Starting phenix.real_space_refine on Sat Aug 8 03:01:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eoe_28373/08_2026/8eoe_28373.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eoe_28373/08_2026/8eoe_28373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eoe_28373/08_2026/8eoe_28373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eoe_28373/08_2026/8eoe_28373.map" model { file = "/net/cci-nas-00/data/ceres_data/8eoe_28373/08_2026/8eoe_28373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eoe_28373/08_2026/8eoe_28373.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8eoe_28373/08_2026/8eoe_28373.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eoe_28373/08_2026/8eoe_28373.cif" } resolution = 3.2 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= 0.003 sd= 0.039 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 88 5.49 5 Mg 1 5.21 5 S 89 5.16 5 C 15585 2.51 5 N 4497 2.21 5 O 5039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25301 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1765 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 8549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8549 Classifications: {'peptide': 1105} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1043} Chain breaks: 1 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: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 9919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1269, 9919 Classifications: {'peptide': 1269} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1208} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 878 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 110, 869 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Conformer: "B" Number of residues, atoms: 110, 869 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} bond proxies already assigned to first conformer: 877 Chain: "T" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 772 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "N" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 713 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain breaks: 2 Chain: "R" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 329 Classifications: {'RNAv2': 15} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 12} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19089 SG CYS D 891 76.718 24.605 87.413 1.00 62.79 S ATOM 19656 SG CYS D 968 75.454 27.919 88.920 1.00 58.47 S ATOM 19698 SG CYS D 975 76.959 27.807 85.389 1.00 56.89 S ATOM 19716 SG CYS D 978 73.604 26.370 86.027 1.00 57.17 S ATOM 12527 SG CYS D 60 108.742 79.963 115.702 1.00 98.93 S ATOM 12545 SG CYS D 62 110.825 82.452 117.535 1.00108.10 S ATOM 12654 SG CYS D 75 111.202 78.681 118.251 1.00 98.26 S ATOM 12680 SG CYS D 78 108.181 80.701 119.486 1.00102.05 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLU G 15 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU G 15 " occ=0.50 Time building chain proxies: 5.01, per 1000 atoms: 0.20 Number of scatterers: 25301 At special positions: 0 Unit cell: (127.89, 141.81, 199.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 89 16.00 P 88 15.00 Mg 1 11.99 O 5039 8.00 N 4497 7.00 C 15585 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: 2.17 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 968 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 75 " Number of angles added : 12 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5564 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 44 sheets defined 35.3% alpha, 13.6% beta 35 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'A' and resid 32 through 43 Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 203 through 219 removed outlier: 3.675A pdb=" N ALA A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 44 removed outlier: 3.653A pdb=" N LEU B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 106 through 110 removed outlier: 3.936A pdb=" N ILE B 110 " --> pdb=" O ALA B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 removed outlier: 3.596A pdb=" N ALA B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 203 through 208' Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.290A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.795A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 removed outlier: 3.704A pdb=" N GLU C 88 " --> pdb=" O GLY C 84 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 226 through 229 Processing helix chain 'C' and resid 233 through 242 removed outlier: 4.219A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 256 through 263 Processing helix chain 'C' and resid 269 through 282 removed outlier: 3.690A pdb=" N LYS C 280 " --> pdb=" O ASP C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.565A pdb=" N LYS C 318 " --> pdb=" O TYR C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 351 removed outlier: 4.026A pdb=" N VAL C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 404 removed outlier: 3.739A pdb=" N ASN C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 420 through 431 Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.622A pdb=" N LYS C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.969A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 539 removed outlier: 3.897A pdb=" N ARG C 538 " --> pdb=" O GLU C 535 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS C 539 " --> pdb=" O GLU C 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 535 through 539' Processing helix chain 'C' and resid 582 through 587 removed outlier: 4.569A pdb=" N MET C 586 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL C 587 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.575A pdb=" N MET C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 590 through 594' Processing helix chain 'C' and resid 596 through 600 removed outlier: 3.500A pdb=" N HIS C 599 " --> pdb=" O PHE C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 632 through 637 removed outlier: 3.568A pdb=" N ILE C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP C 637 " --> pdb=" O ARG C 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 632 through 637' Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 928 through 943 removed outlier: 3.633A pdb=" N LEU C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.564A pdb=" N ALA C 957 " --> pdb=" O ASP C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 989 removed outlier: 3.549A pdb=" N LEU C 985 " --> pdb=" O GLN C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1080 removed outlier: 3.505A pdb=" N CYS C1073 " --> pdb=" O GLY C1069 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA C1075 " --> pdb=" O MET C1071 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET C1076 " --> pdb=" O GLU C1072 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 3.808A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C1086 " --> pdb=" O ALA C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.188A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1130 removed outlier: 4.193A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 7 removed outlier: 3.505A pdb=" N PHE D 7 " --> pdb=" O VAL D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 85 through 90 removed outlier: 3.604A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU D 90 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 147 through 184 Processing helix chain 'D' and resid 191 through 228 Processing helix chain 'D' and resid 237 through 247 Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.531A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.590A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 300 removed outlier: 3.739A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 removed outlier: 3.766A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 342 through 359 Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 406 removed outlier: 3.746A pdb=" N LEU D 405 " --> pdb=" O LEU D 402 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU D 406 " --> pdb=" O SER D 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 402 through 406' Processing helix chain 'D' and resid 411 through 417 removed outlier: 3.659A pdb=" N LEU D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 removed outlier: 3.830A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 478 Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 589 removed outlier: 3.665A pdb=" N THR D 589 " --> pdb=" O LEU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 623 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 667 through 675 removed outlier: 3.602A pdb=" N VAL D 671 " --> pdb=" O THR D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 725 removed outlier: 3.884A pdb=" N VAL D 709 " --> pdb=" O PRO D 705 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA D 710 " --> pdb=" O MET D 706 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP D 714 " --> pdb=" O ALA D 710 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 763 removed outlier: 4.025A pdb=" N ALA D 753 " --> pdb=" O TYR D 749 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL D 756 " --> pdb=" O ARG D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 779 Processing helix chain 'D' and resid 780 through 793 removed outlier: 3.773A pdb=" N GLU D 791 " --> pdb=" O GLN D 787 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR D 793 " --> pdb=" O LEU D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 799 through 804 removed outlier: 4.058A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 819 Processing helix chain 'D' and resid 845 through 853 removed outlier: 3.717A pdb=" N THR D 853 " --> pdb=" O TYR D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 866 removed outlier: 4.008A pdb=" N LYS D 858 " --> pdb=" O HIS D 854 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY D 859 " --> pdb=" O GLY D 855 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU D 860 " --> pdb=" O ALA D 856 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 881 removed outlier: 3.540A pdb=" N ASP D 879 " --> pdb=" O ARG D 875 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL D 880 " --> pdb=" O ARG D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 954 Processing helix chain 'D' and resid 964 through 968 removed outlier: 3.542A pdb=" N CYS D 968 " --> pdb=" O VAL D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1004 removed outlier: 3.711A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 999 " --> pdb=" O VAL D 995 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA D1000 " --> pdb=" O GLY D 996 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE D1003 " --> pdb=" O ALA D 999 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY D1004 " --> pdb=" O ALA D1000 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1119 through 1126 removed outlier: 3.828A pdb=" N ARG D1123 " --> pdb=" O HIS D1119 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1145 removed outlier: 3.746A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN D1131 " --> pdb=" O PRO D1127 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE D1132 " --> pdb=" O ARG D1128 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN D1139 " --> pdb=" O VAL D1135 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1160 removed outlier: 4.176A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL D1156 " --> pdb=" O LYS D1152 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN D1160 " --> pdb=" O VAL D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1197 removed outlier: 3.653A pdb=" N GLU D1196 " --> pdb=" O ARG D1192 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1225 removed outlier: 3.629A pdb=" N SER D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1247 through 1255 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.629A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN E 37 " --> pdb=" O GLY E 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 33 through 37' Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 72 removed outlier: 3.743A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'G' and resid 14 through 28 removed outlier: 4.298A pdb=" N GLU G 27 " --> pdb=" O GLU G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 79 removed outlier: 3.680A pdb=" N TYR G 77 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 112 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 3.636A pdb=" N GLU A 24 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 192 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU A 197 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 94 removed outlier: 6.726A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.848A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 6.967A pdb=" N GLY A 103 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N THR A 127 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 105 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 removed outlier: 3.618A pdb=" N SER A 166 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 10 removed outlier: 3.640A pdb=" N GLU B 24 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS B 191 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 177 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 95 through 100 removed outlier: 6.564A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB1, first strand: chain 'B' and resid 171 through 174 removed outlier: 6.939A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.601A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.623A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB5, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.319A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 185 Processing sheet with id=AB7, first strand: chain 'C' and resid 190 through 191 Processing sheet with id=AB8, first strand: chain 'C' and resid 214 through 215 Processing sheet with id=AB9, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.205A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC2, first strand: chain 'C' and resid 558 through 562 removed outlier: 3.627A pdb=" N GLU C 569 " --> pdb=" O VAL C 561 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.661A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.915A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 676 through 677 Processing sheet with id=AC6, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC7, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 3.502A pdb=" N GLY C 893 " --> pdb=" O LEU C 885 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU C 917 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA C 722 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR C1024 " --> pdb=" O ILE C 723 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 765 through 766 removed outlier: 6.636A pdb=" N SER C 749 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LYS C 876 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N HIS C 751 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ALA C 874 " --> pdb=" O HIS C 751 