Starting phenix.real_space_refine on Tue Mar 19 21:10:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej3_28174/03_2024/8ej3_28174_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej3_28174/03_2024/8ej3_28174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej3_28174/03_2024/8ej3_28174.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej3_28174/03_2024/8ej3_28174.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej3_28174/03_2024/8ej3_28174_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej3_28174/03_2024/8ej3_28174_updated.pdb" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.072 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 81 5.49 5 Mg 2 5.21 5 S 89 5.16 5 C 15625 2.51 5 N 4495 2.21 5 O 5045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25339 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1765 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 8672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8672 Classifications: {'peptide': 1121} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1059} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 10010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1281, 10010 Classifications: {'peptide': 1281} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1220} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "G" Number of atoms: 878 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 110, 869 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Conformer: "B" Number of residues, atoms: 110, 869 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} bond proxies already assigned to first conformer: 877 Chain: "N" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 587 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain breaks: 1 Chain: "R" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 369 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 13} Chain: "T" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 649 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19212 SG CYS D 891 76.582 24.483 87.400 1.00 75.64 S ATOM 19779 SG CYS D 968 75.365 27.766 88.957 1.00 66.53 S ATOM 19821 SG CYS D 975 76.805 27.695 85.403 1.00 56.94 S ATOM 19839 SG CYS D 978 73.436 26.161 86.115 1.00 62.19 S ATOM 12668 SG CYS D 62 109.935 82.237 117.046 1.00151.09 S ATOM 12777 SG CYS D 75 110.795 79.173 118.788 1.00146.09 S ATOM 12803 SG CYS D 78 107.470 80.969 119.174 1.00145.63 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLU G 15 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU G 15 " occ=0.50 Time building chain proxies: 13.94, per 1000 atoms: 0.55 Number of scatterers: 25339 At special positions: 0 Unit cell: (125.28, 133.11, 200.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 89 16.00 P 81 15.00 Mg 2 11.99 O 5045 8.00 N 4495 7.00 C 15625 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 - 3.50 Amino acid : False - 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: 9.42 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 968 " pdb=" ZN D2004 " pdb="ZN ZN D2004 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2004 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2004 " - pdb=" SG CYS D 78 " Number of angles added : 6 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5612 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 27 sheets defined 31.1% alpha, 10.8% beta 29 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 12.15 Creating SS restraints... Processing helix chain 'A' and resid 32 through 42 Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 206 through 218 removed outlier: 3.763A pdb=" N SER A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'B' and resid 35 through 43 Processing helix chain 'B' and resid 74 through 80 Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 204 through 207 No H-bonds generated for 'chain 'B' and resid 204 through 207' Processing helix chain 'B' and resid 213 through 216 No H-bonds generated for 'chain 'B' and resid 213 through 216' Processing helix chain 'C' and resid 55 through 65 removed outlier: 4.262A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 87 through 93 Processing helix chain 'C' and resid 119 through 125 Processing helix chain 'C' and resid 226 through 228 No H-bonds generated for 'chain 'C' and resid 226 through 228' Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'C' and resid 245 through 251 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 310 through 316 Processing helix chain 'C' and resid 335 through 350 removed outlier: 3.665A pdb=" N ILE C 342 " --> pdb=" O VAL C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 405 removed outlier: 3.780A pdb=" N GLN C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 398 " --> pdb=" O SER C 394 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL C 399 " --> pdb=" O ARG C 395 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 417 No H-bonds generated for 'chain 'C' and resid 414 through 417' Processing helix chain 'C' and resid 421 through 431 Processing helix chain 'C' and resid 445 through 451 Processing helix chain 'C' and resid 477 through 479 No H-bonds generated for 'chain 'C' and resid 477 through 479' Processing helix chain 'C' and resid 533 through 538 removed outlier: 4.288A pdb=" N ARG C 538 " --> pdb=" O ASP C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 593 No H-bonds generated for 'chain 'C' and resid 591 through 593' Processing helix chain 'C' and resid 597 through 599 No H-bonds generated for 'chain 'C' and resid 597 through 599' Processing helix chain 'C' and resid 602 through 614 removed outlier: 4.385A pdb=" N ARG C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLN C 614 " --> pdb=" O ASN C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 636 No H-bonds generated for 'chain 'C' and resid 633 through 636' Processing helix chain 'C' and resid 740 through 743 No H-bonds generated for 'chain 'C' and resid 740 through 743' Processing helix chain 'C' and resid 901 through 903 No H-bonds generated for 'chain 'C' and resid 901 through 903' Processing helix chain 'C' and resid 929 through 942 Processing helix chain 'C' and resid 954 through 956 No H-bonds generated for 'chain 'C' and resid 954 through 956' Processing helix chain 'C' and resid 982 through 990 removed outlier: 3.901A pdb=" N SER C 990 " --> pdb=" O GLN C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1037 