Starting phenix.real_space_refine on Fri Feb 6 19:34:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m9e_63731/02_2026/9m9e_63731_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m9e_63731/02_2026/9m9e_63731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m9e_63731/02_2026/9m9e_63731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m9e_63731/02_2026/9m9e_63731.map" model { file = "/net/cci-nas-00/data/ceres_data/9m9e_63731/02_2026/9m9e_63731_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m9e_63731/02_2026/9m9e_63731_neut.cif" } resolution = 3.31 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= -0.000 sd= 0.042 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 99 5.49 5 Mg 1 5.21 5 S 88 5.16 5 C 16579 2.51 5 N 4790 2.21 5 O 5361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26920 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1622 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1753 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 218} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 8530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1125, 8530 Classifications: {'peptide': 1125} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1062} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 14, 'ASN:plan1': 4, 'ASP:plan': 6, 'ARG:plan': 8, 'GLN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 143 Chain: "D" Number of atoms: 9743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1256, 9743 Classifications: {'peptide': 1256} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1195} Chain breaks: 2 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 8, 'GLN:plan1': 2, 'ARG:plan': 6, 'ASP:plan': 6, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 101 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 600 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "G" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 938 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1, ' DT:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "H" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 942 Classifications: {'DNA': 47} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 46} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' DG:plan': 1, ' DG:plan2': 1, ' DT:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "I" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 141 Classifications: {'RNA': 7} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 4} Link IDs: {'rna3p': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "M" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1234 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 154} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 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 12383 SG CYS D 60 106.959 88.198 120.847 1.00157.55 S ATOM 12401 SG CYS D 62 108.186 90.578 122.672 1.00154.01 S ATOM 12510 SG CYS D 75 109.633 86.904 121.986 1.00162.95 S ATOM 18945 SG CYS D 891 89.420 31.033 86.088 1.00133.79 S ATOM 19507 SG CYS D 968 87.612 34.088 87.681 1.00120.45 S ATOM 19549 SG CYS D 975 89.059 34.274 84.248 1.00118.79 S ATOM 19567 SG CYS D 978 86.075 32.182 84.677 1.00117.09 S Time building chain proxies: 6.14, per 1000 atoms: 0.23 Number of scatterers: 26920 At special positions: 0 Unit cell: (143.29, 141.51, 202.92, 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 88 16.00 P 99 15.00 Mg 1 11.99 O 5361 8.00 N 4790 7.00 C 16579 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb=" ZN D1403 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 975 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 978 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 891 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 968 " Number of angles added : 6 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5968 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 42 sheets defined 42.2% alpha, 14.9% beta 15 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 3.38 Creating SS restraints... Processing helix chain 'A' and resid 29 through 45 removed outlier: 4.071A pdb=" N THR A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 203 through 220 removed outlier: 3.642A pdb=" N GLU A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 4.368A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 148 through 153 removed outlier: 3.784A pdb=" N ASN B 152 " --> pdb=" O PRO B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.900A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.140A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 78 Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 234 through 240 removed outlier: 3.672A pdb=" N LEU C 238 " --> pdb=" O VAL C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 253 removed outlier: 4.572A pdb=" N ARG C 251 " --> pdb=" O GLN C 247 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE C 252 " --> pdb=" O ILE C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 removed outlier: 4.064A pdb=" N ARG C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS C 264 " --> pdb=" O SER C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 301 Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 405 Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 420 through 434 removed outlier: 3.584A pdb=" N VAL C 424 " --> pdb=" O ILE C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 452 Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'C' and resid 532 through 537 removed outlier: 3.895A pdb=" N ASP C 537 " --> pdb=" O ALA C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 594 removed outlier: 4.017A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 629 through 639 removed outlier: 4.619A pdb=" N ARG C 633 " --> pdb=" O GLY C 629 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 777 through 782 removed outlier: 3.626A pdb=" N LEU C 781 " --> pdb=" O SER C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 920 through 926 removed outlier: 4.371A pdb=" N ARG C 924 " --> pdb=" O HIS C 920 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 removed outlier: 3.672A pdb=" N LEU C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 960 through 963 Processing helix chain 'C' and resid 981 through 990 removed outlier: 3.790A pdb=" N SER C 990 " --> pdb=" O GLN C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1080 removed outlier: 3.510A pdb=" N TYR C1079 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1091 Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.145A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.603A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 23 removed outlier: 3.928A pdb=" N ILE D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.717A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 141 through 146 removed outlier: 5.667A pdb=" N ASN D 146 " --> pdb=" O MET D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 188 removed outlier: 3.762A pdb=" N LEU D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU D 183 " --> pdb=" O ALA D 179 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU D 184 " --> pdb=" O ASP D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 221 removed outlier: 3.577A pdb=" N VAL D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 240 through 246 removed outlier: 3.606A pdb=" N ASP D 246 " --> pdb=" O ARG D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.713A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 304 removed outlier: 3.658A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.906A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 342 Processing helix chain 'D' and resid 343 through 359 removed outlier: 3.965A