Starting phenix.real_space_refine on Wed Aug 5 23:45:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bdd_44449/08_2026/9bdd_44449.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bdd_44449/08_2026/9bdd_44449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bdd_44449/08_2026/9bdd_44449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bdd_44449/08_2026/9bdd_44449.map" model { file = "/net/cci-nas-00/data/ceres_data/9bdd_44449/08_2026/9bdd_44449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bdd_44449/08_2026/9bdd_44449.cif" } resolution = 2.86 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 64 5.49 5 S 59 5.16 5 C 7666 2.51 5 N 2189 2.21 5 O 2335 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12313 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1723 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 206} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1552 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 194} Chain breaks: 2 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 4, 'GLN:plan1': 4, 'PHE:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "E" Number of atoms: 7746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7746 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 67, 'TRANS': 917} Chain breaks: 2 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 95 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 5, 'GLU:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "N" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 452 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "R" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 6} Chain: "T" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 614 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'APC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.93, per 1000 atoms: 0.16 Number of scatterers: 12313 At special positions: 0 Unit cell: (111.863, 130.229, 103.515, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 P 64 15.00 O 2335 8.00 N 2189 7.00 C 7666 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 471.5 milliseconds 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2674 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 12 sheets defined 58.9% alpha, 7.7% beta 25 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 160 through 166 Processing helix chain 'A' and resid 208 through 223 removed outlier: 3.503A pdb=" N TYR A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 261 removed outlier: 3.722A pdb=" N GLU A 254 " --> pdb=" O PHE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 296 through 306 removed outlier: 3.810A pdb=" N ASP A 306 " --> pdb=" O GLN A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 332 Processing helix chain 'A' and resid 337 through 354 removed outlier: 3.919A pdb=" N TYR A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 166 removed outlier: 3.610A pdb=" N ALA B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 223 removed outlier: 3.847A pdb=" N LYS B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 262 removed outlier: 4.149A pdb=" N HIS B 249 " --> pdb=" O PRO B 245 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 285 Processing helix chain 'B' and resid 296 through 304 Processing helix chain 'B' and resid 321 through 331 Processing helix chain 'B' and resid 338 through 354 removed outlier: 3.757A pdb=" N LEU B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 237 Processing helix chain 'E' and resid 238 through 252 removed outlier: 3.847A pdb=" N GLN E 252 " --> pdb=" O VAL E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 275 removed outlier: 3.536A pdb=" N TYR E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 291 Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 312 through 326 removed outlier: 3.921A pdb=" N ILE E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 335 Processing helix chain 'E' and resid 340 through 355 Processing helix chain 'E' and resid 392 through 409 removed outlier: 3.825A pdb=" N ALA E 409 " --> pdb=" O HIS E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 462 removed outlier: 3.629A 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 490 Processing helix chain 'E' and resid 497 through 520 removed outlier: 4.171A pdb=" N GLN E 517 " --> pdb=" O VAL E 513 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG E 518 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL E 519 " --> pdb=" O GLN E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 538 removed outlier: 3.680A pdb=" N ALA E 525 " --> pdb=" O GLY E 521 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS E 535 " --> pdb=" O ARG E 531 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU E 536 " --> pdb=" O LYS E 532 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU E 537 " --> pdb=" O TYR E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 556 Processing helix chain 'E' and resid 568 through 586 Processing helix chain 'E' and resid 624 through 633 Processing helix chain 'E' and resid 678 through 684 Processing helix chain 'E' and resid 692 through 705 removed outlier: 3.574A pdb=" N ALA E 698 " --> pdb=" O GLY E 694 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS E 705 " --> pdb=" O GLN E 701 " (cutoff:3.500A) Processing helix chain 'E' and resid 711 through 723 removed outlier: 3.655A pdb=" N LEU E 716 " --> pdb=" O ARG E 712 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA E 723 " --> pdb=" O GLN E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 734 through 738 Processing helix chain 'E' and resid 747 through 750 Processing helix chain 'E' and resid 751 through 789 removed outlier: 3.508A pdb=" N LYS E 767 " --> pdb=" O ALA E 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 818 through 824 Processing helix chain 'E' and resid 836 through 850 removed outlier: 3.732A pdb=" N TRP E 840 " --> pdb=" O HIS E 836 " (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 883 through 888 Processing helix chain 'E' and resid 890 through 906 Processing helix chain 'E' and resid 925 through 936 Processing helix chain 'E' and resid 937 