through 1039 No H-bonds generated for 'chain 'C' and resid 1037 through 1039' Processing helix chain 'C' and resid 1070 through 1079 Processing helix chain 'C' and resid 1082 through 1089 Processing helix chain 'C' and resid 1096 through 1108 removed outlier: 4.654A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1120 through 1130 Processing helix chain 'D' and resid 4 through 6 No H-bonds generated for 'chain 'D' and resid 4 through 6' Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 49 through 52 No H-bonds generated for 'chain 'D' and resid 49 through 52' Processing helix chain 'D' and resid 68 through 70 No H-bonds generated for 'chain 'D' and resid 68 through 70' Processing helix chain 'D' and resid 86 through 89 removed outlier: 3.609A pdb=" N ARG D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 86 through 89' Processing helix chain 'D' and resid 115 through 118 No H-bonds generated for 'chain 'D' and resid 115 through 118' Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 141 through 184 removed outlier: 3.565A pdb=" N LEU D 148 " --> pdb=" O ARG D 144 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA D 161 " --> pdb=" O VAL D 157 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU D 163 " --> pdb=" O ARG D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 228 removed outlier: 4.324A pdb=" N LYS D 196 " --> pdb=" O ASP D 192 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY D 201 " --> pdb=" O VAL D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 247 Processing helix chain 'D' and resid 258 through 266 Processing helix chain 'D' and resid 270 through 282 Processing helix chain 'D' and resid 287 through 304 removed outlier: 3.861A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 340 through 360 removed outlier: 3.706A pdb=" N TYR D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG D 345 " --> pdb=" O ASN D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 382 Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 412 through 415 No H-bonds generated for 'chain 'D' and resid 412 through 415' Processing helix chain 'D' and resid 445 through 451 Processing helix chain 'D' and resid 453 through 462 Processing helix chain 'D' and resid 469 through 477 Processing helix chain 'D' and resid 481 through 490 removed outlier: 3.650A pdb=" N ASP D 485 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU D 487 " --> pdb=" O TRP D 484 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU D 488 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 508 No H-bonds generated for 'chain 'D' and resid 506 through 508' Processing helix chain 'D' and resid 526 through 528 No H-bonds generated for 'chain 'D' and resid 526 through 528' Processing helix chain 'D' and resid 549 through 557 Processing helix chain 'D' and resid 580 through 588 Processing helix chain 'D' and resid 615 through 624 removed outlier: 3.527A pdb=" N ARG D 624 " --> pdb=" O MET D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 644 through 650 Processing helix chain 'D' and resid 657 through 659 No H-bonds generated for 'chain 'D' and resid 657 through 659' Processing helix chain 'D' and resid 668 through 676 removed outlier: 4.054A pdb=" N LEU D 676 " --> pdb=" O MET D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 703 Processing helix chain 'D' and resid 706 through 727 removed outlier: 3.958A pdb=" N ASP D 714 " --> pdb=" O ALA D 710 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 762 removed outlier: 3.767A pdb=" N LYS D 755 " --> pdb=" O GLU D 751 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL D 756 " --> pdb=" O ARG D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 792 removed outlier: 3.621A pdb=" N GLU D 776 " --> pdb=" O GLU D 772 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP D 783 " --> pdb=" O LYS D 779 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU D 791 " --> pdb=" O GLN D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 804 removed outlier: 3.637A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 818 Processing helix chain 'D' and resid 846 through 850 Processing helix chain 'D' and resid 854 through 857 No H-bonds generated for 'chain 'D' and resid 854 through 857' Processing helix chain 'D' and resid 868 through 880 removed outlier: 3.696A pdb=" N LEU D 873 " --> pdb=" O ASP D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 955 Processing helix chain 'D' and resid 965 through 967 No H-bonds generated for 'chain 'D' and resid 965 through 967' Processing helix chain 'D' and resid 976 through 979 No H-bonds generated for 'chain 'D' and resid 976 through 979' Processing helix chain 'D' and resid 995 through 1012 Proline residue: D1006 - end of helix Processing helix chain 'D' and resid 1024 through 1036 Proline residue: D1029 - end of helix Processing helix chain 'D' and resid 1118 through 1124 Processing helix chain 'D' and resid 1127 through 1144 removed outlier: 3.871A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1161 removed outlier: 3.749A pdb=" N GLU D1155 " --> pdb=" O LYS D1152 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL D1156 " --> pdb=" O HIS D1153 " (cutoff:3.500A) Processing helix chain 'D' and resid 1171 through 1173 No H-bonds generated for 'chain 'D' and resid 1171 through 1173' Processing helix chain 'D' and resid 1183 through 1194 Processing helix chain 'D' and resid 1220 through 1226 Processing helix chain 'D' and resid 1229 through 1239 Processing helix chain 'D' and resid 1248 through 1254 Processing helix chain 'D' and resid 1261 through 1263 No H-bonds generated for 'chain 'D' and resid 1261 through 1263' Processing helix chain 'D' and resid 1265 through 1268 No H-bonds generated for 'chain 'D' and resid 1265 through 1268' Processing helix chain 'D' and resid 1276 through 1281 Processing helix chain 'E' and resid 34 through 36 No H-bonds generated for 'chain 'E' and resid 34 through 36' Processing helix chain 'E' and resid 40 through 43 No H-bonds generated for 'chain 'E' and resid 40 through 43' Processing helix chain 'E' and resid 50 through 69 removed outlier: 4.049A pdb=" N VAL E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 100 Processing helix chain 'G' and resid 15 through 28 removed outlier: 3.721A pdb=" N GLU G 23 " --> pdb=" O LYS G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 80 Processing helix chain 'G' and