pdb=" N ASN D 349 " --> pdb=" O ARG D 345 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG D 353 " --> pdb=" O ASN D 349 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU D 354 " --> pdb=" O ARG D 350 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS D 355 " --> pdb=" O ASN D 351 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG D 356 " --> pdb=" O ASN D 352 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 377 removed outlier: 3.760A pdb=" N GLN D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU D 376 " --> pdb=" O ARG D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 397 Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 417 removed outlier: 3.618A pdb=" N LEU D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 removed outlier: 3.690A pdb=" N LEU D 463 " --> pdb=" O ARG D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 479 Processing helix chain 'D' and resid 482 through 492 removed outlier: 3.949A pdb=" N VAL D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D 488 " --> pdb=" O TRP D 484 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) 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 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 579 through 589 Processing helix chain 'D' and resid 614 through 623 Processing helix chain 'D' and resid 643 through 650 Processing helix chain 'D' and resid 668 through 675 removed outlier: 3.604A pdb=" N GLU D 675 " --> pdb=" O VAL D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 703 removed outlier: 3.754A pdb=" N ARG D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 726 removed outlier: 3.845A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 751 Processing helix chain 'D' and resid 751 through 762 removed outlier: 3.633A pdb=" N LYS D 755 " --> pdb=" O GLU D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 removed outlier: 3.631A pdb=" N ASN D 771 " --> pdb=" O HIS D 767 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA D 773 " --> pdb=" O GLU D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 805 removed outlier: 3.740A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER D 805 " --> pdb=" O THR D 801 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 819 removed outlier: 3.549A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 3.746A pdb=" N THR D 853 " --> pdb=" O TYR D 849 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA D 856 " --> pdb=" O ASN D 852 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA D 868 " --> pdb=" O ALA D 864 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY D 871 " --> pdb=" O THR D 867 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1005 removed outlier: 3.638A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1006 through 1010 Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1117 through 1126 Processing helix chain 'D' and resid 1126 through 1145 removed outlier: 3.689A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.254A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN D1160 " --> pdb=" O VAL D1156 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET D1161 " --> pdb=" O ILE D1157 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1190 Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1225 removed outlier: 3.712A pdb=" N ALA D1223 " --> pdb=" O SER D1219 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1239 removed outlier: 3.628A pdb=" N ASN D1239 " --> pdb=" O ASP D1235 " (cutoff:3.500A) Processing helix chain 'D' and resid 1247 through 1254 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 removed outlier: 3.648A pdb=" N ASN D1269 " --> pdb=" O ASN D1265 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 36 Processing helix chain 'E' and resid 38 through 44 removed outlier: 3.806A pdb=" N LEU E 42 " --> pdb=" O PRO E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 70 Processing helix chain 'E' and resid 89 through 100 removed outlier: 3.511A pdb=" N ILE E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA E 100 " --> pdb=" O ARG E 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 76 Processing helix chain 'F' and resid 77 through 81 Processing helix chain 'F' and resid 83 through 104 removed outlier: 5.338A pdb=" N ASP F 93 " --> pdb=" O ARG F 89 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ARG F 94 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 124 Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 131 through 153 removed outlier: 3.610A pdb=" N THR F 141 " --> pdb=" O HIS F 137 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASN F 142 " --> pdb=" O ARG F 138 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU F 143 " --> pdb=" O ILE F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 180 Processing helix chain 'F' and resid 183 through 193 Processing helix chain 'F' and resid 194 through 206 Processing helix chain 'F' and resid 210 through 218 Processing helix chain 'F' and resid 221 through 242 Processing helix chain 'M' and resid 52 through 57 removed outlier: 3.912A pdb=" N VAL M 56 " --> pdb=" O ASN M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 75 Processing helix chain 'M' and resid 84 through 97 removed outlier: 3.781A pdb=" N ARG M 88 " --> pdb=" O ASN M 84 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR M 89 " --> pdb=" O TRP M 85 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS M 90 " --> pdb=" O SER M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 118 Processing helix chain 'M' and resid 121 through 144 removed outlier: 3.644A pdb=" N LYS M 125 " --> pdb=" O SER M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 160 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 5.358A pdb=" N GLN A 20 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL A 196 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL A 22 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU A 194 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLU A 24 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU A 192 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 3.939A pdb=" N SER A 53 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY A 143 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ALA A 49 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 removed outlier: 3.516A pdb=" N VAL A 147 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 15 removed outlier: 3.633A pdb=" N SER B 10 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 22 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 12 " --> pdb=" O GLN B 20 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 196 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N THR B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL B 183 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE B 189 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 173 " --> pdb=" O GLU B 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 99 removed outlier: 3.609A pdb=" N LEU B 134 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU B 137 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER B 53 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU B 141 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N VAL B 51 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLY B 143 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ALA B 49 " --> pdb=" O GLY B 143 " (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 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.523A pdb=" N VAL B 147 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.407A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 105 through 112 removed outlier: 