Starting phenix.real_space_refine on Fri Jun 5 23:27:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w3d_65597/06_2026/9w3d_65597.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w3d_65597/06_2026/9w3d_65597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w3d_65597/06_2026/9w3d_65597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w3d_65597/06_2026/9w3d_65597.map" model { file = "/net/cci-nas-00/data/ceres_data/9w3d_65597/06_2026/9w3d_65597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w3d_65597/06_2026/9w3d_65597.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 14807 2.51 5 N 4161 2.21 5 O 4519 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23592 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "B" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 9499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1206, 9499 Classifications: {'peptide': 1206} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1152} Chain breaks: 2 Chain: "D" Number of atoms: 9138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9138 Classifications: {'peptide': 1166} Link IDs: {'PCIS': 2, 'PTRANS': 45, 'TRANS': 1118} Chain breaks: 1 Chain: "G" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 755 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "E" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 666 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Time building chain proxies: 5.37, per 1000 atoms: 0.23 Number of scatterers: 23592 At special positions: 0 Unit cell: (143.99, 133.28, 153.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 4519 8.00 N 4161 7.00 C 14807 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 1.2 seconds 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5560 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 39 sheets defined 42.4% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.623A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.885A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.647A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.429A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 212 through 228 Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.712A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 47 through 57 removed outlier: 3.771A pdb=" N ALA C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.067A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.951A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 409 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.894A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.687A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.743A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 569 removed outlier: 3.843A pdb=" N ASN C 568 " --> pdb=" O GLU C 565 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE C 569 " --> pdb=" O GLY C 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 565 through 569' Processing helix chain 'C' and resid 607 through 612 removed outlier: 4.024A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 660 removed outlier: 3.551A pdb=" N GLN C 659 " --> pdb=" O SER C 656 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 656 through 660' Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.784A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 Processing helix chain 'C' and resid 942 through 983 removed outlier: 4.019A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 Processing helix chain 'C' and resid 993 through 998 removed outlier: 3.517A pdb=" N ARG C 996 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1038 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.135A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1101 through 1106' Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 4.177A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.585A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1332 Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 77 through 81 removed outlier: 3.821A pdb=" N HIS D 80 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D 81 " --> pdb=" O LEU D 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 77 through 81' Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.607A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 180 through 192 Processing helix chain 'D' and resid 193 through 208 removed outlier: 4.035A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.569A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.575A pdb=" N ARG D 250 " --> pdb=" O PRO D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 286 removed outlier: 3.677A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.664A pdb=" N PHE D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 515 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.736A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.610A pdb=" N SER D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 Processing helix chain 'D' and resid 720 through 727 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.216A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.668A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1139 