resid 107 through 110 No H-bonds generated for 'chain 'G' and resid 107 through 110' Processing sheet with id= A, first strand: chain 'A' and resid 18 through 23 removed outlier: 3.856A pdb=" N LYS A 191 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 173 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 85 through 87 Processing sheet with id= C, first strand: chain 'A' and resid 93 through 100 removed outlier: 4.101A pdb=" N SER A 53 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY A 143 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ALA A 49 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 103 through 105 removed outlier: 3.965A pdb=" N GLY A 103 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 8 through 11 removed outlier: 3.599A pdb=" N VAL B 22 " --> pdb=" O SER B 10 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 161 through 163 removed outlier: 6.852A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS B 99 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 93 " --> pdb=" O VAL B 140 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 85 through 87 Processing sheet with id= H, first strand: chain 'B' and resid 103 through 106 Processing sheet with id= I, first strand: chain 'B' and resid 171 through 180 removed outlier: 6.959A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL B 178 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS B 191 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 103 through 108 removed outlier: 3.514A pdb=" N LYS C 148 " --> pdb=" O PHE C 139 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 130 through 132 Processing sheet with id= L, first strand: chain 'C' and resid 166 through 168 Processing sheet with id= M, first strand: chain 'C' and resid 178 through 181 Processing sheet with id= N, first strand: chain 'C' and resid 454 through 456 Processing sheet with id= O, first strand: chain 'C' and resid 528 through 531 Processing sheet with id= P, first strand: chain 'C' and resid 558 through 562 removed outlier: 3.646A pdb=" N GLU C 569 " --> pdb=" O VAL C 561 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 667 through 671 removed outlier: 3.704A pdb=" N GLU C 652 " --> pdb=" O THR C 659 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N MET C 661 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ILE C 650 " --> pdb=" O MET C 661 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 1024 through 1031 removed outlier: 4.594A pdb=" N THR C1024 " --> pdb=" O ILE C 723 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 915 " --> pdb=" O ALA C 722 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 884 through 886 removed outlier: 7.465A pdb=" N LEU C 737 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE C 898 " --> pdb=" O LEU C 737 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 749 through 760 removed outlier: 3.966A pdb=" N GLU C 867 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 93 through 96 Processing sheet with id= V, first strand: chain 'D' and resid 521 through 524 removed outlier: 8.000A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER D 428 " --> pdb=" O MET D 541 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 633 through 637 Processing sheet with id= X, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.937A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 7.264A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 135 through 139 removed outlier: 7.303A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 64 through 68 661 hydrogen bonds defined for protein. 1911 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 12.89 Time building geometry restraints manager: 10.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5409 1.33 - 1.46: 7590 1.46 - 1.59: 12620 1.59 - 1.72: 155 1.72 - 1.85: 159 Bond restraints: 25933 Sorted by residual: bond pdb=" C1' G2P C1201 " pdb=" O4' G2P C1201 " ideal model delta sigma weight residual 1.389 1.603 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C1' G2P C1201 " pdb=" C2' G2P C1201 " ideal model delta sigma weight residual 1.537 1.341 0.196 2.00e-02 2.50e+03 9.61e+01 bond pdb=" C2 G2P C1201 " pdb=" N3 G2P C1201 " ideal model delta sigma weight residual 1.305 1.460 -0.155 2.00e-02 2.50e+03 6.02e+01 bond pdb=" C4 G2P C1201 " pdb=" N3 G2P C1201 " ideal model delta sigma weight residual 1.345 1.492 -0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" C5 G2P C1201 " pdb=" C6 G2P C1201 " ideal model delta sigma weight residual 1.420 1.550 -0.130 2.00e-02 2.50e+03 4.22e+01 ... (remaining 25928 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.26: 1182 106.26 - 113.20: 14118 113.20 - 120.14: 9188 120.14 - 127.08: 10602 127.08 - 134.02: 386 Bond angle restraints: 35476 Sorted by residual: angle pdb=" CA PRO D1029 " pdb=" N PRO D1029 " pdb=" CD PRO D1029 " ideal model delta sigma weight residual 112.00 105.41 6.59 1.40e+00 5.10e-01 2.22e+01 angle pdb=" C3A G2P C1201 " pdb=" PB G2P C1201 " pdb=" O3B G2P C1201 " ideal model delta sigma weight residual 99.71 110.23 -10.52 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C3A G2P C1201 " pdb=" PA G2P C1201 " pdb=" O5' G2P C1201 " ideal model delta sigma weight residual 99.14 109.27 -10.13 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C5 G2P C1201 " pdb=" C6 G2P C1201 " pdb=" N1 G2P C1201 " ideal model delta sigma weight residual 110.74 120.13 -9.39 3.00e+00 1.11e-01 9.80e+00 angle pdb=" N TYR D 793 " pdb=" CA TYR D 793 " pdb=" C TYR D 793 " ideal model delta sigma weight residual 109.57 113.26 -3.69 1.23e+00 6.61e-01 8.98e+00 ... (remaining 35471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 14293 35.31 - 70.62: 1345 70.62 - 105.93: 59 105.93 - 141.25: 1 141.25 - 176.56: 2 Dihedral angle restraints: 15700 sinusoidal: 6959 harmonic: 8741 Sorted by residual: dihedral pdb=" O4' A R 21 " pdb=" C1' A R 21 " pdb=" N9 A R 21 " pdb=" C4 A R 21 " ideal model delta sinusoidal sigma weight residual 254.00 164.62 89.38 1 1.70e+01 3.46e-03 3.29e+01 dihedral pdb=" C4' DC T 23 " pdb=" C3' DC T 23 " pdb=" O3' DC T 23 " pdb=" P DA T 24 " ideal model delta sinusoidal sigma weight residual -140.00 36.56 -176.56 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" O4' U R 15 " pdb=" C1' U R 15 " pdb=" N1 U R 15 " pdb=" C2 U R 15 " ideal model delta sinusoidal sigma weight residual -128.00 -72.32 -55.68 1 1.70e+01 3.46e-03 