Starting phenix.real_space_refine on Sat Aug 23 13:47:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mna_48418/08_2025/9mna_48418.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mna_48418/08_2025/9mna_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 { model { file = "/net/cci-nas-00/data/ceres_data/9mna_48418/08_2025/9mna_48418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mna_48418/08_2025/9mna_48418.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mna_48418/08_2025/9mna_48418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mna_48418/08_2025/9mna_48418.map" } 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-2.0-5787/lib/python3.9/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: 3.02, per 1000 atoms: 0.25 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: 1.11 Conformation dependent library (CDL) restraints added in 516.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.28 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: 2.41 Time building geometry restraints manager: 1.46 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 1.422 1.505 -0.083 3.00e-02 1.11e+03 7.60e+00 bond pdb=" C PRO E1120 " pdb=" N PRO E1121 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.34e+00 bond pdb=" C3' DA N 43 " pdb=" O3' DA N 43 " ideal model delta sigma weight residual 1.422 1.487 -0.065 3.00e-02 1.11e+03 4.76e+00 bond pdb=" CA PRO E 365 " pdb=" C PRO E 365 " ideal model delta sigma weight residual 1.514 1.525 -0.011 5.50e-03 3.31e+04 3.79e+00 bond pdb=" C3' DA N 46 " pdb=" O3' DA N 46 " ideal model delta sigma weight residual 1.422 1.479 -0.057 3.00e-02 1.11e+03 3.57e+00 ... (remaining 12496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 16937 2.68 - 5.36: 326 5.36 - 8.05: 40 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=" 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 angle pdb=" C ARG E 790 " pdb=" N ASP E 791 " pdb=" CA ASP E 791 " ideal model delta sigma weight residual 121.54 129.99 -8.45 1.91e+00 2.74e-01 1.96e+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: 1735 0.069 - 0.139: 226 0.139 - 0.208: 25 0.208 - 0.278: 5 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.430 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5145 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 : 0.004 0.083 12501 Z= 0.198 Angle : 0.868 13.409 17314 Z= 0.453 Chirality : 0.049 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 aren 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 covalent geometry : bond 0.00426 (12501) covalent geometry : angle 0.86755 (17314) hydrogen bonds : bond 0.13411 ( 590) hydrogen bonds : angle 6.00264 ( 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 : 0.386 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: 0.6614 (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: 0.1036 time to fit residues: 32.6871 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 : 0.249 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.188109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.154018 restraints weight = 18874.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.158495 restraints weight = 10086.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.161393 restraints weight = 6259.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.163460 restraints weight = 4434.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.164459 restraints weight = 3495.900| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12501 Z= 0.168 Angle : 0.636 7.898 17314 Z= 0.339 Chirality : 0.040 0.210 1992 Planarity : 0.005 0.053 1962 Dihedral : 20.935 178.171 2306 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.28 % Allowed : 9.25 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.22), residues: 1369 helix: 0.44 (0.19), residues: 722 sheet: -1.29 (0.47), residues: 103 loop : -1.23 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 790 TYR 0.017 0.001 TYR E1140 PHE 0.024 0.002 PHE A 150 TRP 0.037 0.002 TRP E 441 HIS 0.010 0.001 HIS E 624 Details of bonding type rmsd covalent geometry : bond 0.00362 (12501) covalent geometry : angle 