 346 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6696 (pp30) REVERT: E 295 ASP cc_start: 0.8435 (t0) cc_final: 0.8199 (t0) REVERT: E 485 GLN cc_start: 0.7021 (tm-30) cc_final: 0.6720 (tm-30) REVERT: E 685 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6960 (mm-30) REVERT: E 825 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7715 (mt) REVERT: E 831 ARG cc_start: 0.8011 (tpp-160) cc_final: 0.7696 (mmt-90) REVERT: E 892 TRP cc_start: 0.7890 (m100) cc_final: 0.7453 (m100) REVERT: E 987 ARG cc_start: 0.8612 (mtm180) cc_final: 0.8279 (ttp80) REVERT: E 995 MET cc_start: 0.7494 (tmm) cc_final: 0.7246 (tmm) REVERT: E 1043 MET cc_start: 0.1434 (OUTLIER) cc_final: 0.0579 (pmm) REVERT: E 1133 MET cc_start: 0.6529 (mtm) cc_final: 0.6263 (mtm) REVERT: E 1140 TYR cc_start: 0.7674 (t80) cc_final: 0.7419 (t80) REVERT: E 1151 ASP cc_start: 0.5077 (t0) cc_final: 0.4664 (t0) outliers start: 26 outliers final: 16 residues processed: 222 average time/residue: 0.0932 time to fit residues: 29.8138 Evaluate side-chains 224 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 405 HIS Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain E residue 815 HIS Chi-restraints excluded: chain E residue 825 LEU Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 1043 MET Chi-restraints excluded: chain E residue 1071 VAL Chi-restraints excluded: chain E residue 1150 HIS Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 53 optimal weight: 0.0270 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 0.0470 chunk 10 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 251 HIS ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 815 HIS E1009 GLN E1117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.186674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.150499 restraints weight = 19231.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.155237 restraints weight = 10097.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.158584 restraints weight = 6221.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.160514 restraints weight = 4360.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.162018 restraints weight = 3453.203| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12501 Z= 0.132 Angle : 0.622 8.624 17314 Z= 0.324 Chirality : 0.042 0.306 1992 Planarity : 0.005 0.056 1962 Dihedral : 20.740 176.062 2306 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.20 % Allowed : 17.67 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.22), residues: 1369 helix: 1.50 (0.20), residues: 708 sheet: -1.47 (0.47), residues: 95 loop : -1.18 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 518 TYR 0.009 0.001 TYR A 229 PHE 0.040 0.002 PHE E 465 TRP 0.016 0.001 TRP E 885 HIS 0.019 0.001 HIS E 815 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (12501) covalent geometry : angle 0.62164 / 0.32 (17314) hydrogen bonds : bond 0.03778 / 2.58 ( 590) hydrogen bonds : angle 4.30129 / 3.03 ( 1686) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 MET cc_start: 0.7229 (tpp) cc_final: 0.6774 (tpp) REVERT: B 234 THR cc_start: 0.8701 (m) cc_final: 0.8431 (t) REVERT: B 253 MET cc_start: 0.7872 (tpp) cc_final: 0.7322 (tpp) REVERT: B 258 TYR cc_start: 0.7452 (t80) cc_final: 0.6726 (t80) REVERT: B 346 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6725 (pp30) REVERT: E 295 ASP cc_start: 0.8432 (t0) cc_final: 0.8204 (t0) REVERT: E 485 GLN cc_start: 0.7015 (tm-30) cc_final: 0.6725 (tm-30) REVERT: E 685 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6969 (mm-30) REVERT: E 825 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7715 (mt) REVERT: E 892 TRP cc_start: 0.7877 (m100) cc_final: 0.7405 (m100) REVERT: E 966 PHE cc_start: 0.7683 (m-10) cc_final: 0.7479 (m-80) REVERT: E 987 ARG cc_start: 0.8602 (mtm180) cc_final: 0.8270 (ttp80) REVERT: E 995 MET cc_start: 0.7460 (tmm) cc_final: 0.7212 (tmm) REVERT: E 1043 MET cc_start: 0.1405 (OUTLIER) cc_final: 0.0515 (pmm) REVERT: E 1133 MET cc_start: 0.6482 (mtm) cc_final: 0.6196 (mtm) REVERT: E 1135 THR cc_start: 0.7651 (m) cc_final: 0.7377 (m) REVERT: E 1151 ASP cc_start: 0.5087 (t0) cc_final: 0.4657 (t0) REVERT: E 1227 TYR cc_start: 0.6466 (m-10) cc_final: 0.6036 (m-10) outliers start: 24 outliers final: 17 residues processed: 222 average time/residue: 0.0957 time to fit residues: 30.5985 Evaluate side-chains 229 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 405 HIS Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain E residue 815 HIS Chi-restraints excluded: chain E residue 825 LEU Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 1043 MET Chi-restraints excluded: chain E residue 1071 VAL Chi-restraints excluded: chain E residue 1150 HIS Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 132 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 82 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 251 HIS ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN ** E 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1009 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.188162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.152998 restraints weight = 18981.