1.45e+01 ... (remaining 15697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2625 0.035 - 0.070: 953 0.070 - 0.105: 344 0.105 - 0.140: 119 0.140 - 0.175: 7 Chirality restraints: 4048 Sorted by residual: chirality pdb=" CA LEU D1028 " pdb=" N LEU D1028 " pdb=" C LEU D1028 " pdb=" CB LEU D1028 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA ASP C 903 " pdb=" N ASP C 903 " pdb=" C ASP C 903 " pdb=" CB ASP C 903 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CB VAL G 40 " pdb=" CA VAL G 40 " pdb=" CG1 VAL G 40 " pdb=" CG2 VAL G 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.15e-01 ... (remaining 4045 not shown) Planarity restraints: 4391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 746 " -0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C LEU D 746 " 0.055 2.00e-02 2.50e+03 pdb=" O LEU D 746 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP D 747 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D1028 " 0.049 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO D1029 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO D1029 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D1029 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 206 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C ASP B 206 " -0.050 2.00e-02 2.50e+03 pdb=" O ASP B 206 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA B 207 " 0.017 2.00e-02 2.50e+03 ... (remaining 4388 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 164 2.60 - 3.17: 19320 3.17 - 3.75: 36841 3.75 - 4.32: 51099 4.32 - 4.90: 86192 Nonbonded interactions: 193616 Sorted by model distance: nonbonded pdb=" O1B G2P C1201 " pdb="MG MG D2002 " model vdw 2.022 2.170 nonbonded pdb=" OD2 ASP D 535 " pdb="MG MG D2001 " model vdw 2.059 2.170 nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2001 " model vdw 2.171 2.170 nonbonded pdb=" O SER B 37 " pdb=" OG1 THR B 41 " model vdw 2.195 2.440 nonbonded pdb=" OD1 ASP C 909 " pdb=" OG1 THR C 911 " model vdw 2.216 2.440 ... (remaining 193611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 223 o \ r (resid 224 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 25 through 226)) selection = (chain 'B' and resid 1 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.230 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: 14.930 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 79.540 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.080 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 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 : 0.005 0.214 25933 Z= 0.294 Angle : 0.637 10.520 35476 Z= 0.338 Chirality : 0.043 0.175 4048 Planarity : 0.006 0.072 4391 Dihedral : 22.389 176.557 10088 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.89 % Allowed : 9.20 % Favored : 89.91 % Rotamer: Outliers : 15.79 % Allowed : 23.46 % Favored : 60.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.14), residues: 3047 helix: -1.23 (0.16), residues: 1018 sheet: -1.39 (0.25), residues: 410 loop : -2.55 (0.13), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 223 HIS 0.009 0.001 HIS C 889 PHE 0.019 0.001 PHE C 439 TYR 0.016 0.001 TYR D 344 ARG 0.006 0.000 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 404 poor density : 161 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8616 (mt) REVERT: A 91 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: A 151 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7586 (mm-40) REVERT: B 55 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8605 (ttm170) REVERT: B 105 VAL cc_start: 0.9219 (OUTLIER) cc_final: 0.8789 (m) REVERT: B 133 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8695 (mmtt) REVERT: B 218 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.8953 (tt) REVERT: C 201 SER cc_start: 0.9152 (OUTLIER) cc_final: 0.8853 (p) REVERT: C 213 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7479 (tm-30) REVERT: C 251 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8331 (ttt180) REVERT: C 267 THR cc_start: 0.7848 (OUTLIER) cc_final: 0.7647 (p) REVERT: C 275 LEU cc_start: 0.9377 (tp) cc_final: 0.8364 (pp) REVERT: C 297 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: C 304 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8071 (tppp) REVERT: C 758 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8428 (p0) REVERT: C 761 ASP cc_start: 0.9050 (OUTLIER) cc_final: 0.8812 (m-30) REVERT: C 773 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9217 (mm) REVERT: C 805 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8537 (ttpp) REVERT: C 1164 ILE cc_start: 0.5794 (OUTLIER) cc_final: 0.5593 (mt) REVERT: D 151 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8635 (mt) REVERT: D 243 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8564 (mp0) REVERT: D 1050 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7352 (t) REVERT: D 1107 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8861 (p) REVERT: E 70 GLN cc_start: 0.8699 (tp40) cc_final: 0.8104 (tp40) REVERT: G 12 SER cc_start: 0.8395 (OUTLIER) cc_final: 0.8003 (p) REVERT: G 16 ASN cc_start: 0.9160 (OUTLIER) cc_final: 0.8707 (m-40) REVERT: G 31 MET cc_start: 0.7696 (mmp) cc_final: 0.7416 (mmp) REVERT: G 43 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.6501 (tp30) REVERT: G 57 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.7221 (pttt) outliers start: 404 outliers final: 114 residues processed: 528 average time/residue: 0.4319 time to fit residues: 338.9644 Evaluate side-chains 271 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 131 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 229 LYS Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 259 ARG Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain C residue 761 ASP Chi-restraints excluded: chain C residue 762 THR Chi-restraints excluded: chain C residue 773 ILE Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 777 SER Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 847 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 898 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 992 THR Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1147 LEU Chi-restraints excluded: chain C residue 1149 GLU Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1164 ILE Chi-restraints excluded: chain C residue 1167 SER Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 866 ARG Chi-restraints