5.622A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.594A 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: 3.731A pdb=" N SER C 177 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 190 removed outlier: 5.213A pdb=" N HIS C 200 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG C 225 " --> pdb=" O GLU C 213 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.558A pdb=" N MET C 355 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 505 through 506 removed outlier: 6.643A pdb=" N ILE C 512 " --> pdb=" O LEU C 531 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU C 531 " --> pdb=" O ILE C 512 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N THR C 514 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL C 529 " --> pdb=" O THR C 514 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR C 516 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLU C 527 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS C 518 " --> pdb=" O SER C 525 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 505 through 506 removed outlier: 3.695A pdb=" N MET C 579 " --> pdb=" O ARG C 517 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.831A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS C 687 " --> pdb=" O ASP C 704 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 648 through 653 removed outlier: 6.764A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL C 660 " --> pdb=" O ARG C 668 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG C 668 " --> pdb=" O VAL C 660 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 676 through 677 Processing sheet with id=AC4, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC5, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 4.035A pdb=" N ALA C 886 " --> pdb=" O MET C1031 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE C 735 " --> pdb=" O LYS C 897 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU C 899 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU C 737 " --> pdb=" O LEU C 899 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR C1024 " --> pdb=" O ILE C 723 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 749 through 760 removed outlier: 6.851A pdb=" N SER C 749 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LYS C 876 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS C 751 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA C 874 " --> pdb=" O HIS C 751 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLU C 753 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR C 872 " --> pdb=" O GLU C 753 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N HIS C 755 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG C 870 " --> pdb=" O HIS C 755 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE C 757 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU C 868 " --> pdb=" O ILE C 757 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA C 759 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N LYS C 876 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N GLY C 845 " --> pdb=" O LYS C 876 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.856A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 806 through 807 removed outlier: 3.541A pdb=" N ARG C 833 " --> pdb=" O THR C 807 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 944 through 945 Processing sheet with id=AD1, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD2, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.766A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1067 through 1068 Processing sheet with id=AD4, first strand: chain 'C' and resid 1133 through 1138 removed outlier: 3.664A pdb=" N ARG D 11 " --> pdb=" O GLU C1136 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 95 through 102 removed outlier: 11.024A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 327 through 330 Processing sheet with id=AD7, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD8, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AD9, first strand: chain 'D' and resid 897 through 900 Processing sheet with id=AE1, first strand: chain 'D' and resid 981 through 982 removed outlier: 3.868A pdb=" N LYS D 987 " --> pdb=" O SER D 982 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1075 through 1081 removed outlier: 5.467A pdb=" N VAL D1076 " --> pdb=" O ILE D1066 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE D1066 " --> pdb=" O VAL D1076 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASP D1078 " --> pdb=" O ILE D1064 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE D1064 " --> pdb=" O ASP D1078 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY D1051 " --> pdb=" O VAL D1105 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1088 through 1090 Processing sheet with id=AE4, first strand: chain 'D' and resid 1181 through 1182 removed outlier: 4.765A pdb=" N ARG D1164 " --> pdb=" O VAL D1206 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL D1206 " --> pdb=" O ARG D1164 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1271 through 1272 Processing sheet with id=AE6, first strand: chain 'M' and resid 8 through 11 1057 hydrogen bonds defined for protein. 2943 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 6.61 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 4449 1.27 - 1.41: 6448 1.41 - 1.55: 16331 1.55 - 1.69: 202 1.69 - 1.83: 157 Bond restraints: 27587 Sorted by residual: bond pdb=" N PRO F 160 " pdb=" CA PRO F 160 " ideal model delta sigma weight residual 1.466 1.697 -0.231 1.17e-02 7.31e+03 3.88e+02 bond pdb=" N PRO D 41 " pdb=" CA PRO D 41 " ideal model delta sigma weight residual 1.469 1.697 -0.228 1.28e-02 6.10e+03 3.17e+02 bond pdb=" N PRO M 82 " pdb=" CA PRO M 82 " ideal model delta sigma weight residual 1.469 1.685 -0.217 1.28e-02 6.10e+03 2.87e+02 bond pdb=" O3' DG H 9 " pdb=" P DT H 10 " ideal model delta sigma weight residual 1.607 1.406 0.201 1.50e-02 4.44e+03 1.80e+02 bond pdb=" C VAL F 166 " pdb=" N PRO F 167 " ideal model delta sigma weight residual 1.331 1.503 -0.173 1.31e-02 5.83e+03 1.74e+02 ... (remaining 27582 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.66: 37691 6.66 - 13.31: 102 13.31 - 19.97: 27 19.97 - 26.63: 4 26.63 - 33.28: 7 Bond angle restraints: 37831 Sorted by residual: angle pdb=" O THR D 33 " pdb=" C THR D 33 " pdb=" N ILE D 34 " ideal model delta sigma weight residual 122.19 91.33 30.86 1.18e+00 7.18e-01 6.84e+02 angle pdb=" CA THR D 33 " pdb=" C THR D 33 " pdb=" N ILE D 34 " ideal model delta sigma weight residual 117.34 148.24 -30.90 1.22e+00 6.72e-01 6.42e+02 angle pdb=" C ASN M 84 " pdb=" N TRP M 85 " pdb=" CA TRP M 85 " ideal model delta sigma weight residual 120.54 88.20 32.34 1.35e+00 5.49e-01 5.74e+02 angle pdb=" C THR D 33 " pdb=" N ILE D 34 " pdb=" CA ILE D 34 " ideal model delta sigma weight residual 121.95 151.55 -29.60 1.53e+00 4.27e-01 3.74e+02 angle pdb=" O ASN M 84 " pdb=" C ASN M 84 " pdb=" N TRP M 85 " ideal model delta sigma weight residual 122.59 147.17 -24.58 1.33e+00 5.65e-01 3.42e+02 ... (remaining 37826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.23: 15922 35.23 - 70.47: 644 70.47 - 105.70: 47 105.70 - 140.94: 3 140.94 - 176.17: 7 Dihedral angle restraints: 16623 sinusoidal: 7347 harmonic: 9276 Sorted by residual: dihedral pdb=" C LYS F 221 " pdb=" N LYS F 221 " pdb=" CA LYS F 221 " pdb=" CB LYS F 221 " ideal model delta harmonic sigma weight residual -122.60 -159.44 36.84 0 2.50e+00 1.60e-01 2.17e+02 dihedral pdb=" N LYS F 221 " pdb=" C LYS F 221 " pdb=" CA LYS F 221 " pdb=" CB LYS F 221 " ideal model delta harmonic sigma weight residual 122.80 157.01 -34.21 0 2.50e+00 1.60e-01 1.87e+02 dihedral pdb=" C