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLU C 753 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYR C 872 " --> pdb=" O GLU C 753 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N HIS C 755 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG C 870 " --> pdb=" O HIS C 755 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE C 757 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU C 868 " --> pdb=" O ILE C 757 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA C 759 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N LYS C 876 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N GLY C 845 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY C 845 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 768 through 769 removed outlier: 3.601A pdb=" N GLU C 768 " --> pdb=" O VAL C 806 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 3.506A pdb=" N SER D 428 " --> pdb=" O MET D 541 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD3, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.917A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 3.811A pdb=" N GLU D 9 " --> pdb=" O LEU C1138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.619A pdb=" N HIS D 94 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 10.548A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 234 through 235 removed outlier: 5.540A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 443 through 444 removed outlier: 6.173A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD9, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE1, first strand: chain 'D' and resid 897 through 899 removed outlier: 4.608A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 903 through 904 Processing sheet with id=AE3, first strand: chain 'D' and resid 1061 through 1063 removed outlier: 3.617A pdb=" N ILE D1080 " --> pdb=" O TYR D1062 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1180 through 1182 Processing sheet with id=AE5, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AE6, first strand: chain 'G' and resid 5 through 6 removed outlier: 7.139A pdb=" N GLU G 68 " --> pdb=" O PHE G 36 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 43 through 44 removed outlier: 4.307A pdb=" N LYS G 58 " --> pdb=" O GLU G 43 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 48 through 49 790 hydrogen bonds defined for protein. 2190 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 94 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 6.58 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7512 1.33 - 1.45: 3902 1.45 - 1.57: 14178 1.57 - 1.69: 171 1.69 - 1.81: 157 Bond restraints: 25920 Sorted by residual: bond pdb=" C3' DC N 18 " pdb=" C2' DC N 18 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.38e+01 bond pdb=" C3' DG T 31 " pdb=" C2' DG T 31 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DA T 30 " pdb=" C2' DA T 30 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.62e+00 bond pdb=" C3' DC T 23 " pdb=" C2' DC T 23 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.37e+00 bond pdb=" C3' DT T 15 " pdb=" O3' DT T 15 " ideal model delta sigma weight residual 1.435 1.401 0.034 1.30e-02 5.92e+03 6.88e+00 ... (remaining 25915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 34807 2.15 - 4.29: 635 4.29 - 6.44: 44 6.44 - 8.58: 7 8.58 - 10.73: 1 Bond angle restraints: 35494 Sorted by residual: angle pdb=" C ASP G 73 " pdb=" N ASP G 74 " pdb=" CA ASP G 74 " ideal model delta sigma weight residual 120.31 128.71 -8.40 1.52e+00 4.33e-01 3.05e+01 angle pdb=" N VAL B 216 " pdb=" CA VAL B 216 " pdb=" C VAL B 216 " ideal model delta sigma weight residual 112.29 107.33 4.96 9.40e-01 1.13e+00 2.79e+01 angle pdb=" C4' DC T 32 " pdb=" C3' DC T 32 " pdb=" C2' DC T 32 " ideal model delta sigma weight residual 103.10 107.80 -4.70 9.00e-01 1.23e+00 2.73e+01 angle pdb=" O5' DG T 35 " pdb=" C5' DG T 35 " pdb=" C4' DG T 35 " ideal model delta sigma weight residual 109.40 113.29 -3.89 8.00e-01 1.56e+00 2.36e+01 angle pdb=" O4' DC T 17 " pdb=" C4' DC T 17 " pdb=" C3' DC T 17 " ideal model delta sigma weight residual 106.00 103.16 2.84 6.00e-01 2.78e+00 2.24e+01 ... (remaining 35489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 14189 35.35 - 70.70: 1350 70.70 - 106.05: 44 106.05 - 141.40: 2 141.40 - 176.75: 2 Dihedral angle restraints: 15587 sinusoidal: 6923 harmonic: 8664 Sorted by residual: dihedral pdb=" C4' A R 21 " pdb=" C3' A R 21 " pdb=" C2' A R 21 " pdb=" C1' A R 21 " ideal model delta sinusoidal sigma weight residual 36.34 -35.24 71.59 1 3.10e+00 1.04e-01 6.83e+02 dihedral pdb=" C4' C R 20 " pdb=" C3' C R 20 " pdb=" C2' C R 20 " pdb=" C1' C R 20 " ideal model delta sinusoidal sigma weight residual 36.35 -33.04 69.39 1 3.10e+00 1.04e-01 6.47e+02 dihedral pdb=" O4' C R 20 " pdb=" C4' C R 20 " pdb=" C3' C R 20 " pdb=" C2' C R 20 " ideal model delta sinusoidal sigma weight residual -35.15 29.65 -64.80 1 4.00e+00 6.25e-02 3.44e+02 ... (remaining 15584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 4025 0.151 - 0.303: 24 0.303 - 0.454: 1 0.454 - 0.605: 0 0.605 - 0.757: 1 Chirality restraints: 4051 Sorted by residual: chirality pdb=" C3' DC T 32 " pdb=" C4' DC T 32 " pdb=" O3' DC T 32 " pdb=" C2' DC T 32 " both_signs ideal model delta sigma weight residual False -2.73 -1.97 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" C3' DG T 31 " pdb=" C4' DG T 31 " pdb=" O3' DG T 31 " pdb=" C2' DG T 31 " both_signs ideal model delta sigma weight residual False -2.73 -2.41 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C2' C R 20 " pdb=" C3' C R 20 " pdb=" O2' C R 20 " pdb=" C1' C R 20 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 4048 not shown) Planarity restraints: 4358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 81 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO C 82 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO C 82 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 82 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET D 143 " -0.020 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C MET D 143 " 0.071 2.00e-02 2.50e+03 pdb=" O MET D 143 " -0.026 2.00e-02 2.50e+03 pdb=" N ARG D 144 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 197 " -0.020 2.00e-02 2.50e+03 4.02e-02 1.61e+01 pdb=" C VAL D 197 " 0.069 2.00e-02 2.50e+03 pdb=" O VAL D 197 " -0.026 2.00e-02 2.50e+03 pdb=" N ARG D 198 " -0.024 2.00e-02 2.50e+03 ... (remaining 4355 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 118 2.57 - 3.15: 18076 3.15 - 3.73: 36827 3.73 - 4.32: 51266 4.32 - 4.90: 87462 Nonbonded interactions: 193749 Sorted by model distance: nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2001 " model vdw 1.984 2.170 nonbonded pdb=" O3' A R 30 " pdb="MG MG D2001 " model vdw 2.041 2.170 nonbonded pdb=" O ILE D1210 " pdb=" OG SER D1214 " model vdw 2.163 3.040 nonbonded pdb=" OH TYR C 278 " pdb=" OE1 GLU C 285 " model vdw 2.223 3.040 nonbonded pdb=" O THR C 433 " pdb=" OG1 THR C 433 " model vdw 2.237 3.040 ... (remaining 193744 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 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 223 o \ r (resid 224 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 25 through 226)) selection = (chain 'B' and resid 1 through 226) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.990 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: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 29.370 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 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 0.078 25928 Z= 0.227 Angle : 0.658 10.730 35506 Z= 0.413 Chirality : 0.049 0.757 4051 Planarity : 0.006 0.104 4358 Dihedral : 22.356 176.754 10023 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.02 % Favored : 90.44 % Rotamer: Outliers : 17.34 % Allowed : 24.16 % Favored : 58.