0.63604 (17314) hydrogen bonds : bond 0.04653 ( 590) hydrogen bonds : angle 4.86785 ( 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 229 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 215 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 MET cc_start: 0.7924 (tpp) cc_final: 0.7211 (tpp) REVERT: B 258 TYR cc_start: 0.7295 (t80) cc_final: 0.6509 (t80) REVERT: E 456 LEU cc_start: 0.8308 (mm) cc_final: 0.8035 (mt) REVERT: E 701 GLN cc_start: 0.7514 (tt0) cc_final: 0.7272 (tt0) REVERT: E 846 VAL cc_start: 0.7025 (t) cc_final: 0.6795 (m) REVERT: E 995 MET cc_start: 0.7494 (tmm) cc_final: 0.6684 (tmm) REVERT: E 1010 ILE cc_start: 0.8551 (tp) cc_final: 0.8213 (tp) REVERT: E 1111 ASN cc_start: 0.8095 (t0) cc_final: 0.7366 (t0) REVERT: E 1114 LYS cc_start: 0.8196 (mtmm) cc_final: 0.7627 (mtmm) REVERT: E 1133 MET cc_start: 0.6510 (mtm) cc_final: 0.6289 (mtm) REVERT: E 1227 TYR cc_start: 0.6504 (m-10) cc_final: 0.5812 (m-80) outliers start: 14 outliers final: 9 residues processed: 219 average time/residue: 0.1140 time to fit residues: 35.7992 Evaluate side-chains 217 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 208 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 849 THR Chi-restraints excluded: chain E residue 949 SER 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: 3.9990 chunk 99 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 103 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 945 ASN 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 = 0.4318 r_free = 0.4318 target = 0.188225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.154167 restraints weight = 18903.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.158551 restraints weight = 10007.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.161559 restraints weight = 6221.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.163429 restraints weight = 4397.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.164765 restraints weight = 3475.883| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12501 Z= 0.152 Angle : 0.597 6.653 17314 Z= 0.317 Chirality : 0.040 0.238 1992 Planarity : 0.005 0.053 1962 Dihedral : 20.749 177.740 2306 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.65 % Allowed : 12.82 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.22), residues: 1369 helix: 0.92 (0.19), residues: 719 sheet: -1.54 (0.47), residues: 97 loop : -1.23 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 225 TYR 0.015 0.001 TYR E1140 PHE 0.024 0.002 PHE A 150 TRP 0.015 0.001 TRP E 885 HIS 0.010 0.001 HIS E 608 Details of bonding type rmsd covalent geometry : bond 0.00333 (12501) covalent geometry : angle 0.59732 (17314) hydrogen bonds : bond 0.04108 ( 590) hydrogen bonds : angle 4.52193 ( 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 228 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 MET cc_start: 0.7017 (tpp) cc_final: 0.6723 (tpp) REVERT: A 288 MET cc_start: 0.5913 (OUTLIER) cc_final: 0.5701 (mtm) REVERT: B 234 THR cc_start: 0.8713 (m) cc_final: 0.8494 (t) REVERT: B 253 MET cc_start: 0.7887 (tpp) cc_final: 0.7390 (tpp) REVERT: B 258 TYR cc_start: 0.7269 (t80) cc_final: 0.6472 (t80) REVERT: B 346 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6773 (pp30) REVERT: E 407 GLU cc_start: 0.7517 (tp30) cc_final: 0.7238 (tp30) REVERT: E 485 GLN cc_start: 0.6936 (tm-30) cc_final: 0.6632 (tm-30) REVERT: E 701 GLN cc_start: 0.7572 (tt0) cc_final: 0.7320 (tt0) REVERT: E 831 ARG cc_start: 0.8007 (tpp-160) cc_final: 0.7748 (mmt-90) REVERT: E 892 TRP cc_start: 0.7857 (m100) cc_final: 0.7464 (m100) REVERT: E 1043 MET cc_start: 0.1948 (OUTLIER) cc_final: 0.1657 (pmm) REVERT: E 1128 ASP cc_start: 0.6745 (t70) cc_final: 0.6520 (t70) REVERT: E 1133 MET cc_start: 0.6560 (mtm) cc_final: 0.6137 (mtm) REVERT: E 1151 ASP cc_start: 0.5091 (t0) cc_final: 0.4781 (t0) REVERT: E 1227 TYR cc_start: 0.6406 (m-10) cc_final: 0.5960 (m-10) outliers start: 18 outliers final: 11 residues processed: 214 average time/residue: 0.1163 time to fit residues: 35.5652 Evaluate side-chains 223 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 B residue 346 GLN Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 629 GLN 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: 0.7980 chunk 51 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 89 optimal weight: 0.0970 chunk 63 optimal weight: 0.0370 chunk 34 optimal weight: 20.0000 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS E1117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.188787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.153708 restraints weight = 18966.