LYS D 108 " pdb=" N LYS D 108 " pdb=" CA LYS D 108 " pdb=" CB LYS D 108 " ideal model delta harmonic sigma weight residual -122.60 -143.96 21.36 0 2.50e+00 1.60e-01 7.30e+01 ... (remaining 16620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.305: 4301 0.305 - 0.610: 24 0.610 - 0.915: 6 0.915 - 1.220: 1 1.220 - 1.525: 1 Chirality restraints: 4333 Sorted by residual: chirality pdb=" CA LYS F 221 " pdb=" N LYS F 221 " pdb=" C LYS F 221 " pdb=" CB LYS F 221 " both_signs ideal model delta sigma weight residual False 2.51 0.99 1.53 2.00e-01 2.50e+01 5.82e+01 chirality pdb=" C3' C I 5 " pdb=" C4' C I 5 " pdb=" O3' C I 5 " pdb=" C2' C I 5 " both_signs ideal model delta sigma weight residual False -2.48 -1.32 -1.15 2.00e-01 2.50e+01 3.33e+01 chirality pdb=" C1' DA G 18 " pdb=" O4' DA G 18 " pdb=" C2' DA G 18 " pdb=" N9 DA G 18 " both_signs ideal model delta sigma weight residual False 2.42 1.62 0.80 2.00e-01 2.50e+01 1.59e+01 ... (remaining 4330 not shown) Planarity restraints: 4634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG G 15 " 0.191 2.00e-02 2.50e+03 9.71e-02 2.83e+02 pdb=" N9 DG G 15 " -0.037 2.00e-02 2.50e+03 pdb=" C8 DG G 15 " -0.162 2.00e-02 2.50e+03 pdb=" N7 DG G 15 " -0.017 2.00e-02 2.50e+03 pdb=" C5 DG G 15 " 0.081 2.00e-02 2.50e+03 pdb=" C6 DG G 15 " 0.075 2.00e-02 2.50e+03 pdb=" O6 DG G 15 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DG G 15 " 0.061 2.00e-02 2.50e+03 pdb=" C2 DG G 15 " -0.074 2.00e-02 2.50e+03 pdb=" N2 DG G 15 " 0.020 2.00e-02 2.50e+03 pdb=" N3 DG G 15 " -0.162 2.00e-02 2.50e+03 pdb=" C4 DG G 15 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL M 58 " 0.059 2.00e-02 2.50e+03 1.16e-01 1.34e+02 pdb=" C VAL M 58 " -0.200 2.00e-02 2.50e+03 pdb=" O VAL M 58 " 0.077 2.00e-02 2.50e+03 pdb=" N ARG M 59 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU M 81 " 0.055 2.00e-02 2.50e+03 1.08e-01 1.17e+02 pdb=" C GLU M 81 " -0.187 2.00e-02 2.50e+03 pdb=" O GLU M 81 " 0.075 2.00e-02 2.50e+03 pdb=" N PRO M 82 " 0.057 2.00e-02 2.50e+03 ... (remaining 4631 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 103 2.39 - 3.02: 16136 3.02 - 3.65: 42471 3.65 - 4.27: 58841 4.27 - 4.90: 95880 Nonbonded interactions: 213431 Sorted by model distance: nonbonded pdb=" CB ASP D 535 " pdb="MG MG D1401 " model vdw 1.766 2.570 nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D1401 " model vdw 2.018 2.170 nonbonded pdb=" SG CYS D 60 " pdb=" SG CYS D 78 " model vdw 2.051 3.760 nonbonded pdb=" O LYS C1108 " pdb=" NZ LYS C1108 " model vdw 2.076 3.120 nonbonded pdb=" O LYS D 108 " pdb=" NZ LYS D 108 " model vdw 2.078 3.120 ... (remaining 213426 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 5 through 88 or (resid 89 through 91 and (name N or name C \ A or name C or name O or name CB )) or resid 92 through 130 or (resid 131 and (n \ ame N or name CA or name C or name O or name CB )) or resid 132 through 223)) selection = (chain 'B' and (resid 5 through 180 or (resid 181 through 182 and (name N or nam \ e CA or name C or name O or name CB )) or resid 187 through 223)) } 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: 2.210 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 31.570 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: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 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 : 0.007 0.231 27594 Z= 0.426 Angle : 1.199 33.285 37837 Z= 0.771 Chirality : 0.074 1.525 4333 Planarity : 0.007 0.116 4634 Dihedral : 17.733 176.172 10655 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.82 % Favored : 95.59 % Rotamer: Outliers : 1.90 % Allowed : 1.14 % Favored : 96.97 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.03 % 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: -0.12 (0.15), residues: 3218 helix: 0.77 (0.16), residues: 1159 sheet: -0.40 (0.29), residues: 331 loop : -0.54 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 231 TYR 0.051 0.002 TYR F 127 PHE 0.041 0.002 PHE F 144 TRP 0.032 0.002 TRP F 135 HIS 0.006 0.001 HIS F 178 Details of bonding type rmsd covalent geometry : bond 0.00705 (27587) covalent geometry : angle 1.19797 (37831) hydrogen bonds : bond 0.18158 ( 1087) hydrogen bonds : angle 7.18769 ( 3015) metal coordination : bond 0.03664 ( 7) metal coordination : angle 3.22142 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 271 time to evaluate : 1.031 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: C 809 LYS cc_start: 0.8586 (mttp) cc_final: 0.8378 (mmtt) REVERT: D 239 ASN cc_start: 0.9244 (t0) cc_final: 0.8974 (t0) REVERT: D 256 MET cc_start: 0.6064 (tpp) cc_final: 0.5752 (tpp) REVERT: D 312 MET cc_start: 0.9107 (tpp) cc_final: 0.8824 (mmm) REVERT: D 323 GLU cc_start: 0.8122 (tp30) cc_final: 0.7872 (tp30) REVERT: E 34 ILE cc_start: 0.9172 (mm) cc_final: 0.8923 (mm) REVERT: E 107 GLU cc_start: 0.8097 (pp20) cc_final: 0.7892 (tm-30) REVERT: M 11 TYR cc_start: 0.9523 (t80) cc_final: 0.9136 (t80) outliers start: 50 outliers final: 28 residues processed: 310 average time/residue: 0.2159 time to fit residues: 101.3461 Evaluate side-chains 204 residues out of total 2731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 1108 LYS Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 138 ARG Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 165 ARG Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 172 ASN Chi-restraints excluded: chain M residue 72 GLN Chi-restraints excluded: chain M residue 87 ARG Chi-restraints excluded: chain M residue 88 ARG Chi-restraints excluded: chain M residue 95 LYS Chi-restraints excluded: chain M residue 107 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 30.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN C1134 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 ASN E 68 ASN ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.062370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.044855 restraints weight = 132577.828| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 4.18 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27594 Z= 0.187 Angle : 0.686 11.305 37837 Z= 0.364 Chirality : 0.047 0.351 4333 Planarity : 0.005 0.093 4634 Dihedral : 18.698 171.179 4759 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.23 % Favored : 95.62 % Rotamer: Outliers : 1.48 % Allowed : 9.37 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.03 % 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: 0.07 (0.15), residues: 3218 helix: 0.96 (0.15), residues: 1192 sheet: -0.51 (0.27), residues: 359 loop : -0.44 (0.16), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 150 TYR 0.018 0.001 TYR M 55 PHE 0.017 0.001 PHE B 63 TRP 0.012 0.001 TRP D 105 HIS 0.008 0.001 HIS F 178 Details of bonding type rmsd covalent geometry : bond 0.00419 (27587) covalent geometry : angle 0.68563 (37831) hydrogen bonds : bond 0.05140 ( 1087) hydrogen bonds : angle 5.26246 ( 3015) metal coordination : bond 0.00751 ( 7) metal coordination : angle 2.19851 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 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: B 177 LYS cc_start: 0.8551 (tppt) cc_final: 0.8113 (tppt) REVERT: C 410 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8189 (tm-30) REVERT: C 809 LYS cc_start: 0.8665 (mttp) cc_final: 0.8436 (mmtt) REVERT: C 1108 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8773 (tptp) REVERT: D 92 MET cc_start: 0.9163 (mmm) cc_final: 0.8945 (mmm) REVERT: D 239 ASN cc_start: 0.9384 (t0) cc_final: 0.9107 (t0) REVERT: D 312 MET cc_start: 0.9334 (tpp) cc_final: 0.8867 (mmm) REVERT: D 323 GLU cc_start: 0.8574 (tp30) cc_final: 0.8373 (tp30) REVERT: D 515 MET cc_start: 0.8487 (ptp) cc_final: 0.8254 (ptp) REVERT: D 688 MET cc_start: 0.9167 (mmp) cc_final: 0.8952 (mmt) REVERT: E 69 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7698 (tm-30) REVERT: E 82 VAL cc_start: 0.8706 (t) cc_final: 0.8505 (m) outliers start: 39 outliers final: 23 residues processed: 210 average time/residue: 0.1831 time to fit residues: 61.0290 Evaluate side-chains 185 residues out of total 2731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 1108 LYS Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 223 TRP Chi-restraints excluded: chain D residue 241 TYR Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 783 ASP Chi-restraints excluded: chain E residue 67 TYR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 138 ARG Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 172 ASN Chi-restraints excluded: chain M residue 72 GLN Chi-restraints excluded: chain M residue 87 ARG Chi-restraints excluded: chain M residue 95 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 296 optimal weight: 8.9990 chunk 317 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 217 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 224 optimal weight: 3.9990 chunk 313 optimal weight: 7.9990 chunk 262 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1055 GLN ** D 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 854 HIS ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** 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 = 0.3385 r_free = 0.3385 target = 0.058414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.040601 restraints weight = 133480.139| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 4.22 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 27594 Z= 0.315 Angle : 0.755 15.181 37837 Z= 0.395 Chirality : 0.048 0.379 4333 Planarity : 0.006 0.096 4634 Dihedral : 18.470 173.956 4720 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.79 % Favored : 95.03 % Rotamer: Outliers : 2.50 % Allowed : 13.01 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.03 % 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: -0.09 (0.15), residues: 3218 helix: 0.79 (0.15), residues: 1207 sheet: -0.71 (0.27), residues: 376 loop : -0.47 (0.16), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 940 TYR 0.021 0.002 TYR D 749 PHE 0.021 0.002 PHE C 373 TRP 0.024 0.002 TRP D 223 HIS 0.007 0.002 HIS F 91 Details of bonding type rmsd covalent geometry : bond 0.00718 (27587) covalent geometry : angle 0.75376 (37831) hydrogen bonds : bond 0.05796 ( 1087) hydrogen bonds : angle 5.18367 ( 3015) metal coordination : bond 0.01244 ( 7) metal coordination : angle 3.17844 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 173 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.9063 (tmm) cc_final: 0.8672 (ppp) REVERT: C 127 MET cc_start: 0.8775 (pmm) cc_final: 0.8505 (pmm) REVERT: C 732 GLU cc_start: 0.8122 (tt0) cc_final: 0.7812 (tt0) REVERT: C 809 LYS cc_start: 0.8884 (mttp) cc_final: 0.8607 (mmtt) REVERT: D 92 MET cc_start: 0.8985 (mmm) cc_final: 0.8779 (mmm) REVERT: D 105 TRP cc_start: 0.9444 (OUTLIER) cc_final: 0.8498 (t60) REVERT: D 106 TYR cc_start: 0.8877 (m-80) cc_final: 0.8676 (m-80) REVERT: D 239 ASN cc_start: 0.9514 (t0) cc_final: 0.9244 (t0) REVERT: D 323 GLU cc_start: 0.8830 (tp30) cc_final: 0.8477 (tp30) REVERT: D 515 MET cc_start: 0.8589 (ptp) cc_final: 0.8258 (ptp) REVERT: D 541 MET cc_start: 0.8618 (mtp) cc_final: 0.7896 (mtp) REVERT: D 820 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8584 (ppp) REVERT: D 1035 PHE cc_start: 0.9414 (OUTLIER) cc_final: 0.8790 (t80) REVERT: E 40 ASP cc_start: 0.8465 (m-30) cc_final: 0.8262 (m-30) REVERT: E 42 LEU cc_start: 0.9282 (mt) cc_final: 0.8837 (mm) REVERT: E 61 ARG cc_start: 0.8654 (mmt-90) cc_final: 0.8326 (mmt-90) REVERT: E 69 GLN cc_start: 0.7716 (tm-30) cc_final: 0.7465 (tm-30) REVERT: E 89 LYS cc_start: 0.8944 (mmtp) cc_final: 0.8679 (mmtp) REVERT: E 105 HIS cc_start: 0.9191 (p90) cc_final: 0.8770 (p90) REVERT: F 138 ARG cc_start: 0.9589 (OUTLIER) cc_final: 0.9326 (tpp80) REVERT: F 172 ASN cc_start: 0.8209 (t0) cc_final: 0.7990 (t0) outliers start: 66 outliers final: 34 residues processed: 224 average time/residue: 0.1738 time to fit residues: 62.3218 Evaluate side-chains 198 residues out of total 2731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 223 TRP Chi-restraints excluded: chain D residue 241 TYR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 783 ASP Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1035 PHE Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain E residue 67 TYR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 138 ARG Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 72 GLN Chi-restraints excluded: chain M residue 95 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 253 optimal weight: 9.9990 chunk 229 optimal weight: 6.9990 chunk 245 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 238 optimal weight: 7.9990 chunk 301 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 237 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 278 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1055 GLN ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 ASN E 68 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.058732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.040926 restraints weight = 131949.973| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 4.23 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 27594 Z= 0.207 Angle : 0.646 11.068 37837 Z= 0.340 Chirality : 0.045 0.300 4333 Planarity : 0.005 0.080 4634 Dihedral : 18.294 171.948 4705 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.88 % Favored : 95.99 % Rotamer: Outliers : 2.81 % Allowed : 15.02 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.03 % 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: 0.14 (0.15), residues: 3218 helix: 1.05 (0.15), residues: 1204 sheet: -0.59 (0.27), residues: 373 loop : -0.40 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 334 TYR 0.022 0.001 TYR F 177 PHE 0.012 0.001 PHE B 63 TRP 0.020 0.002 TRP D 223 HIS 0.006 0.001 HIS F 178 Details of bonding type rmsd covalent geometry : bond 0.00475 (27587) covalent geometry : angle 0.64539 (37831) hydrogen bonds : bond 0.04625 ( 1087) hydrogen bonds : angle 4.90426 ( 3015) metal coordination : bond 0.00766 ( 7) metal coordination : angle 2.63797 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 171 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.9072 (tmm) cc_final: 0.8714 (ppp) REVERT: C 127 MET cc_start: 0.8744 (pmm) cc_final: 0.8381 (pmm) REVERT: C 214 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8315 (m-80) REVERT: C 580 ASP cc_start: 0.7997 (t0) cc_final: 0.7759 (t0) REVERT: C 732 GLU cc_start: 0.8116 (tt0) cc_final: 0.7778 (tt0) REVERT: C 809 LYS cc_start: 0.8815 (mttp) cc_final: 0.8543 (mmtt) REVERT: C 1072 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8482 (mp0) REVERT: D 105 TRP cc_start: 0.9373 (OUTLIER) cc_final: 0.8779 (t60) REVERT: D 106 TYR cc_start: 0.8892 (m-80) cc_final: 0.8658 (m-80) REVERT: D 239 ASN cc_start: 0.9490 (t0) cc_final: 0.9260 (t0) REVERT: D 323 GLU cc_start: 0.8720 (tp30) cc_final: 0.8271 (tp30) REVERT: D 343 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9096 (mm) REVERT: D 541 MET cc_start: 0.8682 (mtp) cc_final: 0.7799 (mtp) REVERT: D 820 MET cc_start: 0.8806 (ptt) cc_final: 0.8558 (ppp) REVERT: D 1035 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.8666 (t80) REVERT: E 61 ARG cc_start: 0.8708 (mmt-90) cc_final: 0.8350 (mmt-90) REVERT: E 88 GLU cc_start: 0.8217 (pp20) cc_final: 0.7853 (pp20) REVERT: E 89 LYS cc_start: 0.8901 (mmtp) cc_final: 0.8438 (mmtm) REVERT: E 105 HIS cc_start: 0.9192 (p90) cc_final: 0.8798 (p90) REVERT: E 107 GLU cc_start: 0.8204 (pm20) cc_final: 0.7999 (pp20) REVERT: F 153 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8816 (ttm110) outliers start: 74 outliers final: 32 residues processed: 233 average time/residue: 0.1644 time to fit residues: 62.7668 Evaluate side-chains 201 residues out of total 2731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 223 TRP Chi-restraints excluded: chain D residue 241 TYR Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 783 ASP Chi-restraints excluded: chain D residue 1035 PHE Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 95 LYS Chi-restraints excluded: chain M residue 102 ASN Chi-restraints excluded: chain M residue 146 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 94 optimal weight: 0.3980 chunk 274 optimal weight: 7.9990 chunk 191 optimal weight: 0.0870 chunk 55 optimal weight: 9.9990 chunk 302 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 307 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 318 optimal weight: 0.0970 chunk 110 optimal weight: 9.