through 944 removed outlier: 3.731A pdb=" N ALA E 942 " --> pdb=" O SER E 938 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER E 943 " --> pdb=" O VAL E 939 " (cutoff:3.500A) Processing helix chain 'E' and resid 954 through 970 Processing helix chain 'E' and resid 975 through 982 removed outlier: 3.569A pdb=" N LEU E 981 " --> pdb=" O VAL E 977 " (cutoff:3.500A) Processing helix chain 'E' and resid 986 through 997 removed outlier: 3.899A pdb=" N VAL E 990 " --> pdb=" O THR E 986 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLN E 992 " --> pdb=" O LYS E 988 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N THR E 993 " --> pdb=" O VAL E 989 " (cutoff:3.500A) Processing helix chain 'E' and resid 1002 through 1017 removed outlier: 4.157A pdb=" N LYS E1012 " --> pdb=" O LEU E1008 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG E1013 " --> pdb=" O GLN E1009 " (cutoff:3.500A) Processing helix chain 'E' and resid 1024 through 1044 removed outlier: 3.667A pdb=" N ALA E1028 " --> pdb=" O PHE E1024 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR E1031 " --> pdb=" O GLU E1027 " (cutoff:3.500A) Processing helix chain 'E' and resid 1045 through 1065 Processing helix chain 'E' and resid 1111 through 1141 removed outlier: 3.828A pdb=" N PHE E1119 " --> pdb=" O GLN E1115 " (cutoff:3.500A) Proline residue: E1120 - end of helix removed outlier: 3.685A pdb=" N ILE E1124 " --> pdb=" O PRO E1120 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG E1141 " --> pdb=" O LEU E1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 1156 through 1158 No H-bonds generated for 'chain 'E' and resid 1156 through 1158' Processing helix chain 'E' and resid 1159 through 1177 removed outlier: 3.549A pdb=" N GLN E1170 " --> pdb=" O VAL E1166 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE E1171 " --> pdb=" O CYS E1167 " (cutoff:3.500A) removed outlier: 3.975A 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: 3.628A pdb=" N THR E1207 " --> pdb=" O GLN E1203 " (cutoff:3.500A) Processing helix chain 'E' and resid 1221 through 1225 Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 197 removed outlier: 7.207A pdb=" N VAL A 191 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP A 186 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP A 193 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 228 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 232 " --> pdb=" O ILE A 173 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE A 175 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TYR A 229 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N MET A 276 " --> pdb=" O TYR A 229 " (cutoff:3.500A) removed outlier: 6.260A 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 197 removed outlier: 6.249A pdb=" N HIS B 184 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TRP B 194 " --> pdb=" O TRP B 182 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TRP B 182 " --> pdb=" O TRP B 194 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN B 196 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 180 " --> pdb=" O GLN B 196 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N SER B 169 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N VAL B 230 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE B 171 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N GLU B 232 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ILE B 173 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N TYR B 229 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N MET B 276 " --> pdb=" O TYR B 229 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B 231 " --> pdb=" O MET B 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 288 through 289 Processing sheet with id=AA5, first strand: chain 'E' and resid 412 through 415 Processing sheet with id=AA6, first strand: chain 'E' and resid 495 through 496 removed outlier: 3.957A pdb=" N GLU E 495 " --> pdb=" O LEU E 621 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 588 through 590 Processing sheet with id=AA8, first strand: chain 'E' and resid 794 through 795 Processing sheet with id=AA9, first strand: chain 'E' and resid 798 through 800 Processing sheet with id=AB1, first strand: chain 'E' and resid 831 through 832 Processing sheet with id=AB2, first strand: chain 'E' and resid 919 through 922 Processing sheet with id=AB3, first strand: chain 'E' and resid 1069 through 1071 599 hydrogen bonds defined for protein. 1743 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3493 1.34 - 1.46: 2669 1.46 - 1.58: 6344 1.58 - 1.70: 120 1.70 - 1.82: 96 Bond restraints: 12722 Sorted by residual: bond pdb=" C1' DC T 6 " pdb=" N1 DC T 6 " ideal model delta sigma weight residual 1.468 1.526 -0.058 1.40e-02 5.10e+03 1.69e+01 bond pdb=" N ILE E 618 " pdb=" CA ILE E 618 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.08e-02 8.57e+03 1.00e+01 bond pdb=" C3' DC T -2 " pdb=" C2' DC T -2 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.46e+00 bond pdb=" N PHE E1217 " pdb=" CA PHE E1217 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.21e-02 6.83e+03 7.97e+00 bond pdb=" N VAL E 615 " pdb=" CA VAL E 615 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.70e+00 ... (remaining 12717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 16954 1.84 - 3.68: 476 3.68 - 5.52: 68 5.52 - 7.36: 30 7.36 - 9.20: 2 Bond angle restraints: 17530 Sorted by residual: angle pdb=" C LEU B 304 " pdb=" N PHE B 305 " pdb=" CA PHE B 305 " ideal model delta sigma weight residual 121.70 130.90 -9.20 1.80e+00 3.09e-01 2.61e+01 angle pdb=" CA ALA E1216 " pdb=" C ALA E1216 " pdb=" O ALA E1216 " ideal model delta sigma weight residual 121.20 115.95 5.25 1.04e+00 9.25e-01 2.55e+01 angle pdb=" CA ASP E1218 " pdb=" C ASP E1218 " pdb=" O ASP E1218 " ideal model delta sigma weight residual 121.56 116.30 5.26 1.09e+00 8.42e-01 2.32e+01 angle pdb=" CA ASP E1218 " pdb=" C ASP E1218 " pdb=" N LEU E1219 " ideal model delta sigma weight residual 115.51 121.33 -5.82 1.27e+00 6.20e-01 2.10e+01 angle pdb=" N GLN E1221 " pdb=" CA GLN E1221 " pdb=" C GLN E1221 " ideal model delta sigma weight residual 113.17 107.78 5.39 1.26e+00 6.30e-01 1.83e+01 ... (remaining 17525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.27: 7059 28.27 - 56.55: 429 56.55 - 84.82: 85 84.82 - 113.10: 0 113.10 - 141.37: 1 Dihedral angle restraints: 7574 sinusoidal: 3471 harmonic: 4103 Sorted by residual: dihedral pdb=" CA VAL E1149 " pdb=" C VAL E1149 " pdb=" N HIS E1150 " pdb=" CA HIS E1150 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA GLY E 661 " pdb=" C GLY E 661 " pdb=" N ALA E 662 " pdb=" CA ALA E 662 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA TRP A 194 " pdb=" C TRP A 194 " pdb=" N GLN A 195 " pdb=" CA GLN A 195 " ideal model delta harmonic sigma weight residual -180.00 -159.37 -20.63 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 7571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1947 0.129 - 0.258: 27 0.258 - 0.388: 0 0.388 - 0.517: 3 0.517 - 0.646: 10 Chirality restraints: 1987 Sorted by residual: chirality pdb=" P DA N -24 " pdb=" OP1 DA N -24 " pdb=" OP2 DA N -24 " pdb=" O5' DA N -24 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P DC T 2 " pdb=" OP1 DC T 2 " pdb=" OP2 DC T 2 " pdb=" O5' DC T 2 " both_signs ideal model delta sigma weight residual True 2.34 -2.92 -0.58 2.00e-01 2.50e+01 8.48e+00 chirality pdb=" P DG T -1 " pdb=" OP1 DG T -1 " pdb=" OP2 DG T -1 " pdb=" O5' DG T -1 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.54 2.00e-01 2.50e+01 7.31e+00 ... (remaining 1984 not shown) Planarity restraints: 2021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E1215 " 0.022 2.00e-02 2.50e+03 4.54e-02 2.06e+01 pdb=" C GLY E1215 " -0.078 2.00e-02 2.50e+03 pdb=" O GLY E1215 " 0.030 2.00e-02 2.50e+03 pdb=" N ALA E1216 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E1151 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C ASP E1151 " 0.038 2.00e-02 2.50e+03 pdb=" O ASP E1151 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS E1152 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 249 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C HIS B 249 " 0.037 2.00e-02 2.50e+03 pdb=" O HIS B 249 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE B 250 " -0.012 2.00e-02 2.50e+03 ... (remaining 2018 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2364 2.78 - 3.31: 11269 3.31 - 3.84: 20450 3.84 - 4.37: 23275 4.37 - 4.90: 39509 Nonbonded interactions: 96867 Sorted by model distance: nonbonded pdb=" NH1 ARG E 967 " pdb=" O LEU E 981 " model vdw 2.249 3.120 nonbonded pdb=" OH TYR E 530 " pdb=" O PRO E 651 " model vdw 2.274 3.040 nonbonded pdb=" OD2 ASP E 970 " pdb=" OH TYR E1031 " model vdw 2.348 3.040 nonbonded pdb=" OE2 GLU A 232 " pdb=" NH1 ARG A 278 " model vdw 2.349 3.120 nonbonded pdb=" O VAL E1222 " pdb=" OG SER E1225 " model vdw 2.351 3.040 ... (remaining 96862 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 or (resid 152 and (name N or name CA or name C or name \ O or name CB )) or resid 153 through 160 or (resid 161 through 162 and (name N \ or name CA or name C or name O or name CB )) or resid 163 through 169 or (resid \ 170 and (name N or name CA or name C or name O or name CB )) or resid 171 throug \ h 187 or (resid 188 and (name N or name CA or name C or name O or name CB )) or \ resid 189 through 198 or (resid 199 and (name N or name CA or name C or name O o \ r name CB )) or resid 200 through 266 or (resid 267 and (name N or name CA or na \ me C or name O or name CB )) or resid 268 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 or name C or name O or name CB )) or resid 287 or (re \ sid 288 and (name N or name CA or name C or name O or name CB )) or resid 289 th \ rough 296 or (resid 297 and (name N or name CA or name C or name O or name CB )) \ or resid 298 or (resid 299 and (name N or name CA or name C or name O or name C \ B )) or resid 300 through 301 or (resid 302 and (name N or name CA or name C or \ name O or name CB )) or resid 303 through 306 or resid 313 through 316 or (resid \ 317 and (name N or name CA or name C or name O or name CB )) or resid 318 or re \ sid 320 through 326 or (resid 327 and (name N or name CA or name C or name O or \ name CB )) or resid 328 or (resid 329 and (name N or name CA or name C or name O \ or name CB )) or resid 330 through 332 or (resid 333 and (name N or name CA or \ name C or name O or name CB )) or resid 334 or (resid 335 through 336 and (name \ N or name CA or name C or name O or name CB )) or resid 337 through 351 or (resi \ d 352 and (name N or name CA or name C or name O or name CB )) or resid 353 thro \ ugh 355 or (resid 356 through 357 and (name N or name CA or name C or name O or \ name CB )))) selection = (chain 'B' and (resid 151 through 238 or (resid 239 through 240 and (name N or n \ ame CA or name C or name O or name CB )) or resid 241 through 318 or (resid 320 \ and (name N or name CA or name C or name O or name CB )) or resid 321 through 35 \ 7)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.870 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6004 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 0.058 12722 Z= 0.290 Angle : 0.732 9.196 17530 Z= 0.458 Chirality : 0.063 0.646 1987 Planarity : 0.006 0.053 2021 Dihedral : 17.263 141.372 4900 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.26 % Allowed : 0.94 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.21), residues: 1383 helix: 0.88 (0.18), residues: 751 sheet: 0.09 (0.42), residues: 125 loop : -0.88 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 936 TYR 0.020 0.001 TYR B 258 PHE 0.016 0.001 PHE E1024 TRP 0.030 0.002 TRP A 194 HIS 0.014 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.29 (12722) covalent geometry : angle 0.73162 / 0.46 (17530) hydrogen bonds : bond 0.16475 / 10.44 ( 668) hydrogen bonds : angle 5.91204 / 4.20 ( 1881) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 316 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 172 SER cc_start: 0.7356 (t) cc_final: 0.6870 (p) REVERT: B 171 ILE cc_start: 0.7971 (mm) cc_final: 0.7735 (mp) REVERT: B 217 SER cc_start: 0.6539 (t) cc_final: 0.6173 (m) REVERT: B 223 MET cc_start: 0.7480 (mtt) cc_final: 0.7123 (mtm) REVERT: B 304 LEU cc_start: 0.7074 (mt) cc_final: 0.6834 (mt) REVERT: E 225 ARG cc_start: 0.5678 (mtt180) cc_final: 0.5433 (mtp-110) REVERT: E 279 GLU cc_start: 0.6899 (mp0) cc_final: 0.6349 (mp0) REVERT: E 385 SER cc_start: 0.7441 (t) cc_final: 0.6898 (p) REVERT: E 405 HIS cc_start: 0.6670 (t-90) cc_final: 0.6318 (m90) REVERT: E 466 SER cc_start: 0.6832 (t) cc_final: 0.6464 (p) REVERT: E 502 ARG cc_start: 0.6194 (mtm-85) cc_final: 0.5939 (mtm180) REVERT: E 543 VAL cc_start: 0.7139 (m) cc_final: 0.6912 (t) REVERT: E 544 PRO cc_start: 0.7789 (Cg_exo) cc_final: 0.7486 (Cg_endo) REVERT: E 613 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.6295 (mtt90) REVERT: E 638 THR cc_start: 0.6965 (p) cc_final: 0.6755 (m) REVERT: E 682 GLU cc_start: 0.6544 (tt0) cc_final: 0.6105 (tp30) REVERT: E 826 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6727 (tt0) REVERT: E 858 ARG cc_start: 0.6372 (ttp-110) cc_final: 0.6110 (ptp90) REVERT: E 873 ASP cc_start: 0.6742 (t0) cc_final: 0.6467 (t0) REVERT: E 883 LYS cc_start: 0.7211 (mtmm) cc_final: 0.7000 (mtmm) REVERT: E 900 GLU cc_start: 0.6370 (tp30) cc_final: 0.6075 (tp30) REVERT: E 922 ASP cc_start: 0.6415 (p0) cc_final: 0.6106 (p0) REVERT: E 991 LYS cc_start: 0.5936 (ttpt) cc_final: 0.5500 (ttmm) REVERT: E 1064 MET cc_start: 0.6223 (ttp) cc_final: 0.5917 (mtm) outliers start: 3 outliers final: 2 residues processed: 317 average time/residue: 0.4681 time to fit residues: 161.2993 Evaluate side-chains 249 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 246 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 613 ARG Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 1220 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.0870 chunk 55 optimal weight: 0.9980 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN A 251 HIS B 249 HIS B 262 ASN B 346 GLN E 244 HIS E 250 HIS E 265 ASN ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN E 440 GLN E 512 HIS E 515 GLN E 529 HIS E 608 HIS E 617 GLN E 629 GLN E 728 GLN E 812 HIS E 920 HIS E 921 GLN E 930 HIS E 945 ASN E 953 GLN E 969 GLN E 979 GLN E1009 GLN E1030 HIS ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1115 GLN E1117 ASN E1150 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.166120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.133558 restraints weight = 16291.539| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.12 r_work: 0.3540 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12722 Z= 0.141 Angle : 0.574 8.251 17530 Z= 0.311 Chirality : 0.041 0.159 1987 Planarity : 0.005 0.054 2021 Dihedral : 18.552 138.971 2262 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.98 % Allowed : 10.81 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.22), residues: 1383 helix: 1.58 (0.19), residues: 777 sheet: 0.09 (0.42), residues: 125 loop : -0.52 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 411 TYR 0.013 0.001 TYR B 258 PHE 0.019 0.001 PHE E1024 TRP 0.026 0.002 TRP E1026 HIS 0.008 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (12722) covalent geometry : angle 0.57365 / 0.31 (17530) hydrogen bonds : bond 0.05061 / 3.23 ( 668) hydrogen bonds : angle 3.97047 / 2.84 ( 1881) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 245 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 SER cc_start: 0.8233 (m) cc_final: 0.7937 (p) REVERT: A 301 LYS cc_start: 0.8332 (ttpp) cc_final: 0.8075 (ttpp) REVERT: A 339 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7968 (mm-30) REVERT: B 185 LEU cc_start: 0.8081 (tp) cc_final: 0.7861 (mp) REVERT: B 241 SER cc_start: 0.7949 (p) cc_final: 0.7711 (t) REVERT: B 301 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8067 (tppp) REVERT: B 305 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.6063 (m-10) REVERT: E 261 LEU cc_start: 0.7591 (tp) cc_final: 0.7282 (tm) REVERT: E 265 ASN cc_start: 0.7751 (m-40) cc_final: 0.7414 (m-40) REVERT: E 303 LEU cc_start: 0.7904 (mt) cc_final: 0.7640 (mm) REVERT: E 385 SER cc_start: 0.8334 (t) cc_final: 0.8095 (p) REVERT: E 543 VAL cc_start: 0.8178 (m) cc_final: 0.7971 (t) REVERT: E 544 PRO cc_start: 0.8586 (Cg_exo) cc_final: 0.8294 (Cg_endo) REVERT: E 686 THR cc_start: 0.8702 (p) cc_final: 0.8428 (m) REVERT: E 787 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7967 (tp40) REVERT: E 1114 LYS cc_start: 0.8456 (mmtm) cc_final: 0.8145 (mttp) outliers start: 35 outliers final: 11 residues processed: 257 average time/residue: 0.4614 time to fit residues: 129.6051 Evaluate side-chains 247 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 232 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 616 GLN Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 666 SER Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1147 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 0.0000 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 GLN ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN E 454 ASN E 515 GLN E 728 GLN E 920 HIS ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1181 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.164603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.131936 restraints weight = 16447.131| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.07 r_work: 0.3530 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12722 Z= 0.144 Angle : 0.560 7.478 17530 Z= 0.301 Chirality : 0.040 0.166 1987 Planarity : 0.005 0.051 2021 Dihedral : 18.427 138.015 2255 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.06 % Allowed : 14.21 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.22), residues: 1383 helix: 1.89 (0.19), residues: 770 sheet: 0.08 (0.43), residues: 121 loop : -0.49 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 613 TYR 0.016 0.001 TYR B 258 PHE 0.014 0.001 PHE E1024 TRP 0.019 0.002 TRP E1026 HIS 0.004 0.001 HIS E 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (12722) covalent geometry : angle 0.55986 / 0.30 (17530) hydrogen bonds : bond 0.04702 / 3.02 ( 668) hydrogen bonds : angle 3.77680 / 2.71 ( 1881) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 