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.158461 restraints weight = 9892.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.161538 restraints weight = 6053.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.163340 restraints weight = 4254.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.164947 restraints weight = 3372.724| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12501 Z= 0.127 Angle : 0.573 7.512 17314 Z= 0.301 Chirality : 0.038 0.224 1992 Planarity : 0.005 0.052 1962 Dihedral : 20.600 177.136 2306 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.74 % Allowed : 14.74 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.22), residues: 1369 helix: 1.30 (0.19), residues: 713 sheet: -1.46 (0.47), residues: 103 loop : -1.12 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 225 TYR 0.010 0.001 TYR A 229 PHE 0.026 0.002 PHE E 465 TRP 0.012 0.001 TRP E 885 HIS 0.007 0.001 HIS E 608 Details of bonding type rmsd covalent geometry : bond 0.00276 (12501) covalent geometry : angle 0.57302 (17314) hydrogen bonds : bond 0.03701 ( 590) hydrogen bonds : angle 4.33086 ( 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 229 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 210 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.6194 (mp0) cc_final: 0.5937 (mp0) REVERT: A 256 MET cc_start: 0.7110 (tpp) cc_final: 0.6705 (tpp) REVERT: B 234 THR cc_start: 0.8680 (m) cc_final: 0.8455 (t) REVERT: B 253 MET cc_start: 0.7873 (tpp) cc_final: 0.7372 (tpp) REVERT: B 258 TYR cc_start: 0.7316 (t80) cc_final: 0.6534 (t80) REVERT: B 346 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6496 (pp30) REVERT: E 230 PHE cc_start: 0.8216 (m-80) cc_final: 0.7832 (m-80) REVERT: E 263 MET cc_start: 0.7088 (mtt) cc_final: 0.6844 (mtt) REVERT: E 295 ASP cc_start: 0.8482 (t0) cc_final: 0.8241 (t0) REVERT: E 407 GLU cc_start: 0.7544 (tp30) cc_final: 0.7297 (tp30) REVERT: E 485 GLN cc_start: 0.6922 (tm-30) cc_final: 0.6617 (tm-30) REVERT: E 701 GLN cc_start: 0.7574 (tt0) cc_final: 0.7344 (tt0) REVERT: E 800 MET cc_start: 0.5579 (tpp) cc_final: 0.5322 (mmm) REVERT: E 825 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7680 (mt) REVERT: E 831 ARG cc_start: 0.7997 (tpp-160) cc_final: 0.7712 (mmt-90) REVERT: E 995 MET cc_start: 0.7478 (tmm) cc_final: 0.7247 (tmm) REVERT: E 1043 MET cc_start: 0.1803 (OUTLIER) cc_final: 0.0435 (pmm) REVERT: E 1151 ASP cc_start: 0.5073 (t0) cc_final: 0.4686 (t0) outliers start: 19 outliers final: 10 residues processed: 218 average time/residue: 0.1165 time to fit residues: 36.4581 Evaluate side-chains 221 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 208 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU 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 251 HIS Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 629 GLN Chi-restraints excluded: chain E residue 638 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 76 optimal weight: 0.0470 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 42 optimal weight: 0.0670 chunk 138 optimal weight: 6.9990 chunk 104 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS E 704 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 = 0.4296 r_free = 0.4296 target = 0.186096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.149820 restraints weight = 19442.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.154593 restraints weight = 10181.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.157802 restraints weight = 6272.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.159873 restraints weight = 4417.