excluded: chain D residue 966 LEU Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1050 THR Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1060 ARG Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1100 SER Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 16 ASN Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 85 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 0.0970 chunk 234 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 242 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 147 optimal weight: 0.8980 chunk 180 optimal weight: 8.9990 chunk 281 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 120 ASN A 124 HIS A 129 ASN ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 HIS B 151 GLN C 141 ASN C 142 ASN C 169 ASN C 372 HIS C 386 GLN C 451 HIS C 479 HIS C 775 ASN C1066 GLN C1077 GLN C1111 ASN C1165 ASN D 22 GLN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN D 606 HIS D 687 GLN D 882 GLN D 935 ASN D1091 HIS D1110 GLN D1139 GLN E 63 GLN E 106 HIS G 9 HIS G 16 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25933 Z= 0.199 Angle : 0.587 11.153 35476 Z= 0.303 Chirality : 0.043 0.308 4048 Planarity : 0.005 0.080 4391 Dihedral : 17.118 177.156 4559 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.93 % Favored : 94.94 % Rotamer: Outliers : 6.18 % Allowed : 26.27 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.14), residues: 3047 helix: -0.08 (0.16), residues: 1009 sheet: -0.87 (0.27), residues: 384 loop : -2.18 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 223 HIS 0.005 0.001 HIS D 653 PHE 0.011 0.001 PHE C 439 TYR 0.009 0.001 TYR C 129 ARG 0.015 0.000 ARG D1085 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 141 time to evaluate : 2.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8008 (ttm-80) REVERT: B 105 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8430 (m) REVERT: B 218 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9230 (tt) REVERT: C 201 SER cc_start: 0.9148 (OUTLIER) cc_final: 0.8906 (p) REVERT: C 443 ASN cc_start: 0.9083 (OUTLIER) cc_final: 0.8821 (t0) REVERT: C 737 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9059 (mp) REVERT: C 892 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8509 (pttt) REVERT: C 1149 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6528 (pp20) REVERT: D 151 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8794 (mt) REVERT: D 1080 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8564 (pt) REVERT: D 1082 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8445 (mmtp) REVERT: D 1107 VAL cc_start: 0.9166 (OUTLIER) cc_final: 0.8845 (p) REVERT: D 1155 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7869 (mm-30) REVERT: G 12 SER cc_start: 0.8589 (OUTLIER) cc_final: 0.8166 (p) REVERT: G 57 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6809 (pttt) outliers start: 158 outliers final: 98 residues processed: 288 average time/residue: 0.3811 time to fit residues: 174.3129 Evaluate side-chains 237 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 124 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 229 LYS Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 652 GLU Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 762 THR Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 847 VAL Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 892 LYS Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1147 LEU Chi-restraints excluded: chain C residue 1149 GLU Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 966 LEU Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1082 LYS Chi-restraints excluded: chain D residue 1100 SER Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1155 GLU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 20.0000 chunk 87 optimal weight: 7.9990 chunk 234 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 282 optimal weight: 2.9990 chunk 304 optimal weight: 20.0000 chunk 251 optimal weight: 5.9990 chunk 279 optimal weight: 3.9990 chunk 96 optimal weight: 0.3980 chunk 226 optimal weight: 4.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN B 17 ASN C 150 GLN C 662 HIS D 207 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 25933 Z= 0.389 Angle : 0.620 11.856 35476 Z= 0.321 Chirality : 0.045 0.184 4048 Planarity : 0.005 0.052 4391 Dihedral : 16.463 176.398 4432 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.60 % Favored : 93.27 % Rotamer: Outliers : 6.02 % Allowed : 25.45 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.15), residues: 3047 helix: 0.41 (0.17), residues: 1016 sheet: -0.74 (0.27), residues: 400 loop : -2.09 (0.14), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 938 HIS 0.008 0.001 HIS C 889 PHE 0.019 0.002 PHE D1061 TYR 0.039 0.002 TYR D1062 ARG 0.011 0.000 ARG G 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 122 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 VAL cc_start: 0.9169 (OUTLIER) cc_final: 0.8803 (m) REVERT: C 267 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7664 (p) REVERT: C 443 ASN cc_start: 0.9155 (OUTLIER) cc_final: 0.8812 (t0) REVERT: C 604 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8589 (mmm160) REVERT: C 892 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8609 (pttt) REVERT: C 1149 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6529 (pp20) REVERT: D 64 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8448 (ttmt) REVERT: D 155 MET cc_start: 0.7893 (tpt) cc_final: 0.7637 (tpt) REVERT: D 1107 VAL cc_start: 0.9192 (OUTLIER) cc_final: 0.8901 (p) outliers start: 154 outliers final: 99 residues processed: 265 average time/residue: 0.3634 time to fit residues: 158.1000 Evaluate side-chains 227 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 120 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 229 LYS Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 652 GLU Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 762 THR Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 847 VAL Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 892 LYS Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1149 GLU Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1155 GLU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 85 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 6.9990 chunk 212 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 189 optimal weight: 0.9980 chunk 283 optimal weight: 3.9990 chunk 299 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 268 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25933 Z= 0.222 Angle : 0.539 10.297 35476 Z= 0.277 Chirality : 0.042 0.147 4048 Planarity : 0.004 0.051 4391 Dihedral : 15.980 176.247 4391 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.09 % Favored : 94.78 % Rotamer: Outliers : 5.75 % Allowed : 26.08 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.15), residues: 3047 helix: 0.75 (0.17), residues: 1012 sheet: -0.54 (0.27), residues: 389 loop : -1.93 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 723 HIS 0.004 0.001 HIS C 889 PHE 0.011 0.001 PHE C 439 TYR 0.010 0.001 TYR C 129 ARG 0.006 0.000 ARG D1085 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 124 time to evaluate : 2.