245 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 GLU cc_start: 0.7265 (tt0) cc_final: 0.7030 (tt0) REVERT: A 292 SER cc_start: 0.8228 (m) cc_final: 0.7934 (p) REVERT: A 339 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7973 (mm-30) REVERT: A 352 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7561 (mt-10) REVERT: B 241 SER cc_start: 0.7935 (p) cc_final: 0.7727 (t) REVERT: B 301 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8195 (tppp) REVERT: B 305 PHE cc_start: 0.6625 (OUTLIER) cc_final: 0.6092 (m-10) REVERT: B 345 LEU cc_start: 0.8305 (mt) cc_final: 0.8100 (mp) REVERT: E 261 LEU cc_start: 0.7772 (tp) cc_final: 0.7399 (tm) REVERT: E 265 ASN cc_start: 0.7817 (m-40) cc_final: 0.7496 (m-40) REVERT: E 303 LEU cc_start: 0.7845 (mt) cc_final: 0.7601 (mm) REVERT: E 385 SER cc_start: 0.8355 (t) cc_final: 0.8098 (p) REVERT: E 500 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8162 (mp) REVERT: E 544 PRO cc_start: 0.8632 (Cg_exo) cc_final: 0.8332 (Cg_endo) REVERT: E 787 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7976 (tp40) REVERT: E 1016 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: E 1043 MET cc_start: 0.6673 (OUTLIER) cc_final: 0.6326 (mtp) REVERT: E 1114 LYS cc_start: 0.8471 (mmtm) cc_final: 0.8154 (mttp) outliers start: 36 outliers final: 15 residues processed: 260 average time/residue: 0.4812 time to fit residues: 136.6570 Evaluate side-chains 260 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 237 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 616 GLN Chi-restraints excluded: chain E residue 666 SER Chi-restraints excluded: chain E residue 778 GLU Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1043 MET Chi-restraints excluded: chain E residue 1045 SER Chi-restraints excluded: chain E residue 1063 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 74 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 121 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN B 195 GLN B 284 HIS ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN E 614 ASN E 728 GLN E 920 HIS ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.163711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.131279 restraints weight = 16253.628| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.86 r_work: 0.3525 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12722 Z= 0.141 Angle : 0.544 7.515 17530 Z= 0.293 Chirality : 0.040 0.167 1987 Planarity : 0.005 0.048 2021 Dihedral : 18.315 137.560 2255 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.74 % Allowed : 15.06 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.22), residues: 1383 helix: 2.01 (0.19), residues: 772 sheet: 0.25 (0.45), residues: 111 loop : -0.49 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 178 TYR 0.022 0.001 TYR B 258 PHE 0.014 0.001 PHE E1024 TRP 0.017 0.002 TRP E1026 HIS 0.004 0.001 HIS E 815 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (12722) covalent geometry : angle 0.54417 / 0.29 (17530) hydrogen bonds : bond 0.04435 / 2.86 ( 668) hydrogen bonds : angle 3.67786 / 2.64 ( 1881) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 GLU cc_start: 0.7290 (tt0) cc_final: 0.7036 (tt0) REVERT: A 289 ILE cc_start: 0.8430 (mm) cc_final: 0.8092 (mp) REVERT: A 292 SER cc_start: 0.8243 (m) cc_final: 0.7896 (p) REVERT: A 339 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7868 (mm-30) REVERT: A 352 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: A 353 LEU cc_start: 0.7770 (mp) cc_final: 0.7454 (mt) REVERT: B 241 SER cc_start: 0.7950 (p) cc_final: 0.7744 (t) REVERT: B 305 PHE cc_start: 0.6703 (OUTLIER) cc_final: 0.6212 (m-10) REVERT: B 343 SER cc_start: 0.7118 (p) cc_final: 0.6896 (p) REVERT: E 252 GLN cc_start: 0.7696 (mp10) cc_final: 0.7447 (mt0) REVERT: E 303 LEU cc_start: 0.7944 (mt) cc_final: 0.7684 (mm) REVERT: E 385 SER cc_start: 0.8326 (t) cc_final: 0.8076 (p) REVERT: E 686 THR cc_start: 0.8696 (p) cc_final: 0.8457 (m) REVERT: E 787 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7888 (tp40) REVERT: E 853 LYS cc_start: 0.8089 (mtmt) cc_final: 0.7813 (mtpt) REVERT: E 1016 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: E 1114 LYS cc_start: 0.8464 (mmtm) cc_final: 0.8146 (mttp) REVERT: E 1219 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7430 (tp) outliers start: 44 outliers final: 20 residues processed: 261 average time/residue: 0.5152 time to fit residues: 146.8839 Evaluate side-chains 260 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 234 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 616 GLN Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 666 SER Chi-restraints excluded: chain E residue 778 GLU Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1045 SER Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1208 LEU Chi-restraints excluded: chain E residue 1219 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 135 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 GLN ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN E 728 GLN E 920 HIS E1030 HIS ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.161419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.129002 restraints weight = 16408.378| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.86 r_work: 0.3504 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12722 Z= 0.156 Angle : 0.557 8.309 17530 Z= 0.299 Chirality : 0.041 0.170 1987 Planarity : 0.005 0.048 2021 Dihedral : 18.269 137.378 2255 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.83 % Allowed : 16.26 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.22), residues: 1383 helix: 2.04 (0.19), residues: 769 sheet: 0.31 (0.47), residues: 111 loop : -0.49 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 178 TYR 0.021 0.001 TYR B 258 PHE 0.023 0.001 PHE B 305 TRP 0.016 0.002 TRP B 194 HIS 0.004 0.001 HIS E 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (12722) covalent geometry : angle 0.55655 / 0.30 (17530) hydrogen bonds : bond 0.04615 / 2.98 ( 668) hydrogen bonds : angle 3.69088 / 2.65 ( 1881) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 