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -3.14 (0.14), residues: 3017 helix: -1.65 (0.16), residues: 984 sheet: -1.64 (0.26), residues: 401 loop : -2.53 (0.13), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 211 TYR 0.014 0.001 TYR C 314 PHE 0.014 0.001 PHE C 906 TRP 0.010 0.001 TRP D 662 HIS 0.013 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.23 (25920) covalent geometry : angle 0.65641 / 0.41 (35494) hydrogen bonds : bond 0.17644 / 11.62 ( 878) hydrogen bonds : angle 6.07652 / 4.15 ( 2378) metal coordination : bond 0.00315 / 0.14 ( 8) metal coordination : angle 2.45643 / 1.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 440 poor density : 160 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 71 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: C 229 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8663 (mmtm) REVERT: C 262 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8075 (tt) REVERT: C 296 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8538 (tt) REVERT: D 281 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8883 (mt) REVERT: D 1048 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7586 (m-30) REVERT: D 1075 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.6275 (p) REVERT: D 1076 VAL cc_start: 0.9029 (OUTLIER) cc_final: 0.8776 (m) REVERT: D 1081 SER cc_start: 0.8554 (OUTLIER) cc_final: 0.7400 (t) REVERT: G 34 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.5508 (tppt) REVERT: G 102 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.6182 (tt) outliers start: 440 outliers final: 105 residues processed: 556 average time/residue: 0.1882 time to fit residues: 156.7822 Evaluate side-chains 212 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 96 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 229 LYS Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 747 ASP Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 770 ARG Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 899 VAL Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 964 SER Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 972 THR Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1008 THR Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1048 ASP Chi-restraints excluded: chain D residue 1050 THR Chi-restraints excluded: chain D residue 1054 ARG Chi-restraints excluded: chain D residue 1063 LYS Chi-restraints excluded: chain D residue 1074 GLU Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1081 SER Chi-restraints excluded: chain D residue 1082 LYS Chi-restraints excluded: chain D residue 1089 PHE Chi-restraints excluded: chain D residue 1214 SER Chi-restraints excluded: chain D residue 1262 THR Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 98 PRO Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 108 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.0370 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 30.0000 overall best weight: 1.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN A 61 HIS A 79 ASN A 152 ASN B 119 HIS C 247 GLN C 435 GLN C 585 GLN C 610 ASN C 662 HIS C 685 ASN C 751 HIS C1066 GLN C1077 GLN C1111 ASN C1129 GLN D 5 ASN ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 GLN D 352 ASN D 368 ASN D 410 GLN D 505 HIS D 525 HIS D 564 ASN D 759 GLN D 852 ASN D 882 GLN ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1110 GLN D1131 GLN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1273 GLN E 63 GLN G 9 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.067482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.042859 restraints weight = 91765.789| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.56 r_work: 0.2672 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25928 Z= 0.164 Angle : 0.687 21.574 35506 Z= 0.355 Chirality : 0.049 0.735 4051 Planarity : 0.005 0.077 4358 Dihedral : 17.771 179.378 4471 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.41 % Favored : 94.46 % Rotamer: Outliers : 5.68 % Allowed : 26.33 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.23 (0.14), residues: 3017 helix: -0.62 (0.16), residues: 1011 sheet: -1.13 (0.26), residues: 392 loop : -2.20 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 159 TYR 0.021 0.001 TYR C 344 PHE 0.013 0.001 PHE D 47 TRP 0.009 0.001 TRP G 5 HIS 0.012 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (25920) covalent geometry : angle 0.68424 / 0.35 (35494) hydrogen bonds : bond 0.04760 / 3.17 ( 878) hydrogen bonds : angle 4.53795 / 3.09 ( 2378) metal coordination : bond 0.00546 / 0.25 ( 8) metal coordination : angle 3.47782 / 1.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 104 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7232 (ptm) cc_final: 0.7029 (ptm) REVERT: B 208 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9061 (tp) REVERT: C 103 MET cc_start: 0.8679 (ptt) cc_final: 0.8234 (ptt) REVERT: C 296 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8279 (tt) REVERT: C 373 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.7819 (t80) REVERT: C 762 THR cc_start: 0.7746 (OUTLIER) cc_final: 0.7517 (p) REVERT: D 144 ARG cc_start: 0.6112 (OUTLIER) cc_final: 0.5902 (tmm-80) REVERT: D 145 HIS cc_start: 0.8626 (OUTLIER) cc_final: 0.8294 (p90) REVERT: D 155 MET cc_start: 0.8406 (tmm) cc_final: 0.8138 (tpp) REVERT: D 218 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8484 (ttt-90) REVERT: D 281 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8671 (mt) REVERT: D 339 ASP cc_start: 0.7067 (OUTLIER) cc_final: 0.6319 (t70) REVERT: D 679 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8628 (tt) REVERT: D 688 MET cc_start: 0.9169 (mmt) cc_final: 0.8938 (mmt) REVERT: D 1092 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7528 (pm20) REVERT: D 1112 MET cc_start: 0.8889 (mmm) cc_final: 0.8083 (mmm) REVERT: D 1266 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8238 (mtp85) outliers start: 144 outliers final: 74 residues processed: 239 average time/residue: 0.1727 time to fit residues: 66.7482 Evaluate side-chains 182 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 96 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 762 THR Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 620 MET Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 656 TRP Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 747 ASP Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 899 VAL Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1008 THR Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1050 THR Chi-restraints excluded: chain D residue 1054 ARG Chi-restraints excluded: chain D residue 1074 GLU Chi-restraints excluded: chain D residue 1082 LYS Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain D residue 1266 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 97 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 135 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 192 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 257 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 246 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 42 optimal weight: 0.0570 chunk 114 optimal weight: 0.9980 overall best weight: 2.