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.160794 restraints weight = 3469.250| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12501 Z= 0.156 Angle : 0.588 8.218 17314 Z= 0.311 Chirality : 0.040 0.234 1992 Planarity : 0.005 0.051 1962 Dihedral : 20.489 177.209 2306 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.38 % Allowed : 15.75 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.22), residues: 1369 helix: 1.39 (0.19), residues: 710 sheet: -1.55 (0.47), residues: 97 loop : -1.16 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 776 TYR 0.012 0.001 TYR E1140 PHE 0.034 0.002 PHE E 465 TRP 0.013 0.001 TRP E 885 HIS 0.016 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00344 (12501) covalent geometry : angle 0.58842 (17314) hydrogen bonds : bond 0.03877 ( 590) hydrogen bonds : angle 4.34816 ( 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 232 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.6305 (mp0) cc_final: 0.6071 (mp0) REVERT: A 256 MET cc_start: 0.7203 (tpp) cc_final: 0.6755 (tpp) REVERT: B 234 THR cc_start: 0.8710 (m) cc_final: 0.8447 (t) REVERT: B 253 MET cc_start: 0.7966 (tpp) cc_final: 0.7428 (tpp) REVERT: B 258 TYR cc_start: 0.7447 (t80) cc_final: 0.6674 (t80) REVERT: B 346 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.6636 (pp30) REVERT: E 295 ASP cc_start: 0.8520 (t0) cc_final: 0.8274 (t0) REVERT: E 407 GLU cc_start: 0.7573 (tp30) cc_final: 0.7327 (tp30) REVERT: E 478 GLU cc_start: 0.7460 (tp30) cc_final: 0.7253 (tp30) REVERT: E 485 GLN cc_start: 0.7001 (tm-30) cc_final: 0.6703 (tm-30) REVERT: E 701 GLN cc_start: 0.7651 (tt0) cc_final: 0.7386 (tt0) REVERT: E 825 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7679 (mt) REVERT: E 831 ARG cc_start: 0.8024 (tpp-160) cc_final: 0.7733 (mmt-90) REVERT: E 892 TRP cc_start: 0.7870 (m100) cc_final: 0.7537 (m100) REVERT: E 1043 MET cc_start: 0.1463 (OUTLIER) cc_final: 0.0582 (pmm) REVERT: E 1151 ASP cc_start: 0.5171 (t0) cc_final: 0.4746 (t0) outliers start: 26 outliers final: 14 residues processed: 218 average time/residue: 0.1203 time to fit residues: 37.3484 Evaluate side-chains 215 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU 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 405 HIS Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 629 GLN Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 704 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: 3.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS 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 = 0.4292 r_free = 0.4292 target = 0.185778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.149579 restraints weight = 19546.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.154350 restraints weight = 10228.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.157652 restraints weight = 6295.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.159669 restraints weight = 4402.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.161086 restraints weight = 3461.231| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12501 Z= 0.153 Angle : 0.604 9.161 17314 Z= 0.313 Chirality : 0.039 0.178 1992 Planarity : 0.005 0.051 1962 Dihedral : 20.428 177.084 2306 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.29 % Allowed : 16.58 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.22), residues: 1369 helix: 1.44 (0.19), residues: 710 sheet: -1.46 (0.46), residues: 95 loop : -1.16 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 518 TYR 0.013 0.001 TYR E1140 PHE 0.033 0.002 PHE E 465 TRP 0.013 0.001 TRP E 885 HIS 0.012 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00339 (12501) covalent geometry : angle 0.60429 (17314) hydrogen bonds : bond 0.03820 ( 590) hydrogen bonds : angle 4.32359 ( 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 231 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.6298 (mp0) cc_final: 0.6084 (mp0) REVERT: A 256 MET cc_start: 0.7208 (tpp) cc_final: 0.6745 (tpp) REVERT: B 253 MET cc_start: 0.7967 (tpp) cc_final: 0.7426 (tpp) REVERT: B 258 TYR cc_start: 0.7429 (t80) cc_final: 0.6685 (t80) REVERT: B 346 