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.254A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1296 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.638A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.580A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 3.518A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 28 removed outlier: 3.710A pdb=" N VAL G 26 " --> pdb=" O SER G 23 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N MET G 28 " --> pdb=" O THR G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 35 removed outlier: 3.631A pdb=" N VAL G 34 " --> pdb=" O ASP G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 44 removed outlier: 3.681A pdb=" N LEU G 43 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU G 44 " --> pdb=" O GLU G 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 40 through 44' Processing helix chain 'G' and resid 47 through 57 Processing helix chain 'G' and resid 92 through 100 Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 88 removed outlier: 3.507A pdb=" N LEU E 64 " --> pdb=" O ASN E 60 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 4.887A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N HIS A 23 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR A 207 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LYS A 25 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N MET A 205 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N THR A 27 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE A 203 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLU A 29 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU A 201 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N THR A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL A 192 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 198 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 7.818A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 16 removed outlier: 6.696A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS B 23 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR B 207 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LYS B 25 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N MET B 205 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N THR B 27 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE B 203 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLU B 29 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU B 201 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 105 removed outlier: 5.938A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.310A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 7.520A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LEU C 102 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLU C 119 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE C 104 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE C 117 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.900A pdb=" N SER C 147 " --> pdb=" O ARG C 529 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 159 removed outlier: 4.733A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 580 through 581 removed outlier: 6.817A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB8, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.467A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 748 through 752 removed outlier: 5.874A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC2, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC3, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.528A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.794A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AC6, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.646A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.513A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.513A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD1, first strand: chain 'C' and resid 1335 through 1340 removed outlier: 3.552A pdb=" N GLU C1338 " --> pdb=" O LYS D 21 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 103 through 105 removed outlier: 3.791A pdb=" N LEU D 242 " --> pdb=" O ILE D 105 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 158 through 160 removed outlier: 3.674A pdb=" N GLN D 158 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU D 160 " --> pdb=" O TYR D 144 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR D 144 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 252 through 254 Processing sheet with id=AD5, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD6, first strand: chain 'D' and resid 703 through 707 Processing sheet with id=AD7, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AD8, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD9, first strand: chain 'D' and resid 848 through 849 Processing sheet with id=AE1, first strand: chain 'D' and resid 1186 through 1191 removed outlier: 3.804A pdb=" N GLU D1202 " --> pdb=" O VAL D1163 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.898A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 20 through 22 1085 hydrogen bonds defined for protein. 