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN C 323 HIS C 585 GLN ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN D 657 GLN D 693 GLN D1091 HIS ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 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 = 0.3511 r_free = 0.3511 target = 0.066235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.041454 restraints weight = 91696.185| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 3.52 r_work: 0.2630 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25928 Z= 0.178 Angle : 0.628 20.342 35506 Z= 0.322 Chirality : 0.047 0.546 4051 Planarity : 0.005 0.058 4358 Dihedral : 17.026 178.689 4361 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.74 % Favored : 94.19 % Rotamer: Outliers : 5.44 % Allowed : 25.74 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.67 (0.15), residues: 3017 helix: 0.07 (0.17), residues: 1007 sheet: -0.81 (0.26), residues: 391 loop : -2.02 (0.14), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 218 TYR 0.011 0.001 TYR D 872 PHE 0.011 0.001 PHE D 47 TRP 0.008 0.001 TRP D 23 HIS 0.010 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (25920) covalent geometry : angle 0.62631 / 0.32 (35494) hydrogen bonds : bond 0.04615 / 3.08 ( 878) hydrogen bonds : angle 4.24674 / 2.91 ( 2378) metal coordination : bond 0.00711 / 0.34 ( 8) metal coordination : angle 2.66634 / 1.49 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 99 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.7946 (OUTLIER) cc_final: 0.7512 (p) REVERT: B 200 ASN cc_start: 0.9341 (t0) cc_final: 0.8875 (t0) REVERT: C 103 MET cc_start: 0.8692 (ptt) cc_final: 0.8439 (ptt) REVERT: C 296 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8270 (tt) REVERT: C 373 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.7656 (t80) REVERT: D 145 HIS cc_start: 0.8607 (OUTLIER) cc_final: 0.8183 (p90) REVERT: D 181 LEU cc_start: -0.0360 (OUTLIER) cc_final: -0.0963 (pp) REVERT: D 256 MET cc_start: 0.8665 (ptp) cc_final: 0.8349 (ptm) REVERT: D 443 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8663 (mp) REVERT: D 679 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8707 (tt) REVERT: D 1266 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8347 (mtp85) REVERT: G 31 MET cc_start: 0.7788 (ttp) cc_final: 0.6981 (ttp) REVERT: G 71 MET cc_start: 0.7501 (tmm) cc_final: 0.6916 (tpt) REVERT: G 74 ASP cc_start: 0.8730 (p0) cc_final: 0.8461 (p0) REVERT: G 112 ARG cc_start: 0.8263 (mtp-110) cc_final: 0.7901 (mtm-85) outliers start: 138 outliers final: 73 residues processed: 227 average time/residue: 0.1565 time to fit residues: 58.7238 Evaluate side-chains 176 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 95 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 620 MET Chi-restraints excluded: chain D residue 656 TRP Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 747 ASP Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1074 GLU Chi-restraints excluded: chain D residue 1082 LYS Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1266 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 89 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 204 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 23 optimal weight: 0.4980 chunk 299 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 283 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 226 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 543 GLN C 700 GLN ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.066364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.041729 restraints weight = 91755.094| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.41 r_work: 0.2644 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25928 Z= 0.137 Angle : 0.576 10.799 35506 Z= 0.299 Chirality : 0.045 0.368 4051 Planarity : 0.004 0.061 4358 Dihedral : 16.673 177.350 4326 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 3.74 % Allowed : 26.41 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.37 (0.15), residues: 3017 helix: 0.40 (0.17), residues: 1007 sheet: -0.62 (0.26), residues: 405 loop : -1.92 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 80 TYR 0.009 0.001 TYR D1077 PHE 0.011 0.001 PHE G 88 TRP 0.007 0.001 TRP D1220 HIS 0.008 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (25920) covalent geometry : angle 0.57456 / 0.30 (35494) hydrogen bonds : bond 0.04043 / 2.70 ( 878) hydrogen bonds : angle 4.05498 / 2.78 ( 2378) metal coordination : bond 0.00499 / 0.24 ( 8) metal coordination : angle 2.41636 / 1.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 97 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 ASN cc_start: 0.9310 (t0) cc_final: 0.8862 (t0) REVERT: C 103 MET cc_start: 0.8752 (ptt) cc_final: 0.8516 (ptt) REVERT: C 109 ASP cc_start: 0.8853 (OUTLIER) cc_final: 0.8347 (t0) REVERT: C 296 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8281 (tt) REVERT: C 373 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.7777 (t80) REVERT: C 776 ILE cc_start: 0.8316 (tp) cc_final: 0.8091 (tp) REVERT: C 791 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8176 (ptp90) REVERT: D 145 HIS cc_start: 0.8660 (OUTLIER) cc_final: 0.8293 (p90) REVERT: D 159 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8475 (mmm-85) REVERT: D 181 LEU cc_start: -0.0439 (OUTLIER) cc_final: -0.1016 (pp) REVERT: D 256 MET cc_start: 0.8768 (ptp) cc_final: 0.8464 (ptm) REVERT: D 281 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8717 (mt) REVERT: D 443 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8865 (mp) REVERT: D 679 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8712 (tt) REVERT: D 1266 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8454 (mtp85) REVERT: G 31 MET cc_start: 0.7669 (ttp) cc_final: 0.6937 (ttp) REVERT: G 71 MET cc_start: 0.7560 (tmm) cc_final: 0.7118 (tpt) REVERT: G 74 ASP cc_start: 0.8703 (p0) cc_final: 0.8490 (p0) outliers start: 95 outliers final: 56 residues processed: 186 average time/residue: 0.1564 time to fit residues: 48.0162 Evaluate side-chains 162 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 95 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 791 ARG Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 620 MET Chi-restraints excluded: chain D residue 656 TRP Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 747 ASP Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1074 GLU Chi-restraints excluded: chain D residue 1082 LYS Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1266 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 88 PHE Chi-restraints excluded: chain G residue 89 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 122 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 234 optimal weight: 0.0870 chunk 5 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 252 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 657 GLN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.065543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.040778 restraints weight = 91305.967| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 3.52 r_work: 0.2610 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25928 Z= 0.169 Angle : 0.567 8.336 35506 Z= 0.295 Chirality : 0.045 0.234 4051 Planarity : 0.004 0.060 4358 Dihedral : 16.446 177.040 4312 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.44 % Favored : 94.49 % Rotamer: Outliers : 4.06 % Allowed : 26.09 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.17 (0.15), residues: 3017 helix: 0.61 (0.17), residues: 1006 sheet: -0.48 (0.26), residues: 416 loop : -1.84 (0.14), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG D 166 TYR 0.009 0.001 TYR C 731 PHE 0.011 0.001 PHE D 47 TRP 0.007 0.001 TRP D1220 HIS 0.007 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (25920) covalent geometry : angle 0.56529 / 0.30 (35494) hydrogen bonds : bond 0.04314 / 2.88 ( 878) hydrogen bonds : angle 4.00722 / 2.74 ( 2378) metal coordination : bond 0.00675 / 0.33 ( 8) metal coordination : angle 2.34788 / 1.