Starting phenix.real_space_refine on Fri Jul 3 05:36:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bdd_44449/07_2026/9bdd_44449.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bdd_44449/07_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_44449/07_2026/9bdd_44449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bdd_44449/07_2026/9bdd_44449.map" model { file = "/net/cci-nas-00/data/ceres_data/9bdd_44449/07_2026/9bdd_44449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bdd_44449/07_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-dev-6108/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: 2.61, per 1000 atoms: 0.21 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: 0.97 Conformation dependent library (CDL) restraints added in 449.5 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: 1.17 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: 2.23 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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: 16980 1.84 - 3.68: 450 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: 1954 0.129 - 0.258: 20 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.510 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.180 ------------------------------------------------------------------------------- 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= 0.289 Angle : 0.724 9.196 17530 Z= 0.451 Chirality : 0.062 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 0.72436 / 0.45 (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 : 0.387 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: 0.5421 time to fit residues: 187.0898 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 : 0.419 ------------------------------------------------------------------------------- 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 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: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.166138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.133744 restraints weight = 16308.299| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.87 r_work: 0.3558 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12722 Z= 0.143 Angle : 0.571 8.174 17530 Z= 0.311 Chirality : 0.040 0.160 1987 Planarity : 0.005 0.055 2021 Dihedral : 18.588 139.205 2262 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.06 % Allowed : 10.81 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.22), residues: 1383 helix: 1.57 (0.19), residues: 775 sheet: 0.09 (0.42), residues: 125 loop : -0.53 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 967 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 0.00288 / 0.14 (12722) covalent geometry : angle 0.57053 / 0.31 (17530) hydrogen bonds : bond 0.05168 / 3.30 ( 668) hydrogen bonds : angle 4.00573 / 2.86 ( 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 278 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 SER cc_start: 0.8230 (m) cc_final: 0.7941 (p) REVERT: A 301 LYS cc_start: 0.8332 (ttpp) cc_final: 0.8078 (ttpp) REVERT: A 339 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7946 (mm-30) REVERT: B 185 LEU cc_start: 0.8083 (tp) cc_final: 0.7862 (mp) REVERT: B 241 SER cc_start: 0.7934 (p) cc_final: 0.7701 (t) REVERT: B 301 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8092 (tppp) REVERT: B 305 PHE cc_start: 0.6682 (OUTLIER) cc_final: 0.6095 (m-10) REVERT: E 303 LEU cc_start: 0.7939 (mt) cc_final: 0.7675 (mm) REVERT: E 385 SER cc_start: 0.8330 (t) cc_final: 0.8102 (p) REVERT: E 543 VAL cc_start: 0.8184 (m) cc_final: 0.7983 (t) REVERT: E 544 PRO cc_start: 0.8599 (Cg_exo) cc_final: 0.8316 (Cg_endo) REVERT: E 686 THR cc_start: 0.8700 (p) cc_final: 0.8424 (m) REVERT: E 787 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7945 (tp40) REVERT: E 1114 LYS cc_start: 0.8450 (mmtm) cc_final: 0.8142 (mttp) REVERT: E 1220 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7495 (mp0) outliers start: 36 outliers final: 12 residues processed: 254 average time/residue: 0.5356 time to fit residues: 148.2826 Evaluate side-chains 248 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 231 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 1045 SER Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1147 VAL Chi-restraints excluded: chain E residue 1220 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN A 346 GLN ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 E1181 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.162744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.129929 restraints weight = 16375.243| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.87 r_work: 0.3501 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1997 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= 0.192 Angle : 0.599 8.166 17530 Z= 0.322 Chirality : 0.043 0.165 1987 Planarity : 0.005 0.061 2021 Dihedral : 18.504 137.820 2258 