234 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 GLU cc_start: 0.7304 (tt0) cc_final: 0.7057 (tt0) REVERT: A 289 ILE cc_start: 0.8394 (mm) cc_final: 0.8048 (mp) REVERT: A 292 SER cc_start: 0.8234 (m) cc_final: 0.7875 (p) REVERT: A 352 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: B 241 SER cc_start: 0.7978 (p) cc_final: 0.7762 (t) REVERT: B 301 LYS cc_start: 0.8549 (tppp) cc_final: 0.8233 (tppt) REVERT: E 303 LEU cc_start: 0.7928 (mt) cc_final: 0.7674 (mm) REVERT: E 385 SER cc_start: 0.8297 (t) cc_final: 0.8045 (p) REVERT: E 511 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7210 (mpt90) REVERT: E 686 THR cc_start: 0.8663 (p) cc_final: 0.8451 (m) REVERT: E 1016 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: E 1114 LYS cc_start: 0.8462 (mmtm) cc_final: 0.8132 (mttp) outliers start: 45 outliers final: 24 residues processed: 254 average time/residue: 0.5143 time to fit residues: 143.1435 Evaluate side-chains 262 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 511 ARG Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 616 GLN Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 666 SER Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain E residue 778 GLU Chi-restraints excluded: chain E residue 917 LEU Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1045 SER Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1079 ILE Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 51 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 0.0670 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 0.0070 chunk 85 optimal weight: 1.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 249 HIS ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN E 614 ASN E 728 GLN E 920 HIS ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.159934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.127343 restraints weight = 16238.134| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.86 r_work: 0.3475 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12722 Z= 0.201 Angle : 0.613 15.326 17530 Z= 0.321 Chirality : 0.043 0.171 1987 Planarity : 0.005 0.049 2021 Dihedral : 18.253 137.154 2255 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.66 % Allowed : 17.36 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.22), residues: 1383 helix: 1.83 (0.18), residues: 772 sheet: 0.27 (0.47), residues: 110 loop : -0.53 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 936 TYR 0.023 0.002 TYR B 258 PHE 0.017 0.002 PHE A 175 TRP 0.015 0.002 TRP E1070 HIS 0.007 0.001 HIS E 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (12722) covalent geometry : angle 0.61252 / 0.32 (17530) hydrogen bonds : bond 0.05167 / 3.36 ( 668) hydrogen bonds : angle 3.82464 / 2.75 ( 1881) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 235 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 ILE cc_start: 0.8422 (mm) cc_final: 0.8085 (mp) REVERT: A 292 SER cc_start: 0.8251 (m) cc_final: 0.7889 (p) REVERT: B 241 SER cc_start: 0.8085 (p) cc_final: 0.7885 (t) REVERT: B 301 LYS cc_start: 0.8381 (tppp) cc_final: 0.8033 (tppt) REVERT: B 338 GLU cc_start: 0.6734 (mp0) cc_final: 0.6498 (mp0) REVERT: E 256 ARG cc_start: 0.7950 (ttm110) cc_final: 0.7569 (ttp80) REVERT: E 303 LEU cc_start: 0.7948 (mt) cc_final: 0.7654 (mm) REVERT: E 385 SER cc_start: 0.8286 (t) cc_final: 0.7952 (m) REVERT: E 511 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7179 (mpt90) REVERT: E 787 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7917 (tp40) REVERT: E 1016 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: E 1030 HIS cc_start: 0.7493 (OUTLIER) cc_final: 0.7160 (m-70) REVERT: E 1114 LYS cc_start: 0.8479 (mmtm) cc_final: 0.8134 (mttp) REVERT: E 1220 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7410 (mp0) outliers start: 43 outliers final: 27 residues processed: 253 average time/residue: 0.5117 time to fit residues: 141.6370 Evaluate side-chains 266 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 511 ARG Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 616 GLN Chi-restraints excluded: chain E residue 666 SER Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 917 LEU Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1030 HIS Chi-restraints excluded: chain E residue 1045 SER Chi-restraints excluded: chain E residue 1055 THR Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1208 LEU Chi-restraints excluded: chain E residue 1211 VAL Chi-restraints excluded: chain E residue 1220 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 60 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 284 HIS ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 728 GLN E 920 HIS E1030 HIS ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.160792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.128050 restraints weight = 16246.353| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.87 r_work: 0.3491 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12722 Z= 0.151 Angle : 0.566 9.095 17530 Z= 0.300 Chirality : 0.041 0.316 1987 Planarity : 0.005 0.049 2021 Dihedral : 18.186 137.089 2255 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.57 % Allowed : 17.87 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.22), residues: 1383 helix: 1.92 (0.18), residues: 773 sheet: 0.28 (0.49), residues: 105 loop : -0.60 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 507 TYR 0.013 0.001 TYR B 258 PHE 0.014 0.001 PHE A 175 TRP 0.014 0.002 TRP E1070 HIS 0.004 0.001 HIS E 815 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (12722) covalent geometry : angle 0.56615 / 0.30 (17530) hydrogen bonds : bond 0.04587 / 2.95 ( 668) hydrogen bonds : angle 3.73323 / 2.68 ( 1881) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 233 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 ILE cc_start: 0.8408 (mm) cc_final: 0.8068 (mp) REVERT: A 292 SER cc_start: 0.8251 (m) cc_final: 0.7883 (p) REVERT: B 241 SER cc_start: 0.8097 (p) cc_final: 0.7891 (t) REVERT: B 301 LYS cc_start: 0.8276 (tppp) cc_final: 0.7992 (tppt) REVERT: B 338 GLU cc_start: 0.6746 (mp0) cc_final: 