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 99 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 ASN cc_start: 0.9368 (t0) cc_final: 0.8911 (t0) REVERT: C 109 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8313 (t0) REVERT: C 296 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8278 (tt) REVERT: C 373 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.7648 (t80) REVERT: C 454 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.6741 (mpt90) REVERT: C 776 ILE cc_start: 0.8333 (tp) cc_final: 0.8111 (tp) REVERT: C 791 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8055 (ptp90) REVERT: D 140 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7842 (t0) REVERT: D 145 HIS cc_start: 0.8632 (OUTLIER) cc_final: 0.8396 (p90) REVERT: D 181 LEU cc_start: -0.0449 (OUTLIER) cc_final: -0.1054 (pp) REVERT: D 256 MET cc_start: 0.8749 (ptt) cc_final: 0.8290 (ptm) REVERT: D 281 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8551 (mt) REVERT: D 443 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8638 (mp) REVERT: D 506 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8647 (ttp-170) REVERT: D 679 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8752 (tt) REVERT: D 1266 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8419 (mtp85) REVERT: G 31 MET cc_start: 0.7631 (ttp) cc_final: 0.7033 (ttp) REVERT: G 71 MET cc_start: 0.7534 (tmm) cc_final: 0.7188 (tpt) REVERT: G 112 ARG cc_start: 0.8263 (mtp-110) cc_final: 0.7988 (mtm-85) outliers start: 103 outliers final: 65 residues processed: 194 average time/residue: 0.1791 time to fit residues: 55.8070 Evaluate side-chains 175 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 97 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 791 ARG Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 620 MET Chi-restraints excluded: chain D residue 656 TRP Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 747 ASP Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1082 LYS Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1262 THR Chi-restraints excluded: chain D residue 1266 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain G residue 88 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 216 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 130 optimal weight: 0.2980 chunk 116 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 891 ASN ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN D1091 HIS ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 ASN ** G 21 ASN ** 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 = 0.3512 r_free = 0.3512 target = 0.066335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.041806 restraints weight = 91960.971| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.42 r_work: 0.2648 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 25928 Z= 0.105 Angle : 0.537 9.849 35506 Z= 0.280 Chirality : 0.044 0.245 4051 Planarity : 0.004 0.063 4358 Dihedral : 16.244 175.876 4301 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.35 % Favored : 95.59 % Rotamer: Outliers : 3.07 % Allowed : 26.69 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.94 (0.15), residues: 3017 helix: 0.77 (0.17), residues: 1006 sheet: -0.35 (0.27), residues: 413 loop : -1.68 (0.14), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 633 TYR 0.007 0.001 TYR C 731 PHE 0.010 0.001 PHE C 153 TRP 0.007 0.001 TRP C 938 HIS 0.007 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (25920) covalent geometry : angle 0.53543 / 0.28 (35494) hydrogen bonds : bond 0.03565 / 2.40 ( 878) hydrogen bonds : angle 3.84413 / 2.62 ( 2378) metal coordination : bond 0.00298 / 0.14 ( 8) metal coordination : angle 2.09894 / 1.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 97 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 200 ASN cc_start: 0.9325 (t0) cc_final: 0.8855 (t0) REVERT: C 109 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8389 (t0) REVERT: C 296 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8335 (tt) REVERT: C 373 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.7696 (t80) REVERT: C 454 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.6816 (mpt90) REVERT: C 776 ILE cc_start: 0.8384 (tp) cc_final: 0.8165 (tp) REVERT: C 791 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7775 (ptp90) REVERT: D 140 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7958 (t0) REVERT: D 145 HIS cc_start: 0.8648 (OUTLIER) cc_final: 0.8382 (p90) REVERT: D 181 LEU cc_start: -0.0456 (OUTLIER) cc_final: -0.1084 (pp) REVERT: D 256 MET cc_start: 0.8789 (ptt) cc_final: 0.8500 (ptm) REVERT: D 281 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8655 (mt) REVERT: D 443 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8805 (mp) REVERT: D 506 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8802 (ttp-170) REVERT: D 679 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8708 (tt) REVERT: D 747 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8652 (m-30) REVERT: D 1266 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8532 (mtp85) REVERT: G 71 MET cc_start: 0.7477 (tmm) cc_final: 0.7272 (tpt) REVERT: G 112 ARG cc_start: 0.8238 (mtp-110) cc_final: 0.7859 (mtm-85) outliers start: 78 outliers final: 46 residues processed: 171 average time/residue: 0.1735 time to fit residues: 48.2637 Evaluate side-chains 154 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 94 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 791 ARG Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 620 MET Chi-restraints excluded: chain D residue 656 TRP Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 747 ASP Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1082 LYS Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1266 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain G residue 88 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 21 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 177 optimal weight: 30.0000 chunk 163 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 142 optimal weight: 0.9990 chunk 271 optimal weight: 0.6980 chunk 293 optimal weight: 30.0000 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 0.0570 chunk 122 optimal weight: 0.4980 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.066617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.042099 restraints weight = 91530.256| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.41 r_work: 0.2666 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 25928 Z= 0.097 Angle : 0.511 9.312 35506 Z= 0.268 Chirality : 0.043 0.245 4051 Planarity : 0.004 0.062 4358 Dihedral : 16.133 175.501 4296 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.58 % Favored : 95.36 % Rotamer: Outliers : 2.80 % Allowed : 26.84 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.76 (0.15), residues: 3017 helix: 0.94 (0.17), residues: 1000 sheet: -0.19 (0.27), residues: 406 loop : -1.58 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 37 TYR 0.007 0.001 TYR C 731 PHE 0.010 0.001 PHE C 153 TRP 0.007 0.001 TRP C 938 HIS 0.007 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (25920) covalent geometry : angle 0.50965 / 0.27 (35494) hydrogen bonds : bond 0.03384 / 2.28 ( 878) hydrogen bonds : angle 3.76338 / 2.55 ( 2378) metal coordination : bond 0.00267 / 0.12 ( 8) metal coordination : angle 2.01462 / 1.