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.06 % Allowed : 14.38 % Favored : 82.55 % 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: 1.16 (0.22), residues: 1383 helix: 1.72 (0.19), residues: 771 sheet: 0.18 (0.45), residues: 111 loop : -0.57 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 613 TYR 0.023 0.002 TYR B 258 PHE 0.018 0.002 PHE E 612 TRP 0.019 0.002 TRP E1026 HIS 0.006 0.001 HIS E 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (12722) covalent geometry : angle 0.59912 / 0.32 (17530) hydrogen bonds : bond 0.05336 / 3.45 ( 668) hydrogen bonds : angle 3.89649 / 2.79 ( 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 283 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 247 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 GLU cc_start: 0.7233 (tt0) cc_final: 0.7002 (tt0) REVERT: A 289 ILE cc_start: 0.8394 (mm) cc_final: 0.8045 (mp) REVERT: A 292 SER cc_start: 0.8219 (m) cc_final: 0.7917 (p) REVERT: A 339 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7955 (mm-30) REVERT: A 352 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: B 241 SER cc_start: 0.7950 (p) cc_final: 0.7745 (t) REVERT: B 301 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8221 (tppp) REVERT: B 305 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.6023 (m-10) REVERT: E 261 LEU cc_start: 0.7833 (tp) cc_final: 0.7474 (tm) REVERT: E 303 LEU cc_start: 0.7908 (mt) cc_final: 0.7649 (mm) REVERT: E 385 SER cc_start: 0.8344 (t) cc_final: 0.8000 (m) REVERT: E 500 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8234 (mp) REVERT: E 543 VAL cc_start: 0.8261 (m) cc_final: 0.8055 (t) REVERT: E 544 PRO cc_start: 0.8638 (Cg_exo) cc_final: 0.8328 (Cg_endo) REVERT: E 787 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7955 (tp40) REVERT: E 1016 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: E 1114 LYS cc_start: 0.8500 (mmtm) cc_final: 0.8193 (mttp) outliers start: 36 outliers final: 14 residues processed: 260 average time/residue: 0.5261 time to fit residues: 148.8286 Evaluate side-chains 255 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 234 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 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 787 GLN Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 997 VAL 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 1211 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 74 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 124 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 GLN B 262 ASN ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN E 515 GLN E 614 ASN E 728 GLN E 920 HIS ** 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 = 0.4047 r_free = 0.4047 target = 0.163202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.130597 restraints weight = 16217.859| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.86 r_work: 0.3514 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12722 Z= 0.148 Angle : 0.559 9.617 17530 Z= 0.299 Chirality : 0.040 0.176 1987 Planarity : 0.005 0.055 2021 Dihedral : 18.369 137.504 2253 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.49 % Allowed : 15.91 % Favored : 80.60 % 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: 1.32 (0.22), residues: 1383 helix: 1.90 (0.19), residues: 771 sheet: 0.15 (0.45), residues: 111 loop : -0.56 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 178 TYR 0.014 0.001 TYR B 258 PHE 0.014 0.001 PHE B 228 TRP 0.017 0.002 TRP E1026 HIS 0.004 0.001 HIS E 815 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (12722) covalent geometry : angle 0.55909 / 0.30 (17530) hydrogen bonds : bond 0.04693 / 3.02 ( 668) hydrogen bonds : angle 3.77839 / 2.71 ( 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 278 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 237 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 GLU cc_start: 0.7298 (tt0) cc_final: 0.7089 (tt0) REVERT: A 289 ILE cc_start: 0.8423 (mm) cc_final: 0.8082 (mp) REVERT: A 292 SER cc_start: 0.8215 (m) cc_final: 0.7865 (p) REVERT: A 339 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7872 (mm-30) REVERT: A 352 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: B 241 SER cc_start: 0.7957 (p) cc_final: 0.7752 (t) REVERT: B 305 PHE cc_start: 0.6687 (OUTLIER) cc_final: 0.6209 (m-10) REVERT: B 343 SER cc_start: 0.7109 (p) cc_final: 0.6885 (p) REVERT: E 303 LEU cc_start: 0.7944 (mt) cc_final: 0.7676 (mm) REVERT: E 385 SER cc_start: 0.8301 (t) cc_final: 0.8046 (p) REVERT: E 500 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8204 (mp) REVERT: E 544 PRO cc_start: 0.8649 (Cg_exo) cc_final: 0.8345 (Cg_endo) REVERT: E 787 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7896 (tp40) REVERT: E 1016 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6992 (mp0) REVERT: E 1114 LYS cc_start: 0.8472 (mmtm) cc_final: 0.8149 (mttp) outliers start: 41 outliers