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6680 (pp30) REVERT: E 235 LEU cc_start: 0.7637 (mt) cc_final: 0.7360 (mp) REVERT: E 295 ASP cc_start: 0.8479 (t0) cc_final: 0.8239 (t0) REVERT: E 478 GLU cc_start: 0.7456 (tp30) cc_final: 0.7254 (tp30) REVERT: E 485 GLN cc_start: 0.7007 (tm-30) cc_final: 0.6706 (tm-30) REVERT: E 542 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7245 (tm-30) REVERT: E 648 MET cc_start: 0.6853 (mmp) cc_final: 0.6300 (mmt) REVERT: E 701 GLN cc_start: 0.7639 (tt0) cc_final: 0.7352 (tt0) REVERT: E 825 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7688 (mt) REVERT: E 831 ARG cc_start: 0.8009 (tpp-160) cc_final: 0.7704 (mmt-90) REVERT: E 892 TRP cc_start: 0.7887 (m100) cc_final: 0.7563 (m100) REVERT: E 995 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.7012 (tmm) REVERT: E 1043 MET cc_start: 0.1549 (OUTLIER) cc_final: 0.1016 (pmm) REVERT: E 1151 ASP cc_start: 0.5069 (t0) cc_final: 0.4677 (t0) outliers start: 25 outliers final: 16 residues processed: 215 average time/residue: 0.1157 time to fit residues: 35.4435 Evaluate side-chains 220 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 589 MET Chi-restraints excluded: chain E residue 629 GLN Chi-restraints excluded: chain E residue 638 THR 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 995 MET 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: 1.9990 chunk 99 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4278 r_free = 0.4278 target = 0.184523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.148405 restraints weight = 19365.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.153127 restraints weight = 10133.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.156390 restraints weight = 6241.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.158305 restraints weight = 4365.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.159758 restraints weight = 3452.764| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.2171 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= 0.176 Angle : 0.630 13.415 17314 Z= 0.324 Chirality : 0.040 0.176 1992 Planarity : 0.005 0.054 1962 Dihedral : 20.422 177.278 2306 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.66 % Allowed : 16.30 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.22), residues: 1369 helix: 1.42 (0.19), residues: 707 sheet: -1.52 (0.45), residues: 101 loop : -1.16 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 803 TYR 0.014 0.001 TYR E1140 PHE 0.036 0.002 PHE E 465 TRP 0.013 0.001 TRP E 885 HIS 0.016 0.001 HIS E 815 Details of bonding type rmsd covalent geometry : bond 0.00390 (12501) covalent geometry : angle 0.62972 (17314) hydrogen bonds : bond 0.03989 ( 590) hydrogen bonds : angle 4.36601 ( 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 244 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 MET cc_start: 0.7216 (tpp) cc_final: 0.6740 (tpp) REVERT: B 234 THR cc_start: 0.8725 (m) cc_final: 0.8448 (t) REVERT: B 253 MET cc_start: 0.8011 (tpp) cc_final: 0.7511 (tpp) REVERT: B 258 TYR cc_start: 0.7421 (t80) cc_final: 0.6740 (t80) REVERT: B 346 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6732 (pp30) REVERT: E 230 PHE cc_start: 0.8293 (m-80) cc_final: 0.7880 (m-80) REVERT: E 295 ASP cc_start: 0.8456 (t0) cc_final: 0.8246 (t0) REVERT: E 478 GLU cc_start: 0.7518 (tp30) cc_final: 0.7300 (tp30) REVERT: E 485 GLN cc_start: 0.7021 (tm-30) cc_final: 0.6723 (tm-30) REVERT: E 542 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7214 (tm-30) REVERT: E 574 GLU cc_start: 0.6662 (tm-30) cc_final: 0.6453 (tm-30) REVERT: E 648 MET cc_start: 0.6938 (mmp) cc_final: 0.6358 (mmt) REVERT: E 701 GLN cc_start: 0.7618 (tt0) cc_final: 0.7335 (tt0) REVERT: E 825 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7700 (mt) REVERT: E 892 TRP cc_start: 0.7893 (m100) cc_final: 0.7567 (m100) REVERT: E 995 MET cc_start: 0.7421 (ttt) cc_final: 0.7101 (tmm) REVERT: E 1043 MET cc_start: 0.1588 (OUTLIER) cc_final: 0.0682 (pmm) REVERT: E 1111 ASN cc_start: 0.8294 (t0) cc_final: 0.7426 (t0) REVERT: E 1114 LYS cc_start: 0.8296 (mtmm) cc_final: 0.7642 (mtmm) REVERT: E 1151 ASP cc_start: 0.5170 (t0) cc_final: 0.4774 (t0) REVERT: E 1227 TYR cc_start: 0.6542 (m-10) cc_final: 0.6046 (m-10) outliers start: 29 outliers final: 21 residues processed: 227 average time/residue: 0.1142 time to fit residues: 37.2387 Evaluate side-chains 238 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 234 THR 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 406 MET Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 629 GLN Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 762 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 0.0060 chunk 88 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 136 optimal weight: 0.3980 chunk 86 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN E 704 ASN E 773 HIS E 815 HIS E1009 GLN E1117 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.185487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.149389 restraints weight = 19405.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.154193 restraints weight = 10117.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.157364 restraints weight = 6206.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.159293 restraints weight = 4363.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.160840 restraints weight = 3437.266| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12501 Z= 0.135 Angle : 0.607 9.798 17314 Z= 0.311 Chirality : 0.039 0.181 1992 Planarity : 0.005 0.056 1962 Dihedral : 20.363 177.693 2306 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.38 % Allowed : 16.58 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.23), residues: 1369 helix: 1.51 (0.19), residues: 707 sheet: -1.39 (0.47), residues: 95 loop : -1.15 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 518 TYR 0.011 0.001 TYR A 229 PHE 0.033 0.002 PHE E 465 TRP 0.012 0.001 TRP E 885 HIS 0.009 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00300 (12501) covalent geometry : angle 0.60730 (17314) hydrogen bonds : bond 0.03665 ( 590) hydrogen bonds : angle 4.27515 ( 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 233 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.6315 (mp0) cc_final: 0.6114 (mp0) REVERT: A 256 MET cc_start: 0.7268 (tpp) cc_final: 0.6756 (tpp) REVERT: B 234 THR cc_start: 0.8693 (m) cc_final: 0.8409 (t) REVERT: B 253 MET cc_start: 0.7944 (tpp) cc_final: 0.7412 (tpp) REVERT: B 258 TYR cc_start: 0.7456 (t80) cc_final: 0.6737 (t80) REVERT: B 346 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6699 (pp30) REVERT: E 230 PHE cc_start: 0.8229 (m-80) cc_final: 0.7875 (m-80) REVERT: E 468 TYR cc_start: 0.7438 (t80) cc_final: 0.7180 (t80) REVERT: E 485 GLN cc_start: 0.6991 (tm-30) cc_final: 0.6708 (tm-30) REVERT: E 542 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7164 (tm-30) REVERT: E 648 MET cc_start: 0.6818 (mmp) cc_final: 0.6221 (mmt) REVERT: E 701 GLN cc_start: 0.7577 (tt0) cc_final: 0.7291 (tt0) REVERT: E 825 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7667 (mt) REVERT: E 892 TRP cc_start: 0.7856 (m100) cc_final: 0.7378 (m100) REVERT: E 995 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7123 (tmm) REVERT: E 1043 MET cc_start: 0.1487 (OUTLIER) cc_final: 0.0531 (pmm) REVERT: E 1151 ASP cc_start: 0.5128 (t0) cc_final: 0.4706 (t0) outliers start: 26 outliers final: 19 residues processed: 218 average time/residue: 0.1132 time to fit residues: 35.2111 Evaluate side-chains 229 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 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 406 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 629 GLN 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 871 ILE Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 995 MET 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: 0.0070 chunk 69 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 0.0040 overall best weight: 0.5012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4295 r_free = 0.4295 target = 0.186143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.149931 restraints weight = 19343.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.154634 restraints weight = 10149.