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 95 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 200 ASN cc_start: 0.9314 (t0) cc_final: 0.8851 (t0) REVERT: C 62 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: C 109 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8441 (t0) REVERT: C 258 MET cc_start: 0.8799 (mmp) cc_final: 0.8580 (tpt) REVERT: C 296 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8374 (tt) REVERT: C 373 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.7711 (t80) REVERT: C 454 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.7002 (mpt90) REVERT: C 776 ILE cc_start: 0.8439 (tp) cc_final: 0.8220 (tp) REVERT: C 791 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7854 (ptp90) REVERT: D 140 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.8058 (t0) REVERT: D 145 HIS cc_start: 0.8626 (OUTLIER) cc_final: 0.8358 (p90) REVERT: D 181 LEU cc_start: -0.0352 (OUTLIER) cc_final: -0.0984 (pp) REVERT: D 256 MET cc_start: 0.8798 (ptt) cc_final: 0.8545 (ptm) REVERT: D 281 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8696 (mt) REVERT: D 443 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8880 (mp) REVERT: D 679 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8693 (tt) REVERT: D 1266 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8534 (mtp85) REVERT: G 29 MET cc_start: 0.7929 (mtm) cc_final: 0.7611 (ttp) REVERT: G 112 ARG cc_start: 0.8247 (mtp-110) cc_final: 0.8035 (mtm-85) outliers start: 71 outliers final: 48 residues processed: 162 average time/residue: 0.1371 time to fit residues: 36.8235 Evaluate side-chains 153 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 92 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 791 ARG Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 620 MET Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1082 LYS Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1266 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain G residue 88 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 242 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 95 optimal weight: 0.0870 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 31 optimal weight: 0.0470 chunk 214 optimal weight: 0.0270 overall best weight: 0.8316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.066704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.042170 restraints weight = 91748.192| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.44 r_work: 0.2665 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 25928 Z= 0.100 Angle : 0.508 9.609 35506 Z= 0.266 Chirality : 0.043 0.251 4051 Planarity : 0.004 0.064 4358 Dihedral : 15.978 175.520 4290 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.41 % Favored : 95.52 % Rotamer: Outliers : 2.60 % Allowed : 27.04 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.64 (0.15), residues: 3017 helix: 1.05 (0.17), residues: 1002 sheet: -0.10 (0.27), residues: 403 loop : -1.52 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1085 TYR 0.007 0.001 TYR C 731 PHE 0.010 0.001 PHE D 107 TRP 0.007 0.001 TRP C 938 HIS 0.006 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (25920) covalent geometry : angle 0.50672 / 0.27 (35494) hydrogen bonds : bond 0.03302 / 2.23 ( 878) hydrogen bonds : angle 3.68133 / 2.50 ( 2378) metal coordination : bond 0.00284 / 0.13 ( 8) metal coordination : angle 1.87280 / 1.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 96 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.8455 (OUTLIER) cc_final: 0.8182 (p) REVERT: B 200 ASN cc_start: 0.9303 (t0) cc_final: 0.8839 (t0) REVERT: C 62 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8086 (mp0) REVERT: C 109 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8445 (t0) REVERT: C 296 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8348 (tt) REVERT: C 373 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.7715 (t80) REVERT: C 454 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.6988 (mpt90) REVERT: C 776 ILE cc_start: 0.8431 (tp) cc_final: 0.8215 (tp) REVERT: D 145 HIS cc_start: 0.8607 (OUTLIER) cc_final: 0.8239 (p-80) REVERT: D 155 MET cc_start: 0.7923 (tpt) cc_final: 0.7570 (tpp) REVERT: D 181 LEU cc_start: -0.0192 (OUTLIER) cc_final: -0.0759 (pp) REVERT: D 252 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8431 (p90) REVERT: D 256 MET cc_start: 0.8825 (ptt) cc_final: 0.8567 (ptm) REVERT: D 281 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8706 (mt) REVERT: D 460 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8113 (mp) REVERT: D 506 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8880 (ttp-170) REVERT: D 656 TRP cc_start: 0.7576 (t-100) cc_final: 0.7132 (m100) REVERT: D 679 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8677 (tt) REVERT: D 1266 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8525 (mtp85) REVERT: G 29 MET cc_start: 0.8012 (mtm) cc_final: 0.7710 (ttp) REVERT: G 31 MET cc_start: 0.7956 (ttp) cc_final: 0.7476 (ttp) REVERT: G 74 ASP cc_start: 0.8966 (p0) cc_final: 0.8548 (p0) REVERT: G 112 ARG cc_start: 0.8331 (mtp-110) cc_final: 0.7944 (mtm-85) outliers start: 66 outliers final: 44 residues processed: 160 average time/residue: 0.1429 time to fit residues: 38.4388 Evaluate side-chains 149 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 91 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 620 MET Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1082 LYS Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1266 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain G residue 88 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 129 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 250 optimal weight: 0.0770 chunk 92 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 854 HIS ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.065656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.041021 restraints weight = 91824.240| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.43 r_work: 0.2630 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25928 Z= 0.160 Angle : 0.539 9.518 35506 Z= 0.281 Chirality : 0.044 0.257 4051 Planarity : 0.004 0.059 4358 Dihedral : 15.919 176.344 4290 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.18 % Favored : 94.76 % Rotamer: Outliers : 2.80 % Allowed : 26.76 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.63 (0.15), residues: 3017 helix: 1.08 (0.17), residues: 1001 sheet: -0.13 (0.26), residues: 431 loop : -1.54 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1085 TYR 0.008 0.001 TYR D 586 PHE 0.011 0.001 PHE C 906 TRP 0.007 0.001 TRP C 243 HIS 0.006 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (25920) covalent geometry : angle 0.53770 / 0.28 (35494) hydrogen bonds : bond 0.03944 / 2.65 ( 878) hydrogen bonds : angle 3.77743 / 2.56 ( 2378) metal coordination : bond 0.00604 / 0.30 ( 8) metal coordination : angle 1.90102 / 1.