final: 20 residues processed: 255 average time/residue: 0.5153 time to fit residues: 143.7657 Evaluate side-chains 255 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 331 SER 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 305 PHE 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 500 LEU 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 787 GLN Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 951 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 83 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 135 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** 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 = 0.4042 r_free = 0.4042 target = 0.162660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.129947 restraints weight = 16373.412| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.87 r_work: 0.3510 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2370 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= 0.146 Angle : 0.565 12.736 17530 Z= 0.299 Chirality : 0.040 0.170 1987 Planarity : 0.005 0.051 2021 Dihedral : 18.310 137.283 2253 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.98 % Allowed : 17.62 % Favored : 79.40 % 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: 1.42 (0.22), residues: 1383 helix: 2.00 (0.18), residues: 771 sheet: 0.33 (0.47), residues: 110 loop : -0.57 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 447 TYR 0.013 0.001 TYR B 258 PHE 0.020 0.001 PHE B 305 TRP 0.016 0.002 TRP E1026 HIS 0.004 0.001 HIS E 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (12722) covalent geometry : angle 0.56525 / 0.30 (17530) hydrogen bonds : bond 0.04522 / 2.91 ( 668) hydrogen bonds : angle 3.72169 / 2.67 ( 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 271 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 GLU cc_start: 0.7284 (tt0) cc_final: 0.7083 (tt0) REVERT: A 289 ILE cc_start: 0.8449 (mm) cc_final: 0.8121 (mp) REVERT: A 292 SER cc_start: 0.8232 (m) cc_final: 0.7881 (p) REVERT: A 339 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7855 (mm-30) REVERT: A 352 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7502 (mt-10) REVERT: B 241 SER cc_start: 0.7970 (p) cc_final: 0.7766 (t) REVERT: B 301 LYS cc_start: 0.8530 (tppp) cc_final: 0.8191 (tppt) REVERT: B 338 GLU cc_start: 0.6698 (mp0) cc_final: 0.6443 (mp0) REVERT: E 303 LEU cc_start: 0.7950 (mt) cc_final: 0.7692 (mm) REVERT: E 385 SER cc_start: 0.8298 (t) cc_final: 0.7972 (m) REVERT: E 500 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8224 (mp) REVERT: E 686 THR cc_start: 0.8688 (p) cc_final: 0.8473 (m) REVERT: E 1016 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7097 (mt-10) REVERT: E 1114 LYS cc_start: 0.8440 (mmtm) cc_final: 0.8110 (mttp) outliers start: 35 outliers final: 21 residues processed: 254 average time/residue: 0.5467 time to fit residues: 151.8360 Evaluate side-chains 258 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 233 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 331 SER Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 230 VAL 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 500 LEU 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 778 GLU Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1063 HIS 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: 5.9990 chunk 19 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 0.0270 chunk 65 optimal weight: 0.6980 chunk 1 optimal weight: 0.0470 chunk 85 optimal weight: 1.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- 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 614 ASN E 728 GLN E 920 HIS ** 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 = 0.4030 r_free = 0.4030 target = 0.161575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128954 restraints weight = 16234.790| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.87 r_work: 0.3491 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12722 Z= 0.172 Angle : 0.571 12.023 17530 Z= 0.304 Chirality : 0.042 0.180 1987 Planarity : 0.005 0.050 2021 Dihedral : 18.270 137.140 2253 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.49 % Allowed : 17.87 % Favored : 78.64 % 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: 1.36 (0.22), residues: 1383 helix: 1.93 (0.18), residues: 771 sheet: 0.37 (0.48), residues: 110 loop : -0.58 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 447 TYR 0.017 0.001 TYR B 258 PHE 0.013 0.001 PHE A 175 TRP 0.015 0.002 TRP E1026 HIS 0.005 0.001 HIS E 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (12722) covalent geometry : angle 0.57146 / 0.30 (17530) hydrogen bonds : bond 0.04776 / 3.10 ( 668) hydrogen bonds : angle 3.75738 / 2.70 ( 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 272 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 231 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 ILE cc_start: 0.8431 (mm) cc_final: 