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.157714 restraints weight = 9862.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.160926 restraints weight = 6017.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.162969 restraints weight = 4199.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.164276 restraints weight = 3288.767| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12501 Z= 0.143 Angle : 0.647 15.393 17314 Z= 0.331 Chirality : 0.042 0.304 1992 Planarity : 0.005 0.057 1962 Dihedral : 20.719 176.115 2306 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.01 % Allowed : 18.13 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.22), residues: 1369 helix: 1.48 (0.20), residues: 706 sheet: -1.50 (0.47), residues: 95 loop : -1.24 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 518 TYR 0.011 0.001 TYR E1140 PHE 0.041 0.002 PHE E 465 TRP 0.017 0.001 TRP E 885 HIS 0.012 0.001 HIS E 815 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (12501) covalent geometry : angle 0.64700 / 0.33 (17314) hydrogen bonds : bond 0.03805 / 2.60 ( 590) hydrogen bonds : angle 4.30960 / 3.04 ( 1686) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 211 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 MET cc_start: 0.7194 (tpp) cc_final: 0.6745 (tpp) REVERT: B 253 MET cc_start: 0.7939 (tpp) cc_final: 0.7383 (tpp) REVERT: B 258 TYR cc_start: 0.7444 (t80) cc_final: 0.6729 (t80) REVERT: B 346 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6707 (pp30) REVERT: E 230 PHE cc_start: 0.8266 (m-80) cc_final: 0.7933 (m-80) REVERT: E 478 GLU cc_start: 0.7317 (tp30) cc_final: 0.7115 (tp30) REVERT: E 485 GLN cc_start: 0.7018 (tm-30) cc_final: 0.6722 (tm-30) REVERT: E 685 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6970 (mm-30) REVERT: E 825 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7731 (mt) REVERT: E 892 TRP cc_start: 0.7883 (m100) cc_final: 0.7425 (m100) REVERT: E 966 PHE cc_start: 0.7685 (m-10) cc_final: 0.7469 (m-80) REVERT: E 987 ARG cc_start: 0.8607 (mtm180) cc_final: 0.8270 (ttp80) REVERT: E 995 MET cc_start: 0.7457 (tmm) cc_final: 0.7207 (tmm) REVERT: E 1043 MET cc_start: 0.1396 (OUTLIER) cc_final: 0.0416 (pmm) REVERT: E 1135 THR cc_start: 0.7653 (m) cc_final: 0.7375 (m) REVERT: E 1151 ASP cc_start: 0.5138 (t0) cc_final: 0.4697 (t0) REVERT: E 1227 TYR cc_start: 0.6472 (m-10) cc_final: 0.6043 (m-10) outliers start: 22 outliers final: 18 residues processed: 220 average time/residue: 0.0961 time to fit residues: 30.5121 Evaluate side-chains 231 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 405 HIS Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain E residue 815 HIS Chi-restraints excluded: chain E residue 825 LEU Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 1043 MET Chi-restraints excluded: chain E residue 1071 VAL Chi-restraints excluded: chain E residue 1150 HIS Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 74 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 99 optimal weight: 0.0370 chunk 66 optimal weight: 0.0020 chunk 69 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.5666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 251 HIS ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1009 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.186070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.149782 restraints weight = 19337.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.154599 restraints weight = 10141.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.157807 restraints weight = 6245.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.159787 restraints weight = 4399.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.161339 restraints weight = 3481.405| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12501 Z= 0.135 Angle : 0.636 10.692 17314 Z= 0.328 Chirality : 0.042 0.305 1992 Planarity : 0.005 0.058 1962 Dihedral : 20.690 175.922 2306 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.01 % Allowed : 18.32 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.22), residues: 1369 helix: 1.50 (0.20), residues: 706 sheet: -1.50 (0.46), residues: 101 loop : -1.19 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 518 TYR 0.010 0.001 TYR A 229 PHE 0.034 0.002 PHE E 465 TRP 0.020 0.001 TRP E 885 HIS 0.008 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (12501) covalent geometry : angle 0.63630 / 0.33 (17314) hydrogen bonds : bond 0.03763 / 2.57 ( 590) hydrogen bonds : angle 4.28834 / 3.03 ( 1686) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1920.35 seconds wall clock time: 33 minutes 49.62 seconds (2029.62 seconds total)