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.157884 restraints weight = 6279.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.159851 restraints weight = 4426.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.161372 restraints weight = 3485.238| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12501 Z= 0.132 Angle : 0.616 14.611 17314 Z= 0.312 Chirality : 0.039 0.173 1992 Planarity : 0.005 0.056 1962 Dihedral : 20.310 177.677 2306 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.47 % Allowed : 17.31 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.23), residues: 1369 helix: 1.58 (0.20), residues: 704 sheet: -1.36 (0.46), residues: 101 loop : -1.13 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 518 TYR 0.011 0.001 TYR A 229 PHE 0.033 0.001 PHE E 465 TRP 0.013 0.001 TRP E 885 HIS 0.008 0.001 HIS E 815 Details of bonding type rmsd covalent geometry : bond 0.00293 (12501) covalent geometry : angle 0.61583 (17314) hydrogen bonds : bond 0.03558 ( 590) hydrogen bonds : angle 4.23451 ( 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 238 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 MET cc_start: 0.7255 (tpp) cc_final: 0.6749 (tpp) REVERT: B 234 THR cc_start: 0.8690 (m) cc_final: 0.8404 (t) REVERT: B 253 MET cc_start: 0.7962 (tpp) cc_final: 0.7434 (tpp) REVERT: B 258 TYR cc_start: 0.7470 (t80) cc_final: 0.6799 (t80) REVERT: B 346 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.6727 (pp30) REVERT: E 230 PHE cc_start: 0.8239 (m-80) cc_final: 0.7873 (m-80) REVERT: E 295 ASP cc_start: 0.8190 (t0) cc_final: 0.7945 (t0) REVERT: E 485 GLN cc_start: 0.6980 (tm-30) cc_final: 0.6712 (tm-30) REVERT: E 542 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7152 (tm-30) REVERT: E 648 MET cc_start: 0.6781 (mmp) cc_final: 0.6233 (mmt) REVERT: E 685 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6984 (mm-30) REVERT: E 701 GLN cc_start: 0.7572 (tt0) cc_final: 0.7285 (tt0) REVERT: E 825 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7704 (mt) REVERT: E 892 TRP cc_start: 0.7866 (m100) cc_final: 0.7448 (m100) REVERT: E 995 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.7150 (tmm) REVERT: E 1043 MET cc_start: 0.1408 (OUTLIER) cc_final: 0.0469 (pmm) REVERT: E 1151 ASP cc_start: 0.5144 (t0) cc_final: 0.4701 (t0) outliers start: 27 outliers final: 20 residues processed: 224 average time/residue: 0.1166 time to fit residues: 37.6240 Evaluate side-chains 235 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 234 THR 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 406 MET Chi-restraints excluded: chain E residue 629 GLN Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain E residue 825 LEU Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain E residue 871 ILE Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 995 MET 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: 2.9990 chunk 95 optimal weight: 0.5980 chunk 142 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 82 optimal weight: 0.0010 chunk 57 optimal weight: 0.0570 chunk 114 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 overall best weight: 0.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1009 GLN E1131 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.186911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.150790 restraints weight = 19489.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.155549 restraints weight = 10212.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.158832 restraints weight = 6286.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.160878 restraints weight = 4402.