0.8103 (mp) REVERT: A 292 SER cc_start: 0.8234 (m) cc_final: 0.7879 (p) REVERT: B 301 LYS cc_start: 0.8334 (tppp) cc_final: 0.8003 (tppt) REVERT: B 338 GLU cc_start: 0.6730 (mp0) cc_final: 0.6437 (mp0) REVERT: E 256 ARG cc_start: 0.7936 (ttm110) cc_final: 0.7582 (ttp80) REVERT: E 303 LEU cc_start: 0.7944 (mt) cc_final: 0.7679 (mm) REVERT: E 385 SER cc_start: 0.8291 (t) cc_final: 0.7960 (m) REVERT: E 500 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8258 (mp) REVERT: E 787 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7908 (tp40) REVERT: E 1016 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7079 (mt-10) REVERT: E 1114 LYS cc_start: 0.8434 (mmtm) cc_final: 0.8096 (mttp) outliers start: 41 outliers final: 24 residues processed: 250 average time/residue: 0.5459 time to fit residues: 148.9763 Evaluate side-chains 255 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 228 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 502 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 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 922 ASP Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1055 THR Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 60 optimal weight: 3.9990 chunk 82 optimal weight: 0.0060 chunk 79 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 GLN E 249 HIS ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 485 GLN E 728 GLN E 920 HIS E1030 HIS ** 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 = 0.4035 r_free = 0.4035 target = 0.161983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.129321 restraints weight = 16258.688| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.86 r_work: 0.3501 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2658 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= 0.143 Angle : 0.551 10.634 17530 Z= 0.293 Chirality : 0.041 0.304 1987 Planarity : 0.005 0.049 2021 Dihedral : 18.213 137.079 2253 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.66 % Allowed : 18.13 % Favored : 78.21 % 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: 1.43 (0.22), residues: 1383 helix: 2.02 (0.18), residues: 772 sheet: 0.50 (0.48), residues: 107 loop : -0.63 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 936 TYR 0.011 0.001 TYR B 258 PHE 0.013 0.001 PHE B 305 TRP 0.015 0.002 TRP E1026 HIS 0.005 0.001 HIS E 815 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (12722) covalent geometry : angle 0.55080 / 0.29 (17530) hydrogen bonds : bond 0.04449 / 2.86 ( 668) hydrogen bonds : angle 3.69939 / 2.65 ( 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 274 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 231 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 ILE cc_start: 0.8432 (mm) cc_final: 0.8102 (mp) REVERT: A 292 SER cc_start: 0.8251 (m) cc_final: 0.7893 (p) REVERT: A 352 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7493 (mt-10) REVERT: B 301 LYS cc_start: 0.8224 (tppp) cc_final: 0.7949 (tppt) REVERT: B 338 GLU cc_start: 0.6708 (mp0) cc_final: 0.6424 (mp0) REVERT: E 256 ARG cc_start: 0.7964 (ttm110) cc_final: 0.7587 (ttp80) REVERT: E 303 LEU cc_start: 0.7927 (mt) cc_final: 0.7666 (mm) REVERT: E 385 SER cc_start: 0.8289 (t) cc_final: 0.7972 (m) REVERT: E 500 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8235 (mp) REVERT: E 787 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7881 (tp40) REVERT: E 854 ARG cc_start: 0.7852 (mtp-110) cc_final: 0.7608 (mtp180) REVERT: E 886 MET cc_start: 0.8755 (mtt) cc_final: 0.8218 (mtt) REVERT: E 985 ILE cc_start: 0.7652 (tp) cc_final: 0.7434 (pp) REVERT: E 1016 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7082 (mt-10) REVERT: E 1114 LYS cc_start: 0.8432 (mmtm) cc_final: 0.8087 (mttp) outliers start: 43 outliers final: 21 residues processed: 251 average time/residue: 0.5455 time to fit residues: 149.4834 Evaluate side-chains 253 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 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 500 LEU Chi-restraints excluded: chain E residue 502 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 853 LYS 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 997 VAL Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1063 HIS 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: 3.9990 chunk 107 optimal weight: 0.3980 chunk 106 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 134 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 903 ASN E 920 HIS E1030 HIS ** 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 = 0.4033 r_free = 0.4033 target = 0.161673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.128936 restraints weight = 16135.856| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.86 r_work: 0.3501 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12722 Z= 0.140 Angle : 0.559 11.458 17530 Z= 0.293 Chirality : 0.040 0.329 1987 Planarity : 0.005 0.048 2021 