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN C1077 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.059981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.042459 restraints weight = 130113.620| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 4.16 r_work: 0.2694 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27594 Z= 0.123 Angle : 0.602 10.528 37837 Z= 0.314 Chirality : 0.043 0.266 4333 Planarity : 0.004 0.070 4634 Dihedral : 18.095 172.873 4698 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.67 % Favored : 96.18 % Rotamer: Outliers : 2.09 % Allowed : 16.12 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.03 % 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: 0.33 (0.15), residues: 3218 helix: 1.12 (0.15), residues: 1224 sheet: -0.29 (0.29), residues: 343 loop : -0.28 (0.16), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 334 TYR 0.032 0.001 TYR E 55 PHE 0.015 0.001 PHE C 153 TRP 0.021 0.001 TRP D 223 HIS 0.004 0.001 HIS F 178 Details of bonding type rmsd covalent geometry : bond 0.00272 (27587) covalent geometry : angle 0.60106 (37831) hydrogen bonds : bond 0.03863 ( 1087) hydrogen bonds : angle 4.65709 ( 3015) metal coordination : bond 0.00339 ( 7) metal coordination : angle 2.36403 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 172 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.9290 (tmm) cc_final: 0.8751 (ppp) REVERT: A 213 LYS cc_start: 0.9453 (OUTLIER) cc_final: 0.9198 (ttmt) REVERT: C 214 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8508 (m-80) REVERT: C 580 ASP cc_start: 0.8641 (t0) cc_final: 0.8316 (t0) REVERT: C 732 GLU cc_start: 0.8594 (tt0) cc_final: 0.8280 (tt0) REVERT: C 809 LYS cc_start: 0.8845 (mttp) cc_final: 0.8584 (mmtt) REVERT: D 27 GLU cc_start: 0.8731 (pp20) cc_final: 0.8156 (pp20) REVERT: D 92 MET cc_start: 0.9187 (mmm) cc_final: 0.8901 (mmm) REVERT: D 105 TRP cc_start: 0.9352 (OUTLIER) cc_final: 0.8887 (t60) REVERT: D 106 TYR cc_start: 0.9120 (m-80) cc_final: 0.8876 (m-80) REVERT: D 256 MET cc_start: 0.6826 (tpp) cc_final: 0.6578 (tpp) REVERT: D 323 GLU cc_start: 0.9108 (tp30) cc_final: 0.8677 (tp30) REVERT: D 576 MET cc_start: 0.9319 (ttm) cc_final: 0.9072 (mtp) REVERT: D 693 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8080 (mp10) REVERT: D 1035 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8456 (t80) REVERT: E 61 ARG cc_start: 0.8603 (mmt-90) cc_final: 0.8176 (mmt-90) REVERT: E 88 GLU cc_start: 0.8031 (pp20) cc_final: 0.7696 (pp20) REVERT: E 89 LYS cc_start: 0.8808 (mmtp) cc_final: 0.8350 (mmtp) REVERT: F 133 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8739 (pm20) outliers start: 55 outliers final: 26 residues processed: 220 average time/residue: 0.1639 time to fit residues: 59.8196 Evaluate side-chains 202 residues out of total 2731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 755 HIS Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 223 TRP Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 783 ASP Chi-restraints excluded: chain D residue 1035 PHE Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 95 LYS Chi-restraints excluded: chain M residue 146 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 312 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 310 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 chunk 143 optimal weight: 8.9990 chunk 324 optimal weight: 20.0000 chunk 125 optimal weight: 8.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 826 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 = 0.3369 r_free = 0.3369 target = 0.057831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.040124 restraints weight = 132246.425| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 4.20 r_work: 0.2598 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 27594 Z= 0.258 Angle : 0.675 9.052 37837 Z= 0.350 Chirality : 0.045 0.330 4333 Planarity : 0.005 0.068 4634 Dihedral : 18.057 171.321 4695 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.35 % Favored : 95.53 % Rotamer: Outliers : 2.96 % Allowed : 16.27 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 3218 helix: 1.12 (0.15), residues: 1216 sheet: -0.48 (0.27), residues: 381 loop : -0.34 (0.16), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 940 TYR 0.021 0.002 TYR E 55 PHE 0.014 0.002 PHE C 214 TRP 0.018 0.002 TRP D 223 HIS 0.005 0.001 HIS F 178 Details of bonding type rmsd covalent geometry : bond 0.00593 (27587) covalent geometry : angle 0.67419 (37831) hydrogen bonds : bond 0.04872 ( 1087) hydrogen bonds : angle 4.79654 ( 3015) metal coordination : bond 0.00985 ( 7) metal coordination : angle 2.17754 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 169 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: A 213 LYS cc_start: 0.9441 (OUTLIER) cc_final: 0.9202 (ttmt) REVERT: C 214 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8588 (m-80) REVERT: C 580 ASP cc_start: 0.8707 (t0) cc_final: 0.8339 (t0) REVERT: C 614 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.8983 (mt0) REVERT: C 732 GLU cc_start: 0.8609 (tt0) cc_final: 0.8274 (tt0) REVERT: C 809 LYS cc_start: 0.8999 (mttp) cc_final: 0.8715 (mmtt) REVERT: C 1072 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8728 (mp0) REVERT: D 105 TRP cc_start: 0.9487 (OUTLIER) cc_final: 0.8465 (t60) REVERT: D 106 TYR cc_start: 0.9236 (m-80) cc_final: 0.8930 (m-80) REVERT: D 205 MET cc_start: 0.8955 (tmm) cc_final: 0.8486 (ppp) REVERT: D 256 MET cc_start: 0.7156 (tpp) cc_final: 0.6679 (tpp) REVERT: D 323 GLU cc_start: 0.9214 (tp30) cc_final: 0.8893 (tp30) REVERT: D 576 MET cc_start: 0.9386 (ttm) cc_final: 0.9162 (mtp) REVERT: D 693 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8562 (mp10) REVERT: D 1035 PHE cc_start: 0.9470 (OUTLIER) cc_final: 0.8730 (t80) REVERT: E 28 TYR cc_start: 0.8357 (p90) cc_final: 0.7724 (p90) REVERT: E 89 LYS cc_start: 0.8793 (mmtp) cc_final: 0.8332 (mmtm) outliers start: 78 outliers final: 42 residues processed: 235 average time/residue: 0.1529 time to fit residues: 60.7987 Evaluate side-chains 213 residues out of total 2731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 755 HIS Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 223 TRP Chi-restraints excluded: chain D residue 241 TYR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 783 ASP Chi-restraints excluded: chain D residue 1035 PHE Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 95 LYS Chi-restraints excluded: chain M residue 102 ASN Chi-restraints excluded: chain M residue 146 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 