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.162359 restraints weight = 3448.221| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12501 Z= 0.128 Angle : 0.612 10.239 17314 Z= 0.311 Chirality : 0.039 0.171 1992 Planarity : 0.005 0.056 1962 Dihedral : 20.254 177.702 2306 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.20 % Allowed : 18.32 % Favored : 79.49 % 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 aren not related in a simple way. whole: 0.44 (0.23), residues: 1369 helix: 1.62 (0.20), residues: 707 sheet: -1.37 (0.46), residues: 98 loop : -1.12 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 518 TYR 0.020 0.001 TYR E 627 PHE 0.029 0.001 PHE E 465 TRP 0.020 0.001 TRP E 885 HIS 0.008 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00286 (12501) covalent geometry : angle 0.61166 (17314) hydrogen bonds : bond 0.03437 ( 590) hydrogen bonds : angle 4.18944 ( 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 229 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 MET cc_start: 0.7235 (tpp) cc_final: 0.6743 (tpp) REVERT: B 234 THR cc_start: 0.8680 (m) cc_final: 0.8392 (t) REVERT: B 253 MET cc_start: 0.7912 (tpp) cc_final: 0.7385 (tpp) REVERT: B 346 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.6745 (pp30) REVERT: E 230 PHE cc_start: 0.8242 (m-80) cc_final: 0.7852 (m-80) REVERT: E 295 ASP cc_start: 0.8180 (t0) cc_final: 0.7932 (t0) REVERT: E 485 GLN cc_start: 0.6979 (tm-30) cc_final: 0.6698 (tm-30) REVERT: E 542 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7150 (tm-30) REVERT: E 582 MET cc_start: 0.7230 (tpp) cc_final: 0.6913 (ttm) REVERT: E 648 MET cc_start: 0.6785 (mmp) cc_final: 0.6254 (mmt) REVERT: E 671 MET cc_start: 0.8353 (mtt) cc_final: 0.8138 (mtm) REVERT: E 701 GLN cc_start: 0.7561 (tt0) cc_final: 0.7293 (tt0) REVERT: E 825 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7686 (mt) REVERT: E 882 ARG cc_start: 0.6838 (ttm110) cc_final: 0.6454 (ttp80) REVERT: E 892 TRP cc_start: 0.7848 (m100) cc_final: 0.7430 (m100) REVERT: E 995 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.7034 (tmm) REVERT: E 1043 MET cc_start: 0.1403 (OUTLIER) cc_final: 0.0430 (pmm) REVERT: E 1151 ASP cc_start: 0.5151 (t0) cc_final: 0.4715 (t0) outliers start: 24 outliers final: 20 residues processed: 216 average time/residue: 0.1216 time to fit residues: 37.2470 Evaluate side-chains 229 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 260 LEU 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 406 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 629 GLN Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain E residue 772 MET Chi-restraints excluded: chain E residue 825 LEU Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain E residue 871 ILE Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 995 MET 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: 0.9980 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 66 optimal weight: 0.0010 chunk 69 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 0.0980 chunk 130 optimal weight: 1.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 680 HIS ** E 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1009 GLN E1131 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.185783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.149578 restraints weight = 19333.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.154393 restraints weight = 10139.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.157655 restraints weight = 6230.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.159656 restraints weight = 4351.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.161162 restraints weight = 3415.677| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12501 Z= 0.152 Angle : 0.618 10.214 17314 Z= 0.316 Chirality : 0.039 0.167 1992 Planarity : 0.005 0.056 1962 Dihedral : 20.229 178.068 2306 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.29 % Allowed : 18.32 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.23), residues: 1369 helix: 1.59 (0.20), residues: 707 sheet: -1.36 (0.47), residues: 98 loop : -1.12 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 518 TYR 0.012 0.001 TYR E1140 PHE 0.028 0.002 PHE E 465 TRP 0.018 0.001 TRP E 885 HIS 0.010 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00337 (12501) covalent geometry : angle 0.61844 (17314) hydrogen bonds : bond 0.03605 ( 590) hydrogen bonds : angle 4.21790 ( 1686) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2308.92 seconds wall clock time: 40 minutes 42.78 seconds (2442.78 seconds total)