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8845 (m) REVERT: C 366 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8105 (pt0) REVERT: C 443 ASN cc_start: 0.9134 (OUTLIER) cc_final: 0.8838 (t0) REVERT: C 604 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8498 (mmt180) REVERT: C 737 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9134 (mp) REVERT: C 892 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8523 (pttt) REVERT: C 1149 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6547 (pp20) REVERT: D 155 MET cc_start: 0.7822 (tpt) cc_final: 0.7577 (tpt) REVERT: D 1107 VAL cc_start: 0.9203 (OUTLIER) cc_final: 0.8926 (p) REVERT: G 43 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7515 (tp30) REVERT: G 71 MET cc_start: 0.6980 (tpt) cc_final: 0.6541 (ttp) outliers start: 147 outliers final: 104 residues processed: 262 average time/residue: 0.3694 time to fit residues: 157.6299 Evaluate side-chains 234 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 121 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 229 LYS Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 652 GLU Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 762 THR Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 847 VAL Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 892 LYS Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1084 THR Chi-restraints excluded: chain C residue 1149 GLU Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1164 ILE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 267 ASN Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 606 HIS Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1082 LYS Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1155 GLU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 223 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 255 optimal weight: 0.9990 chunk 207 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 268 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 150 GLN D 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 25933 Z= 0.381 Angle : 0.583 11.955 35476 Z= 0.301 Chirality : 0.044 0.153 4048 Planarity : 0.005 0.052 4391 Dihedral : 15.924 176.227 4381 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.34 % Favored : 93.53 % Rotamer: Outliers : 5.98 % Allowed : 25.92 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.15), residues: 3047 helix: 0.76 (0.17), residues: 1023 sheet: -0.59 (0.26), residues: 408 loop : -1.91 (0.14), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 944 HIS 0.006 0.001 HIS C 889 PHE 0.016 0.001 PHE C 431 TYR 0.032 0.001 TYR D1062 ARG 0.008 0.000 ARG D 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 120 time to evaluate : 4.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 VAL cc_start: 0.9230 (OUTLIER) cc_final: 0.8989 (m) REVERT: C 267 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7603 (p) REVERT: C 297 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8016 (tp30) REVERT: C 366 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7662 (pp20) REVERT: C 443 ASN cc_start: 0.9147 (OUTLIER) cc_final: 0.8822 (t0) REVERT: C 604 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8594 (mmm160) REVERT: C 737 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9167 (mp) REVERT: C 892 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8628 (pttt) REVERT: C 1149 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6568 (pp20) REVERT: D 64 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8421 (ttmt) REVERT: D 506 ARG cc_start: 0.9530 (OUTLIER) cc_final: 0.8094 (ttm170) outliers start: 153 outliers final: 109 residues processed: 265 average time/residue: 0.3361 time to fit residues: 147.0298 Evaluate side-chains 240 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 120 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 229 LYS Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 652 GLU Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 847 VAL Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 892 LYS Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1084 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1149 GLU Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain C residue 1164 ILE Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 304 GLN Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 606 HIS Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 768 ASP Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1155 GLU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 5.9990 chunk 269 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 175 optimal weight: 30.0000 chunk 73 optimal weight: 4.9990 chunk 299 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25933 Z= 0.237 Angle : 0.526 10.505 35476 Z= 0.272 Chirality : 0.042 0.165 4048 Planarity : 0.004 0.052 4391 Dihedral : 15.710 175.810 4370 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.09 % Favored : 94.78 % Rotamer: Outliers : 5.32 % Allowed : 26.78 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.15), residues: 3047 helix: 0.97 (0.17), residues: 1015 sheet: -0.53 (0.27), residues: 396 loop : -1.76 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 723 HIS 0.004 0.001 HIS D 505 PHE 0.011 0.001 PHE C 431 TYR 0.010 0.001 TYR C 129 ARG 0.006 0.000 ARG G 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 125 time to evaluate : 4.