94 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 301 optimal weight: 6.9990 chunk 195 optimal weight: 8.9990 chunk 196 optimal weight: 0.9990 chunk 209 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 263 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.057691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.039990 restraints weight = 131261.364| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 4.20 r_work: 0.2596 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- 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 = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 27594 Z= 0.228 Angle : 0.663 12.142 37837 Z= 0.344 Chirality : 0.045 0.312 4333 Planarity : 0.004 0.070 4634 Dihedral : 18.037 172.345 4692 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.26 % Favored : 95.65 % Rotamer: Outliers : 2.58 % Allowed : 17.64 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.03 % 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: 0.25 (0.15), residues: 3218 helix: 1.17 (0.15), residues: 1215 sheet: -0.47 (0.27), residues: 389 loop : -0.39 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 45 TYR 0.022 0.001 TYR E 55 PHE 0.013 0.001 PHE F 121 TRP 0.018 0.002 TRP D 223 HIS 0.006 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00525 (27587) covalent geometry : angle 0.66257 (37831) hydrogen bonds : bond 0.04496 ( 1087) hydrogen bonds : angle 4.75806 ( 3015) metal coordination : bond 0.00829 ( 7) metal coordination : angle 2.48821 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 165 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9201 (ttmt) REVERT: C 214 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8577 (m-80) REVERT: C 410 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8206 (tm-30) REVERT: C 580 ASP cc_start: 0.8747 (t0) cc_final: 0.8360 (t0) REVERT: C 614 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8951 (mt0) REVERT: C 732 GLU cc_start: 0.8640 (tt0) cc_final: 0.8338 (tt0) REVERT: C 797 ARG cc_start: 0.9273 (ttp-110) cc_final: 0.9052 (ptp-110) REVERT: C 809 LYS cc_start: 0.8988 (mttp) cc_final: 0.8700 (mmtt) REVERT: C 1072 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8739 (mp0) REVERT: D 105 TRP cc_start: 0.9458 (OUTLIER) cc_final: 0.8583 (t60) REVERT: D 323 GLU cc_start: 0.9213 (tp30) cc_final: 0.8711 (tp30) REVERT: D 576 MET cc_start: 0.9380 (ttm) cc_final: 0.9160 (mtp) REVERT: D 688 MET cc_start: 0.9477 (mmm) cc_final: 0.9063 (mmm) REVERT: D 693 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8412 (mp10) REVERT: D 1035 PHE cc_start: 0.9438 (OUTLIER) cc_final: 0.8608 (t80) REVERT: D 1208 MET cc_start: 0.9043 (ppp) cc_final: 0.8529 (ppp) REVERT: E 28 TYR cc_start: 0.8422 (p90) cc_final: 0.7652 (p90) REVERT: E 61 ARG cc_start: 0.8603 (mmt-90) cc_final: 0.8375 (mmt-90) REVERT: E 107 GLU cc_start: 0.6671 (pp20) cc_final: 0.6350 (tm-30) REVERT: F 153 ARG cc_start: 0.9263 (OUTLIER) cc_final: 0.8906 (ttm110) outliers start: 68 outliers final: 43 residues processed: 225 average time/residue: 0.1593 time to fit residues: 58.9457 Evaluate side-chains 214 residues out of total 2731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 755 HIS Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 223 TRP Chi-restraints excluded: chain D residue 241 TYR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 783 ASP Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 1035 PHE Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 95 LYS Chi-restraints excluded: chain M residue 146 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 44 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 321 optimal weight: 1.9990 chunk 158 optimal weight: 0.0670 chunk 136 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 239 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 overall best weight: 1.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.058959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.041287 restraints weight = 131439.118| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 4.25 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27594 Z= 0.129 Angle : 0.610 10.235 37837 Z= 0.316 Chirality : 0.043 0.294 4333 Planarity : 0.004 0.064 4634 Dihedral : 17.953 173.238 4692 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.33 % Rotamer: Outliers : 2.35 % Allowed : 17.72 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.03 % 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: 0.42 (0.15), residues: 3218 helix: 1.31 (0.15), residues: 1223 sheet: -0.33 (0.28), residues: 365 loop : -0.31 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 45 TYR 0.021 0.001 TYR E 66 PHE 0.014 0.001 PHE C 153 TRP 0.016 0.001 TRP D 223 HIS 0.005 0.001 HIS F 178 Details of bonding type rmsd covalent geometry : bond 0.00289 (27587) covalent geometry : angle 0.60944 (37831) hydrogen bonds : bond 0.03816 ( 1087) hydrogen bonds : angle 4.55712 ( 3015) metal coordination : bond 0.00360 ( 7) metal coordination : angle 2.31056 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 172 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.9051 (tmm) cc_final: 0.8573 (ppp) REVERT: A 213 LYS cc_start: 0.9410 (OUTLIER) cc_final: 0.9161 (ttmt) REVERT: C 214 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8269 (m-80) REVERT: C 355 MET cc_start: 0.8662 (ppp) cc_final: 0.8270 (ppp) REVERT: C 410 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: C 580 ASP cc_start: 0.8157 (t0) cc_final: 0.7704 (t0) REVERT: C 614 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8539 (mt0) REVERT: C 732 GLU cc_start: 0.8022 (tt0) cc_final: 0.7672 (tt0) REVERT: C 809 LYS cc_start: 0.8831 (mttp) cc_final: 0.8524 (mmtt) REVERT: C 1072 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8477 (mp0) REVERT: D 27 GLU cc_start: 0.8276 (pp20) cc_final: 0.7760 (pp20) REVERT: D 105 TRP cc_start: 0.9290 (OUTLIER) cc_final: 0.8752 (t60) REVERT: D 205 MET cc_start: 0.8828 (tmm) cc_final: 0.8432 (ppp) REVERT: D 256 MET cc_start: 0.6331 (tpp) cc_final: 0.5921 (tpp) REVERT: D 312 MET cc_start: 0.9410 (tpp) cc_final: 0.9019 (mmt) REVERT: D 1035 PHE cc_start: 0.9340 (OUTLIER) cc_final: 0.8414 (t80) REVERT: D 1208 MET cc_start: 0.8654 (ppp) cc_final: 0.8125 (ppp) REVERT: E 28 TYR cc_start: 0.8481 (p90) cc_final: 0.7714 (p90) REVERT: E 89 LYS cc_start: 0.8742 (mmtp) cc_final: 0.8341 (mmtm) REVERT: E 107 GLU cc_start: 0.6724 (pp20) cc_final: 0.6455 (tm-30) REVERT: F 78 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.8746 (tppt) outliers start: 62 outliers final: 39 residues processed: 225 average time/residue: 0.1681 time to fit residues: 61.5252 Evaluate side-chains 209 residues out of total 2731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 755 HIS Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 223 TRP Chi-restraints excluded: chain D residue 241 TYR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 1035 PHE Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 95 LYS Chi-restraints excluded: chain M residue 146 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 228 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 319 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 302 optimal weight: 20.0000 chunk 262 optimal weight: 30.0000 chunk 132 optimal weight: 8.9990 chunk 241 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN ** D 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.057690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.040003 restraints weight = 132194.900| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 4.22 r_work: 0.2597 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- 