Dihedral : 18.174 137.047 2253 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.23 % Allowed : 18.55 % Favored : 78.21 % 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: 1.44 (0.22), residues: 1383 helix: 2.04 (0.18), residues: 774 sheet: 0.48 (0.48), residues: 107 loop : -0.65 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 613 TYR 0.011 0.001 TYR B 258 PHE 0.012 0.001 PHE E1024 TRP 0.015 0.002 TRP E1026 HIS 0.004 0.001 HIS E 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (12722) covalent geometry : angle 0.55893 / 0.29 (17530) hydrogen bonds : bond 0.04358 / 2.80 ( 668) hydrogen bonds : angle 3.68017 / 2.65 ( 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 265 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 289 ILE cc_start: 0.8405 (mm) cc_final: 0.8057 (mp) REVERT: A 292 SER cc_start: 0.8270 (m) cc_final: 0.7908 (p) REVERT: B 301 LYS cc_start: 0.8274 (tppp) cc_final: 0.8000 (tppt) REVERT: B 338 GLU cc_start: 0.6713 (mp0) cc_final: 0.6460 (mp0) REVERT: E 256 ARG cc_start: 0.7978 (ttm110) cc_final: 0.7617 (ttp80) REVERT: E 279 GLU cc_start: 0.7950 (mp0) cc_final: 0.7496 (mp0) REVERT: E 303 LEU cc_start: 0.7910 (mt) cc_final: 0.7657 (mm) REVERT: E 385 SER cc_start: 0.8269 (t) cc_final: 0.7947 (m) REVERT: E 500 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8201 (mp) REVERT: E 615 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7996 (t) REVERT: E 787 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7899 (tp40) REVERT: E 854 ARG cc_start: 0.7789 (mtp-110) cc_final: 0.7543 (mtp180) REVERT: E 886 MET cc_start: 0.8744 (mtt) cc_final: 0.8189 (mtt) REVERT: E 985 ILE cc_start: 0.7630 (tp) cc_final: 0.7352 (pp) REVERT: E 1016 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7111 (mt-10) REVERT: E 1114 LYS cc_start: 0.8410 (mmtm) cc_final: 0.8047 (mttp) outliers start: 38 outliers final: 23 residues processed: 245 average time/residue: 0.5111 time to fit residues: 136.8133 Evaluate side-chains 254 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 227 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 B residue 206 ILE Chi-restraints excluded: chain B residue 230 VAL 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 500 LEU Chi-restraints excluded: chain E residue 502 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 922 ASP Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1055 THR Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 133 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 91 optimal weight: 0.0870 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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 617 GLN E 728 GLN E 920 HIS E1030 HIS ** 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 = 0.4030 r_free = 0.4030 target = 0.161458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.128641 restraints weight = 16151.659| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.87 r_work: 0.3494 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2804 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= 0.147 Angle : 0.561 11.385 17530 Z= 0.294 Chirality : 0.041 0.331 1987 Planarity : 0.005 0.048 2021 Dihedral : 18.138 137.002 2253 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.89 % Allowed : 19.06 % 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: 1.43 (0.22), residues: 1383 helix: 2.04 (0.18), residues: 774 sheet: 0.48 (0.49), residues: 107 loop : -0.68 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 936 TYR 0.011 0.001 TYR B 258 PHE 0.020 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 0.00327 / 0.15 (12722) covalent geometry : angle 0.56073 / 0.29 (17530) hydrogen bonds : bond 0.04386 / 2.83 ( 668) hydrogen bonds : angle 3.66581 / 2.64 ( 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 257 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 289 ILE cc_start: 0.8404 (mm) cc_final: 0.8066 (mp) REVERT: A 292 SER cc_start: 0.8278 (m) cc_final: 0.7918 (p) REVERT: A 352 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: B 301 LYS cc_start: 0.8169 (tppp) cc_final: 0.7926 (tppt) REVERT: B 338 GLU cc_start: 0.6707 (mp0) cc_final: 0.6456 (mp0) REVERT: E 256 ARG cc_start: 0.7992 (ttm110) cc_final: 0.7620 (ttp80) REVERT: E 279 GLU cc_start: 0.7967 (mp0) cc_final: 0.7511 (mp0) REVERT: E 303 LEU cc_start: 0.7912 (mt) cc_final: 0.7659 (mm) REVERT: E 385 SER cc_start: 0.8262 (t) cc_final: 0.7977 (m) REVERT: E 500 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8213 (mp) REVERT: E 615 VAL cc_start: 0.8232 (OUTLIER) cc_final: 0.8010 (t) REVERT: E 787 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7904 (tp40) REVERT: E 854 ARG cc_start: 0.7795 (mtp-110) cc_final: 0.7552 (mtp180) REVERT: E 886 MET cc_start: 0.8734 (mtt) cc_final: 0.8474 (mtt) REVERT: E 985 ILE cc_start: 0.7603 (tp) cc_final: 0.7311 (pp) REVERT: E 1016 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7169 (mt-10) outliers