0.6451 (mp0) REVERT: E 256 ARG cc_start: 0.7996 (ttm110) cc_final: 0.7643 (ttp80) REVERT: E 303 LEU cc_start: 0.7898 (mt) cc_final: 0.7630 (mm) REVERT: E 385 SER cc_start: 0.8280 (t) cc_final: 0.7959 (m) REVERT: E 511 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7187 (mpt90) REVERT: E 787 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7905 (tp40) REVERT: E 858 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.6893 (ptp90) REVERT: E 1016 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7151 (mt-10) REVERT: E 1114 LYS cc_start: 0.8423 (mmtm) cc_final: 0.8079 (mttp) outliers start: 42 outliers final: 25 residues processed: 254 average time/residue: 0.4929 time to fit residues: 136.2701 Evaluate side-chains 255 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 511 ARG Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 616 GLN Chi-restraints excluded: chain E residue 666 SER Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 853 LYS Chi-restraints excluded: chain E residue 858 ARG Chi-restraints excluded: chain E residue 917 LEU Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1002 THR Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1045 SER Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1079 ILE Chi-restraints excluded: chain E residue 1152 CYS Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 117 optimal weight: 0.0980 chunk 107 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 92 optimal weight: 0.0370 chunk 8 optimal weight: 0.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 GLN ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN E 485 GLN E 728 GLN E 920 HIS E1030 HIS ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.162124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.129695 restraints weight = 16196.864| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.86 r_work: 0.3512 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12722 Z= 0.123 Angle : 0.549 12.354 17530 Z= 0.288 Chirality : 0.040 0.346 1987 Planarity : 0.005 0.046 2021 Dihedral : 18.088 137.100 2255 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.06 % Allowed : 18.21 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.22), residues: 1383 helix: 2.05 (0.18), residues: 774 sheet: 0.39 (0.48), residues: 109 loop : -0.59 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 613 TYR 0.009 0.001 TYR A 258 PHE 0.012 0.001 PHE E1024 TRP 0.014 0.002 TRP E1026 HIS 0.004 0.001 HIS E 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (12722) covalent geometry : angle 0.54920 / 0.29 (17530) hydrogen bonds : bond 0.04083 / 2.62 ( 668) hydrogen bonds : angle 3.61532 / 2.60 ( 1881) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 ILE cc_start: 0.8403 (mm) cc_final: 0.8056 (mp) REVERT: A 292 SER cc_start: 0.8243 (m) cc_final: 0.7872 (p) REVERT: A 352 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: B 241 SER cc_start: 0.8072 (p) cc_final: 0.7866 (t) REVERT: B 301 LYS cc_start: 0.8273 (tppp) cc_final: 0.7984 (tppt) REVERT: B 338 GLU cc_start: 0.6701 (mp0) cc_final: 0.6448 (mp0) REVERT: E 256 ARG cc_start: 0.7976 (ttm110) cc_final: 0.7623 (ttp80) REVERT: E 303 LEU cc_start: 0.7919 (mt) cc_final: 0.7649 (mm) REVERT: E 385 SER cc_start: 0.8271 (t) cc_final: 0.7960 (m) REVERT: E 511 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7198 (mpt90) REVERT: E 615 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.8013 (t) REVERT: E 854 ARG cc_start: 0.7795 (mtp-110) cc_final: 0.7552 (mtp180) REVERT: E 858 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6883 (ptp90) REVERT: E 886 MET cc_start: 0.8737 (mtt) cc_final: 0.8473 (mtt) REVERT: E 1016 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7140 (mt-10) REVERT: E 1114 LYS cc_start: 0.8409 (mmtm) cc_final: 0.8062 (mttp) outliers start: 36 outliers final: 24 residues processed: 247 average time/residue: 0.5086 time to fit residues: 136.7627 Evaluate side-chains 257 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 511 ARG Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 616 GLN Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 666 SER Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain E residue 858 ARG Chi-restraints excluded: chain E residue 917 LEU Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1002 THR Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1079 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 133 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 136 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 90 optimal weight: 0.0970 chunk 50 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 91 optimal weight: 0.0470 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 GLN ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN E 485 GLN E 617 GLN E 728 GLN E 920 HIS E1030 HIS ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.162362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.129888 restraints weight = 16202.396| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.85 r_work: 0.3514 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12722 Z= 0.123 Angle : 0.544 11.102 17530 Z= 0.285 Chirality : 0.040 0.312 1987 Planarity : 0.005 0.055 2021 Dihedral : 18.034 137.114 2255 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.98 % Allowed : 18.98 % Favored : 78.04 % 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 are not related in a simple way. whole: 1.51 (0.22), residues: 1383 helix: 2.08 (0.18), residues: 780 sheet: 0.35 (0.48), residues: 109 loop : -0.59 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 613 TYR 0.010 0.001 TYR A 258 PHE 0.018 0.001 PHE B 305 TRP 0.014 0.001 TRP E1026 HIS 0.005 0.001 HIS E 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (12722) covalent geometry : angle 0.54405 / 0.29 (17530) hydrogen bonds : bond 0.04033 / 2.59 ( 668) hydrogen bonds : angle 3.57464 / 2.57 ( 1881) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 0.427 Fit side-chains REVERT: A 289 ILE cc_start: 0.8398 (mm) cc_final: 0.8065 (mp) REVERT: A 292 SER cc_start: 0.8243 (m) cc_final: 0.7884 (p) REVERT: B 241 SER cc_start: 