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 = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 27594 Z= 0.215 Angle : 0.656 13.242 37837 Z= 0.338 Chirality : 0.044 0.332 4333 Planarity : 0.004 0.077 4634 Dihedral : 17.949 172.793 4690 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 2.28 % Allowed : 17.91 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.03 % 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: 0.36 (0.15), residues: 3218 helix: 1.31 (0.15), residues: 1212 sheet: -0.39 (0.27), residues: 391 loop : -0.36 (0.16), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 467 TYR 0.022 0.001 TYR E 66 PHE 0.012 0.001 PHE F 121 TRP 0.016 0.001 TRP D 223 HIS 0.006 0.001 HIS F 178 Details of bonding type rmsd covalent geometry : bond 0.00494 (27587) covalent geometry : angle 0.65530 (37831) hydrogen bonds : bond 0.04430 ( 1087) hydrogen bonds : angle 4.67216 ( 3015) metal coordination : bond 0.00767 ( 7) metal coordination : angle 2.21731 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 161 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LYS cc_start: 0.9454 (OUTLIER) cc_final: 0.9249 (ttmt) REVERT: C 214 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8570 (m-80) REVERT: C 355 MET cc_start: 0.8738 (ppp) cc_final: 0.8343 (ppp) REVERT: C 580 ASP cc_start: 0.8765 (t0) cc_final: 0.8368 (t0) REVERT: C 614 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8954 (mt0) REVERT: C 732 GLU cc_start: 0.8568 (tt0) cc_final: 0.8258 (tt0) REVERT: C 809 LYS cc_start: 0.9038 (mttp) cc_final: 0.8731 (mmtt) REVERT: C 1072 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8745 (mp0) REVERT: D 105 TRP cc_start: 0.9463 (OUTLIER) cc_final: 0.8352 (t60) REVERT: D 205 MET cc_start: 0.8852 (tmm) cc_final: 0.8535 (ppp) REVERT: D 256 MET cc_start: 0.6902 (tpp) cc_final: 0.6478 (tpp) REVERT: D 688 MET cc_start: 0.9544 (mmm) cc_final: 0.9155 (mmm) REVERT: D 1035 PHE cc_start: 0.9423 (OUTLIER) cc_final: 0.8667 (t80) REVERT: D 1208 MET cc_start: 0.9045 (ppp) cc_final: 0.8597 (ppp) REVERT: E 28 TYR cc_start: 0.8482 (p90) cc_final: 0.7976 (p90) REVERT: E 107 GLU cc_start: 0.6626 (pp20) cc_final: 0.6366 (tm-30) REVERT: F 153 ARG cc_start: 0.9263 (OUTLIER) cc_final: 0.8913 (ttm110) outliers start: 60 outliers final: 48 residues processed: 214 average time/residue: 0.1607 time to fit residues: 56.3840 Evaluate side-chains 215 residues out of total 2731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 160 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 755 HIS Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 223 TRP Chi-restraints excluded: chain D residue 241 TYR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 1035 PHE Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 95 LYS Chi-restraints excluded: chain M residue 146 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 291 optimal weight: 5.9990 chunk 277 optimal weight: 5.9990 chunk 286 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 293 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 232 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 chunk 262 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 826 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 = 0.3387 r_free = 0.3387 target = 0.057506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.040040 restraints weight = 130791.743| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 4.06 r_work: 0.2628 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 27594 Z= 0.237 Angle : 0.676 9.466 37837 Z= 0.350 Chirality : 0.045 0.314 4333 Planarity : 0.005 0.130 4634 Dihedral : 18.002 174.716 4690 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.66 % Favored : 95.25 % Rotamer: Outliers : 2.16 % Allowed : 18.10 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 3218 helix: 1.20 (0.15), residues: 1220 sheet: -0.33 (0.28), residues: 367 loop : -0.47 (0.16), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 153 TYR 0.023 0.002 TYR F 177 PHE 0.016 0.002 PHE F 121 TRP 0.018 0.002 TRP D 105 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00544 (27587) covalent geometry : angle 0.67555 (37831) hydrogen bonds : bond 0.04639 ( 1087) hydrogen bonds : angle 4.77610 ( 3015) metal coordination : bond 0.00893 ( 7) metal coordination : angle 2.48438 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 160 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LYS cc_start: 0.9477 (OUTLIER) cc_final: 0.9223 (ttmt) REVERT: C 214 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8614 (m-80) REVERT: C 355 MET cc_start: 0.8631 (ppp) cc_final: 0.8337 (ppp) REVERT: C 580 ASP cc_start: 0.8782 (t0) cc_final: 0.8456 (t0) REVERT: C 614 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.8964 (mt0) REVERT: C 732 GLU cc_start: 0.8517 (tt0) cc_final: 0.8254 (tt0) REVERT: C 809 LYS cc_start: 0.9034 (mttp) cc_final: 0.8701 (mmtt) REVERT: C 1072 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8744 (mp0) REVERT: D 105 TRP cc_start: 0.9444 (OUTLIER) cc_final: 0.8329 (t60) REVERT: D 205 MET cc_start: 0.8871 (tmm) cc_final: 0.8558 (ppp) REVERT: D 256 MET cc_start: 0.6904 (tpp) cc_final: 0.6454 (tpp) REVERT: D 688 MET cc_start: 0.9496 (mmm) cc_final: 0.9121 (mmm) REVERT: D 1035 PHE cc_start: 0.9411 (OUTLIER) cc_final: 0.8619 (t80) REVERT: D 1208 MET cc_start: 0.9086 (ppp) cc_final: 0.8427 (ppp) REVERT: E 28 TYR cc_start: 0.8573 (p90) cc_final: 0.8066 (p90) REVERT: E 107 GLU cc_start: 0.6606 (pp20) cc_final: 0.6368 (tm-30) REVERT: F 153 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.8914 (ttm110) outliers start: 57 outliers final: 47 residues processed: 212 average time/residue: 0.1713 time to fit residues: 59.2876 Evaluate side-chains 212 residues out of total 2731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 158 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 755 HIS Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 223 TRP Chi-restraints excluded: chain D residue 241 TYR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 1035 PHE Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 95 LYS Chi-restraints excluded: chain M residue 146 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 144 optimal weight: 1.9990 chunk 96 optimal weight: 0.0040 chunk 131 optimal weight: 8.9990 chunk 155 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 167 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 257 optimal weight: 1.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.059418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.041635 restraints weight = 131016.723| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 4.17 r_work: 0.2699 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27594 Z= 0.120 Angle : 0.624 14.297 37837 Z= 0.320 Chirality : 0.043 0.298 4333 Planarity : 0.004 0.068 4634 Dihedral : 17.861 175.456 4690 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.23 % Favored : 96.67 % Rotamer: Outliers : 1.86 % Allowed : 18.59 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.40 (0.15), residues: 3218 helix: 1.30 (0.15), residues: 1231 sheet: -0.18 (0.28), residues: 351 loop : -0.38 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 153 TYR 0.023 0.001 TYR E 66 PHE 0.013 0.001 PHE C 153 TRP 0.015 0.001 TRP D 58 HIS 0.005 0.001 HIS F 178 Details of bonding type rmsd covalent geometry : bond 0.00268 (27587) covalent geometry : angle 0.62343 (37831) hydrogen bonds : bond 0.03658 ( 1087) hydrogen bonds : angle 4.53431 ( 3015) metal coordination : bond 0.00267 ( 7) metal coordination : angle 2.43193 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5564.85 seconds wall clock time: 96 minutes 11.39 seconds (5771.39 seconds total)