start: 34 outliers final: 22 residues processed: 237 average time/residue: 0.5768 time to fit residues: 148.8450 Evaluate side-chains 250 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 223 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 230 VAL 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 500 LEU Chi-restraints excluded: chain E residue 502 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 922 ASP Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1152 CYS Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 42 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 141 optimal weight: 30.0000 chunk 64 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 617 GLN E 728 GLN E 920 HIS E1030 HIS ** 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 = 0.4022 r_free = 0.4022 target = 0.160699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.127950 restraints weight = 16243.482| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.87 r_work: 0.3484 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12722 Z= 0.171 Angle : 0.585 11.821 17530 Z= 0.304 Chirality : 0.042 0.248 1987 Planarity : 0.005 0.049 2021 Dihedral : 18.128 136.913 2253 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.89 % Allowed : 19.32 % Favored : 77.79 % 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: 1.34 (0.22), residues: 1383 helix: 1.96 (0.18), residues: 776 sheet: 0.48 (0.51), residues: 101 loop : -0.73 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 481 TYR 0.013 0.001 TYR B 258 PHE 0.012 0.001 PHE E 794 TRP 0.026 0.002 TRP B 194 HIS 0.005 0.001 HIS B 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (12722) covalent geometry : angle 0.58529 / 0.30 (17530) hydrogen bonds : bond 0.04672 / 3.01 ( 668) hydrogen bonds : angle 3.70922 / 2.67 ( 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 253 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 289 ILE cc_start: 0.8401 (mm) cc_final: 0.8063 (mp) REVERT: A 292 SER cc_start: 0.8284 (m) cc_final: 0.7920 (p) REVERT: A 352 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: B 301 LYS cc_start: 0.8265 (tppp) cc_final: 0.7973 (tppt) REVERT: E 256 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7589 (ttp80) REVERT: E 279 GLU cc_start: 0.7973 (mp0) cc_final: 0.7514 (mp0) REVERT: E 303 LEU cc_start: 0.7919 (mt) cc_final: 0.7660 (mm) REVERT: E 385 SER cc_start: 0.8256 (t) cc_final: 0.7978 (m) REVERT: E 500 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8234 (mp) REVERT: E 602 LEU cc_start: 0.8387 (mm) cc_final: 0.8123 (mt) REVERT: E 615 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.8004 (t) REVERT: E 787 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7912 (tp40) REVERT: E 886 MET cc_start: 0.8734 (mtt) cc_final: 0.8475 (mtt) REVERT: E 1016 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7190 (mt-10) outliers start: 34 outliers final: 25 residues processed: 237 average time/residue: 0.5643 time to fit residues: 145.8092 Evaluate side-chains 249 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 164 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 256 ARG 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 500 LEU Chi-restraints excluded: chain E residue 502 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 922 ASP Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1055 THR Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1152 CYS Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 62 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 0.0370 chunk 78 optimal weight: 0.0770 chunk 14 optimal weight: 0.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 304 GLN E 369 ASN E 617 GLN E 728 GLN E 920 HIS E1030 HIS ** 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 = 0.4042 r_free = 0.4042 target = 0.162015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.129358 restraints weight = 16201.724| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.87 r_work: 0.3514 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12722 Z= 0.119 Angle : 0.548 11.513 17530 Z= 0.286 Chirality : 0.039 0.288 1987 Planarity : 0.005 0.048 2021 Dihedral : 18.051 136.889 2253 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.38 % Allowed : 20.00 % 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: 1.53 (0.22), residues: 1383 helix: 2.16 (0.18), residues: 775 sheet: 0.38 (0.48), residues: 109 loop : -0.68 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 411 TYR 0.009 0.001 TYR A 258 PHE 0.013 0.001 PHE B 305 TRP 0.016 0.002 TRP E1026 HIS 0.004 0.001 HIS E 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (12722) covalent geometry : angle 0.54784 / 0.29 (17530) hydrogen bonds : bond 0.03981 / 2.55 ( 668) hydrogen bonds : angle 3.62001 / 2.61 ( 1881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4947.11 seconds wall clock time: 84 minutes 49.91 seconds (5089.91 seconds total)