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 94 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.8525 (OUTLIER) cc_final: 0.8268 (p) REVERT: B 200 ASN cc_start: 0.9331 (t0) cc_final: 0.8876 (t0) REVERT: C 62 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8092 (mp0) REVERT: C 109 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8478 (t0) REVERT: C 154 MET cc_start: 0.9088 (mmm) cc_final: 0.8659 (mtt) REVERT: C 296 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8395 (tt) REVERT: C 373 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.7742 (t80) REVERT: C 454 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.7058 (mpt90) REVERT: C 611 MET cc_start: 0.9266 (mtm) cc_final: 0.9036 (mtm) REVERT: C 776 ILE cc_start: 0.8507 (tp) cc_final: 0.8297 (tp) REVERT: C 791 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7903 (ptp90) REVERT: D 140 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8098 (t0) REVERT: D 145 HIS cc_start: 0.8689 (OUTLIER) cc_final: 0.8406 (p90) REVERT: D 155 MET cc_start: 0.8061 (tpt) cc_final: 0.7668 (tpp) REVERT: D 181 LEU cc_start: -0.0272 (OUTLIER) cc_final: -0.0800 (pp) REVERT: D 252 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8579 (p90) REVERT: D 256 MET cc_start: 0.8861 (ptt) cc_final: 0.8617 (ptm) REVERT: D 281 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8754 (mt) REVERT: D 460 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8064 (mp) REVERT: D 506 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8860 (ttp-170) REVERT: D 679 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8716 (tt) REVERT: D 1266 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8459 (mtp85) REVERT: G 29 MET cc_start: 0.8092 (mtm) cc_final: 0.7744 (ttp) REVERT: G 31 MET cc_start: 0.7841 (ttp) cc_final: 0.7332 (ttp) REVERT: G 74 ASP cc_start: 0.8946 (p0) cc_final: 0.8507 (p0) REVERT: G 112 ARG cc_start: 0.8348 (mtp-110) cc_final: 0.8049 (mtm-85) outliers start: 71 outliers final: 49 residues processed: 160 average time/residue: 0.1518 time to fit residues: 40.2807 Evaluate side-chains 156 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 91 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 791 ARG Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 620 MET Chi-restraints excluded: chain D residue 656 TRP Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1082 LYS Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1262 THR Chi-restraints excluded: chain D residue 1266 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain G residue 88 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 190 optimal weight: 0.8980 chunk 291 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 172 optimal weight: 40.0000 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 268 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 143 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.066068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.041527 restraints weight = 91245.386| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 3.42 r_work: 0.2644 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25928 Z= 0.113 Angle : 0.517 9.509 35506 Z= 0.269 Chirality : 0.043 0.260 4051 Planarity : 0.004 0.065 4358 Dihedral : 15.841 175.732 4290 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.25 % Favored : 95.69 % Rotamer: Outliers : 2.56 % Allowed : 27.04 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.53 (0.15), residues: 3017 helix: 1.15 (0.17), residues: 1006 sheet: -0.09 (0.27), residues: 408 loop : -1.46 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1085 TYR 0.008 0.001 TYR C 731 PHE 0.009 0.001 PHE D 107 TRP 0.007 0.001 TRP C 938 HIS 0.007 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (25920) covalent geometry : angle 0.51604 / 0.27 (35494) hydrogen bonds : bond 0.03505 / 2.36 ( 878) hydrogen bonds : angle 3.69940 / 2.51 ( 2378) metal coordination : bond 0.00373 / 0.18 ( 8) metal coordination : angle 1.84102 / 1.02 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 98 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.8527 (OUTLIER) cc_final: 0.8290 (p) REVERT: B 200 ASN cc_start: 0.9328 (t0) cc_final: 0.8876 (t0) REVERT: C 62 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: C 109 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8454 (t0) REVERT: C 296 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8434 (tt) REVERT: C 373 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.7718 (t80) REVERT: C 454 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.7056 (mpt90) REVERT: C 611 MET cc_start: 0.9257 (mtm) cc_final: 0.9029 (mtm) REVERT: C 776 ILE cc_start: 0.8529 (tp) cc_final: 0.8317 (tp) REVERT: C 791 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7888 (ptp90) REVERT: D 140 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.8064 (t0) REVERT: D 145 HIS cc_start: 0.8725 (OUTLIER) cc_final: 0.8456 (p90) REVERT: D 155 MET cc_start: 0.8037 (tpt) cc_final: 0.7648 (tpp) REVERT: D 181 LEU cc_start: -0.0367 (OUTLIER) cc_final: -0.0895 (pp) REVERT: D 252 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8593 (p90) REVERT: D 256 MET cc_start: 0.8866 (ptt) cc_final: 0.8606 (ptm) REVERT: D 281 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8755 (mt) REVERT: D 460 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8130 (mp) REVERT: D 656 TRP cc_start: 0.7518 (OUTLIER) cc_final: 0.7107 (m100) REVERT: D 679 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8692 (tt) REVERT: D 1266 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8527 (mtp85) REVERT: G 29 MET cc_start: 0.8080 (mtm) cc_final: 0.7565 (ttp) REVERT: G 74 ASP cc_start: 0.8915 (p0) cc_final: 0.8547 (p0) REVERT: G 112 ARG cc_start: 0.8331 (mtp-110) cc_final: 0.7976 (mtm-85) outliers start: 65 outliers final: 43 residues processed: 160 average time/residue: 0.1581 time to fit residues: 41.7800 Evaluate side-chains 154 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 95 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 791 ARG Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 620 MET Chi-restraints excluded: chain D residue 656 TRP Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 943 ASP Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1082 LYS Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1266 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain G residue 88 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 18 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1091 HIS ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.065116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.040488 restraints weight = 91565.817| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.39 r_work: 0.2609 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25928 Z= 0.182 Angle : 0.553 9.610 35506 Z= 0.288 Chirality : 0.044 0.260 4051 Planarity : 0.004 0.058 4358 Dihedral : 15.807 176.317 4289 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.31 % Favored : 94.63 % Rotamer: Outliers : 2.68 % Allowed : 27.04 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.58 (0.15), residues: 3017 helix: 1.12 (0.17), residues: 1014 sheet: -0.15 (0.26), residues: 413 loop : -1.51 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1085 TYR 0.009 0.001 TYR D 793 PHE 0.012 0.001 PHE D 47 TRP 0.007 0.001 TRP C 243 HIS 0.007 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (25920) covalent geometry : angle 0.55214 / 0.29 (35494) hydrogen bonds : bond 0.04213 / 2.82 ( 878) hydrogen bonds : angle 3.82427 / 2.60 ( 2378) metal coordination : bond 0.00741 / 0.37 ( 8) metal coordination : angle 1.97894 / 1.11 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7532.93 seconds wall clock time: 128 minutes 55.67 seconds (7735.67 seconds total)