3108 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.17 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8088 1.34 - 1.46: 4734 1.46 - 1.59: 10948 1.59 - 1.71: 0 1.71 - 1.83: 182 Bond restraints: 23952 Sorted by residual: bond pdb=" C GLU D 925 " pdb=" N PRO D 926 " ideal model delta sigma weight residual 1.334 1.375 -0.041 8.40e-03 1.42e+04 2.44e+01 bond pdb=" N MET C 124 " pdb=" CA MET C 124 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.16e-02 7.43e+03 6.55e+00 bond pdb=" N MET C 515 " pdb=" CA MET C 515 " ideal model delta sigma weight residual 1.458 1.486 -0.029 1.25e-02 6.40e+03 5.28e+00 bond pdb=" N MET D 466 " pdb=" CA MET D 466 " ideal model delta sigma weight residual 1.456 1.484 -0.027 1.23e-02 6.61e+03 4.98e+00 bond pdb=" CB ASP G 93 " pdb=" CG ASP G 93 " ideal model delta sigma weight residual 1.516 1.569 -0.053 2.50e-02 1.60e+03 4.45e+00 ... (remaining 23947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 31953 2.96 - 5.92: 289 5.92 - 8.88: 66 8.88 - 11.84: 21 11.84 - 14.80: 18 Bond angle restraints: 32347 Sorted by residual: angle pdb=" CA MET C 951 " pdb=" CB MET C 951 " pdb=" CG MET C 951 " ideal model delta sigma weight residual 114.10 124.09 -9.99 2.00e+00 2.50e-01 2.49e+01 angle pdb=" CB MET D 821 " pdb=" CG MET D 821 " pdb=" SD MET D 821 " ideal model delta sigma weight residual 112.70 127.50 -14.80 3.00e+00 1.11e-01 2.43e+01 angle pdb=" CB MET E 30 " pdb=" CG MET E 30 " pdb=" SD MET E 30 " ideal model delta sigma weight residual 112.70 127.44 -14.74 3.00e+00 1.11e-01 2.41e+01 angle pdb=" CB MET B 51 " pdb=" CG MET B 51 " pdb=" SD MET B 51 " ideal model delta sigma weight residual 112.70 127.26 -14.56 3.00e+00 1.11e-01 2.36e+01 angle pdb=" CB MET C1232 " pdb=" CG MET C1232 " pdb=" SD MET C1232 " ideal model delta sigma weight residual 112.70 127.01 -14.31 3.00e+00 1.11e-01 2.27e+01 ... (remaining 32342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 13040 17.86 - 35.71: 1391 35.71 - 53.57: 268 53.57 - 71.43: 47 71.43 - 89.28: 13 Dihedral angle restraints: 14759 sinusoidal: 6118 harmonic: 8641 Sorted by residual: dihedral pdb=" CA MET D 237 " pdb=" C MET D 237 " pdb=" N ILE D 238 " pdb=" CA ILE D 238 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA SER A 49 " pdb=" C SER A 49 " pdb=" N SER A 50 " pdb=" CA SER A 50 " ideal model delta harmonic sigma weight residual 180.00 -155.80 -24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual -180.00 -156.39 -23.61 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 14756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 3436 0.099 - 0.198: 235 0.198 - 0.297: 5 0.297 - 0.397: 1 0.397 - 0.496: 1 Chirality restraints: 3678 Sorted by residual: chirality pdb=" CG LEU E 80 " pdb=" CB LEU E 80 " pdb=" CD1 LEU E 80 " pdb=" CD2 LEU E 80 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.14e+00 chirality pdb=" CB ILE D 500 " pdb=" CA ILE D 500 " pdb=" CG1 ILE D 500 " pdb=" CG2 ILE D 500 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB VAL C 980 " pdb=" CA VAL C 980 " pdb=" CG1 VAL C 980 " pdb=" CG2 VAL C 980 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 3675 not shown) Planarity restraints: 4245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 596 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.09e+01 pdb=" C ASP C 596 " 0.057 2.00e-02 2.50e+03 pdb=" O ASP C 596 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY C 597 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP G 30 " 0.015 2.00e-02 2.50e+03 3.10e-02 9.59e+00 pdb=" CG ASP G 30 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASP G 30 " 0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP G 30 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 50 " 0.046 5.00e-02 4.00e+02 7.07e-02 7.99e+00 pdb=" N PRO D 51 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 51 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 51 " 0.039 5.00e-02 4.00e+02 ... (remaining 4242 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6533 2.81 - 3.33: 20925 3.33 - 3.85: 41297 3.85 - 4.38: 46184 4.38 - 4.90: 78413 Nonbonded interactions: 193352 Sorted by model distance: nonbonded pdb=" O GLN C1111 " pdb=" OG1 THR C1115 " model vdw 2.285 3.040 nonbonded pdb=" NH2 ARG C1331 " pdb=" O ILE C1335 " model vdw 2.288 3.120 nonbonded pdb=" OG SER C 646 " pdb=" OD1 ASP C 648 " model vdw 2.308 3.040 nonbonded pdb=" O THR G 42 " pdb=" OG1 THR G 42 " model vdw 2.318 3.040 nonbonded pdb=" O LEU D 8 " pdb=" OG1 THR D 12 " model vdw 2.320 3.040 ... (remaining 193347 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 232) selection = (chain 'B' and resid 7 through 232) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 23.120 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 23952 Z= 0.183 Angle : 0.867 14.797 32347 Z= 0.440 Chirality : 0.050 0.496 3678 Planarity : 0.006 0.094 4245 Dihedral : 14.854 89.284 9199 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.16 % Allowed : 15.93 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.14), residues: 2986 helix: -1.03 (0.13), residues: 1152 sheet: 0.12 (0.26), residues: 403 loop : -0.51 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D1372 TYR 0.031 0.002 TYR G 20 PHE 0.015 0.001 PHE D1319 TRP 0.018 0.002 TRP D 580 HIS 0.007 