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 VAL cc_start: 0.9211 (OUTLIER) cc_final: 0.8972 (m) REVERT: C 366 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7522 (pp20) REVERT: C 443 ASN cc_start: 0.9133 (OUTLIER) cc_final: 0.8820 (t0) REVERT: C 604 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.8501 (mmt180) REVERT: C 737 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9139 (mp) REVERT: C 892 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8584 (pttt) REVERT: C 1149 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6536 (pp20) REVERT: D 155 MET cc_start: 0.7920 (tpt) cc_final: 0.7689 (tpt) REVERT: G 71 MET cc_start: 0.6986 (tpt) cc_final: 0.6632 (ttp) outliers start: 136 outliers final: 108 residues processed: 252 average time/residue: 0.3417 time to fit residues: 141.4788 Evaluate side-chains 236 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 121 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 229 LYS Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 652 GLU Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 847 VAL Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 892 LYS Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1149 GLU Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1164 ILE Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain D residue 606 HIS Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 768 ASP Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1155 GLU Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 85 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 219 optimal weight: 0.4980 chunk 169 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 chunk 186 optimal weight: 8.9990 chunk 182 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 841 HIS D 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25933 Z= 0.181 Angle : 0.504 11.978 35476 Z= 0.259 Chirality : 0.041 0.143 4048 Planarity : 0.004 0.052 4391 Dihedral : 15.409 175.198 4363 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.22 % Favored : 94.65 % Rotamer: Outliers : 4.14 % Allowed : 27.91 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.15), residues: 3047 helix: 1.12 (0.17), residues: 1022 sheet: -0.33 (0.27), residues: 401 loop : -1.64 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 723 HIS 0.003 0.001 HIS D 653 PHE 0.010 0.001 PHE C 431 TYR 0.011 0.001 TYR D1062 ARG 0.006 0.000 ARG G 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 123 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 VAL cc_start: 0.9228 (OUTLIER) cc_final: 0.8999 (m) REVERT: B 131 LYS cc_start: 0.8979 (mmtm) cc_final: 0.8696 (mmtm) REVERT: C 443 ASN cc_start: 0.9119 (OUTLIER) cc_final: 0.8807 (t0) REVERT: C 737 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9113 (mp) REVERT: C 892 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8505 (pttt) REVERT: C 1149 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6530 (pp20) REVERT: D 155 MET cc_start: 0.7888 (tpt) cc_final: 0.7658 (tpt) REVERT: D 1053 VAL cc_start: 0.9219 (OUTLIER) cc_final: 0.8967 (p) REVERT: G 71 MET cc_start: 0.7046 (tpt) cc_final: 0.6779 (ttp) outliers start: 106 outliers final: 89 residues processed: 224 average time/residue: 0.3529 time to fit residues: 129.7580 Evaluate side-chains 215 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 120 time to evaluate : 3.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 652 GLU Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 847 VAL Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 892 LYS Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1149 GLU Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1164 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 606 HIS Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1067 VAL Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1155 GLU Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 85 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 189 optimal weight: 0.1980 chunk 203 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 234 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 841 HIS D 341 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25933 Z= 0.250 Angle : 0.526 12.607 35476 Z= 0.270 Chirality : 0.042 0.145 4048 Planarity : 0.004 0.053 4391 Dihedral : 15.312 175.095 4343 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.32 % Favored : 94.55 % Rotamer: Outliers : 4.46 % Allowed : 28.03 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.15), residues: 3047 helix: 1.11 (0.17), residues: 1029 sheet: -0.23 (0.27), residues: 397 loop : -1.63 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 723 HIS 0.004 0.001 HIS D 505 PHE 0.012 0.001 PHE C 431 TYR 0.035 0.001 TYR D1062 ARG 0.007 0.000 ARG G 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 120 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8450 (p0) REVERT: B 105 VAL cc_start: 0.9272 (OUTLIER) cc_final: 0.9057 (m) REVERT: B 131 LYS cc_start: 0.9031 (mmtm) cc_final: 0.8724 (mmtm) REVERT: C 443 ASN cc_start: 0.9134 (OUTLIER) cc_final: 0.8826 (t0) REVERT: C 604 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8511 (mmt180) REVERT: C 737 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9131 (mp) REVERT: C 892 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8556 (pttt) REVERT: C 1149 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6506 (pp20) REVERT: D 64 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8433 (ttmt) REVERT: D 155 MET cc_start: 0.7903 (tpt) cc_final: 0.7674 (tpt) REVERT: D 1053 VAL cc_start: 0.9254 (OUTLIER) cc_final: 0.9022 (p) REVERT: G 71 MET cc_start: 0.6995 (tpt) cc_final: 0.6604 (ttp) outliers start: 114 outliers final: 93 residues processed: 225 average time/residue: 0.3678 time to fit residues: 136.3267 Evaluate side-chains 221 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 119 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 652 GLU Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 847 VAL Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 892 LYS Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1149 GLU Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1164 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain D residue 606 HIS Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 917 GLU Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1067 VAL Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1155 GLU Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 4.9990 chunk 286 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 278 optimal weight: 0.0020 chunk 167 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 218 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 251 optimal weight: 0.8980 chunk 263 optimal weight: 9.9990 chunk 277 optimal weight: 6.