0.8029 (p) cc_final: 0.7816 (t) REVERT: B 301 LYS cc_start: 0.8146 (tppp) cc_final: 0.7940 (tppt) REVERT: B 338 GLU cc_start: 0.6707 (mp0) cc_final: 0.6442 (mp0) REVERT: E 279 GLU cc_start: 0.7950 (mp0) cc_final: 0.7484 (mp0) REVERT: E 303 LEU cc_start: 0.7916 (mt) cc_final: 0.7651 (mm) REVERT: E 385 SER cc_start: 0.8267 (t) cc_final: 0.7961 (m) REVERT: E 511 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7205 (mpt90) REVERT: E 602 LEU cc_start: 0.8364 (mm) cc_final: 0.8096 (mt) REVERT: E 615 VAL cc_start: 0.8215 (OUTLIER) cc_final: 0.7994 (t) REVERT: E 787 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7862 (tp40) REVERT: E 854 ARG cc_start: 0.7787 (mtp-110) cc_final: 0.7545 (mtp180) REVERT: E 858 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.6879 (ptp90) REVERT: E 1016 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7145 (mt-10) outliers start: 35 outliers final: 22 residues processed: 247 average time/residue: 0.5015 time to fit residues: 135.0149 Evaluate side-chains 257 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 230 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 511 ARG Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 616 GLN Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 666 SER Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 858 ARG Chi-restraints excluded: chain E residue 917 LEU Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1002 THR Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1079 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 141 optimal weight: 30.0000 chunk 64 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 GLN E 250 HIS ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN E 485 GLN E 617 GLN E 728 GLN E 903 ASN E 920 HIS E1030 HIS ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.162062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.129677 restraints weight = 16273.598| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.85 r_work: 0.3496 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12722 Z= 0.163 Angle : 0.592 14.051 17530 Z= 0.304 Chirality : 0.042 0.363 1987 Planarity : 0.005 0.047 2021 Dihedral : 18.013 137.051 2255 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.89 % Allowed : 19.57 % Favored : 77.53 % 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 are not related in a simple way. whole: 1.35 (0.22), residues: 1383 helix: 1.93 (0.18), residues: 781 sheet: 0.41 (0.48), residues: 107 loop : -0.66 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 613 TYR 0.011 0.001 TYR B 258 PHE 0.013 0.001 PHE A 175 TRP 0.012 0.002 TRP E1070 HIS 0.005 0.001 HIS E 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (12722) covalent geometry : angle 0.59162 / 0.30 (17530) hydrogen bonds : bond 0.04379 / 2.81 ( 668) hydrogen bonds : angle 3.64926 / 2.63 ( 1881) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 225 time to evaluate : 0.446 Fit side-chains REVERT: A 289 ILE cc_start: 0.8414 (mm) cc_final: 0.8088 (mp) REVERT: A 292 SER cc_start: 0.8257 (m) cc_final: 0.7897 (p) REVERT: B 241 SER cc_start: 0.8047 (p) cc_final: 0.7834 (t) REVERT: B 338 GLU cc_start: 0.6677 (mp0) cc_final: 0.6427 (mp0) REVERT: E 279 GLU cc_start: 0.7967 (mp0) cc_final: 0.7485 (mp0) REVERT: E 303 LEU cc_start: 0.7935 (mt) cc_final: 0.7668 (mm) REVERT: E 385 SER cc_start: 0.8271 (t) cc_final: 0.7964 (m) REVERT: E 511 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7210 (mpt90) REVERT: E 602 LEU cc_start: 0.8374 (mm) cc_final: 0.8109 (mt) REVERT: E 615 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.8019 (t) REVERT: E 787 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7859 (tp40) REVERT: E 854 ARG cc_start: 0.7804 (mtp-110) cc_final: 0.7541 (mtp180) REVERT: E 858 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.6900 (ptp90) REVERT: E 886 MET cc_start: 0.8783 (mtt) cc_final: 0.8381 (mtm) REVERT: E 1016 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7178 (mt-10) outliers start: 34 outliers final: 25 residues processed: 242 average time/residue: 0.5177 time to fit residues: 136.4510 Evaluate side-chains 256 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 511 ARG Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 616 GLN Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 666 SER Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain E residue 778 GLU Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 858 ARG Chi-restraints excluded: chain E residue 917 LEU Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1002 THR Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1079 ILE Chi-restraints excluded: chain E residue 1152 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 62 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 78 optimal weight: 0.0000 chunk 14 optimal weight: 1.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 250 HIS ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN E 617 GLN E 728 GLN E 920 HIS E1030 HIS ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.161475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.128951 restraints weight = 16215.557| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.86 r_work: 0.3502 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12722 Z= 0.137 Angle : 0.565 11.635 17530 Z= 0.293 Chirality : 0.041 0.350 1987 Planarity : 0.005 0.051 2021 Dihedral : 17.945 136.979 2255 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.23 % Allowed : 19.15 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.22), residues: 1383 helix: 1.96 (0.18), residues: 781 sheet: 0.36 (0.48), residues: 107 loop : -0.65 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 326 TYR 0.009 0.001 TYR E 533 PHE 0.013 0.001 PHE A 175 TRP 0.013 0.002 TRP E1026 HIS 0.004 0.001 HIS E 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (12722) covalent geometry : angle 0.56507 / 0.29 (17530) hydrogen bonds : bond 0.04195 / 2.70 ( 668) hydrogen bonds : angle 3.63291 / 2.62 ( 1881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4392.90 seconds wall clock time: 75 minutes 14.80 seconds (4514.80 seconds total)