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 841 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25933 Z= 0.187 Angle : 0.505 12.753 35476 Z= 0.257 Chirality : 0.041 0.143 4048 Planarity : 0.004 0.052 4391 Dihedral : 15.164 174.892 4340 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.83 % Favored : 95.04 % Rotamer: Outliers : 3.75 % Allowed : 28.77 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 3047 helix: 1.23 (0.17), residues: 1021 sheet: -0.09 (0.28), residues: 397 loop : -1.52 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 723 HIS 0.003 0.001 HIS D 653 PHE 0.010 0.001 PHE C 431 TYR 0.024 0.001 TYR D1062 ARG 0.007 0.000 ARG G 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 120 time to evaluate : 3.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8395 (p0) REVERT: B 105 VAL cc_start: 0.9246 (OUTLIER) cc_final: 0.9032 (m) REVERT: B 131 LYS cc_start: 0.8990 (mmtm) cc_final: 0.8687 (mmtm) REVERT: C 443 ASN cc_start: 0.9131 (OUTLIER) cc_final: 0.8821 (t0) REVERT: C 604 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8489 (mmm160) REVERT: C 737 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9094 (mp) REVERT: C 892 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8548 (pttt) REVERT: C 1149 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6539 (pp20) REVERT: D 64 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8449 (ttmt) REVERT: D 155 MET cc_start: 0.7829 (tpt) cc_final: 0.7605 (tpt) REVERT: D 1053 VAL cc_start: 0.9261 (OUTLIER) cc_final: 0.9026 (p) REVERT: G 71 MET cc_start: 0.7039 (tpt) cc_final: 0.6672 (ttp) outliers start: 96 outliers final: 82 residues processed: 211 average time/residue: 0.3436 time to fit residues: 119.1890 Evaluate side-chains 211 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 120 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 652 GLU Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 847 VAL Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 892 LYS Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1149 GLU Chi-restraints excluded: chain C residue 1164 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 606 HIS Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 917 GLU Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1067 VAL Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1155 GLU Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 6.9990 chunk 294 optimal weight: 9.9990 chunk 179 optimal weight: 8.9990 chunk 139 optimal weight: 0.1980 chunk 204 optimal weight: 0.9990 chunk 308 optimal weight: 5.9990 chunk 284 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 189 optimal weight: 0.0870 chunk 150 optimal weight: 2.9990 overall best weight: 1.0564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 841 HIS D1032 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25933 Z= 0.161 Angle : 0.496 12.605 35476 Z= 0.252 Chirality : 0.040 0.145 4048 Planarity : 0.004 0.052 4391 Dihedral : 14.980 174.680 4329 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.80 % Favored : 95.07 % Rotamer: Outliers : 3.40 % Allowed : 29.24 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3047 helix: 1.32 (0.17), residues: 1022 sheet: 0.03 (0.28), residues: 395 loop : -1.45 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 938 HIS 0.003 0.000 HIS D 653 PHE 0.011 0.001 PHE C 252 TYR 0.023 0.001 TYR D1062 ARG 0.008 0.000 ARG G 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 121 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8315 (p0) REVERT: B 131 LYS cc_start: 0.8968 (mmtm) cc_final: 0.8646 (mmtm) REVERT: C 443 ASN cc_start: 0.9109 (OUTLIER) cc_final: 0.8797 (t0) REVERT: C 737 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9083 (mp) REVERT: C 892 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8498 (pttt) REVERT: C 1149 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6543 (pp20) REVERT: D 64 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8470 (ttmt) REVERT: D 155 MET cc_start: 0.7746 (tpt) cc_final: 0.7535 (tpt) REVERT: G 71 MET cc_start: 0.7063 (tpt) cc_final: 0.6764 (ttp) outliers start: 87 outliers final: 76 residues processed: 202 average time/residue: 0.3408 time to fit residues: 113.7849 Evaluate side-chains 201 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 119 time to evaluate : 2.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 652 GLU Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 847 VAL Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 892 LYS Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1149 GLU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 606 HIS Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 917 GLU Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1067 VAL Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1155 GLU Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 110 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 0.0000 chunk 261 optimal weight: 9.9990 chunk 75 optimal weight: 0.0470 chunk 226 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 chunk 246 optimal weight: 3.9990 chunk 103 optimal weight: 0.1980 chunk 252 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 729 HIS C 841 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.072680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.044887 restraints weight = 75197.271| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 3.29 r_work: 0.2544 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25933 Z= 0.142 Angle : 0.488 12.634 35476 Z= 0.247 Chirality : 0.040 0.144 4048 Planarity : 0.004 0.057 4391 Dihedral : 14.854 174.585 4326 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.24 % Favored : 95.63 % Rotamer: Outliers : 2.70 % Allowed : 29.95 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.16), residues: 3047 helix: 1.41 (0.17), residues: 1019 sheet: 0.22 (0.29), residues: 376 loop : -1.37 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 938 HIS 0.003 0.000 HIS D 653 PHE 0.010 0.001 PHE C 153 TYR 0.020 0.001 TYR D1062 ARG 0.008 0.000 ARG G 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5208.59 seconds wall clock time: 94 minutes 16.95 seconds (5656.95 seconds total)