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 (23952) covalent geometry : angle 0.86683 / 0.44 (32347) hydrogen bonds : bond 0.12998 / 9.12 ( 1080) hydrogen bonds : angle 6.71847 / 4.79 ( 3108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 681 MET cc_start: 0.8829 (ptp) cc_final: 0.8623 (ptp) REVERT: C 1232 MET cc_start: 0.8330 (mmm) cc_final: 0.7980 (mmm) REVERT: D 697 MET cc_start: 0.8978 (tmm) cc_final: 0.8306 (ttp) REVERT: D 1145 PHE cc_start: 0.8821 (m-80) cc_final: 0.8408 (m-80) REVERT: G 20 TYR cc_start: 0.8822 (t80) cc_final: 0.8514 (m-80) outliers start: 4 outliers final: 2 residues processed: 111 average time/residue: 0.1465 time to fit residues: 28.1107 Evaluate side-chains 104 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 369 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 overall best weight: 9.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 720 ASN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1279 GLN G 21 ASN G 106 HIS E 73 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.031165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.022552 restraints weight = 283193.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.023208 restraints weight = 166363.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.023634 restraints weight = 117634.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.023907 restraints weight = 94057.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.024074 restraints weight = 81655.597| |-----------------------------------------------------------------------------| r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 23952 Z= 0.302 Angle : 0.683 7.840 32347 Z= 0.352 Chirality : 0.042 0.219 3678 Planarity : 0.005 0.059 4245 Dihedral : 4.725 26.900 3299 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.10 % Allowed : 14.10 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.15), residues: 2986 helix: 0.59 (0.14), residues: 1179 sheet: 0.03 (0.25), residues: 398 loop : -0.13 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 26 TYR 0.014 0.002 TYR D 723 PHE 0.021 0.002 PHE C1221 TRP 0.014 0.002 TRP D 580 HIS 0.006 0.001 HIS G 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.30 (23952) covalent geometry : angle 0.68275 / 0.35 (32347) hydrogen bonds : bond 0.04318 / 2.96 ( 1080) hydrogen bonds : angle 5.34363 / 3.78 ( 3108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 99 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 205 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8502 (tmm) REVERT: C 492 MET cc_start: 0.8974 (tmm) cc_final: 0.8356 (tmm) REVERT: C 768 MET cc_start: 0.7369 (tmm) cc_final: 0.7152 (tmm) REVERT: C 800 MET cc_start: 0.8844 (mmm) cc_final: 0.8616 (mmm) REVERT: C 805 MET cc_start: 0.8874 (ppp) cc_final: 0.8312 (ppp) REVERT: C 985 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7424 (pp20) REVERT: C 1230 MET cc_start: 0.8751 (tmm) cc_final: 0.8286 (tmm) REVERT: C 1232 MET cc_start: 0.8435 (mmm) cc_final: 0.7973 (mmm) REVERT: C 1324 ASN cc_start: 0.9528 (OUTLIER) cc_final: 0.9294 (m-40) REVERT: D 102 MET cc_start: 0.8774 (ppp) cc_final: 0.8113 (ppp) REVERT: D 306 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8455 (mm) REVERT: D 466 MET cc_start: 0.9205 (mmm) cc_final: 0.8864 (mmm) REVERT: D 485 MET cc_start: 0.9175 (tpp) cc_final: 0.8849 (tpp) REVERT: D 698 MET cc_start: 0.9374 (mmm) cc_final: 0.9045 (mmm) REVERT: D 807 LEU cc_start: 0.9462 (tp) cc_final: 0.9196 (tp) REVERT: G 86 MET cc_start: 0.8507 (mpp) cc_final: 0.7992 (mpp) outliers start: 54 outliers final: 31 residues processed: 148 average time/residue: 0.1438 time to fit residues: 36.4771 Evaluate side-chains 133 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 985 GLU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1324 ASN Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 11 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 1257 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 102 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 92 optimal weight: 9.9990 chunk 264 optimal weight: 40.0000 chunk 61 optimal weight: 20.0000 chunk 154 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 106 optimal weight: 0.0670 chunk 8 optimal weight: 7.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.031646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.023083 restraints weight = 278220.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.023743 restraints weight = 160408.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.024178 restraints weight = 112730.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.024443 restraints weight = 89931.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.024630 restraints weight = 78277.003| |-----------------------------------------------------------------------------| r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23952 Z= 0.136 Angle : 0.512 7.184 32347 Z= 0.264 Chirality : 0.041 0.241 3678 Planarity : 0.004 0.052 4245 Dihedral : 4.326 28.946 3296 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.17 % Allowed : 15.04 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.15), residues: 2986 helix: 1.11 (0.15), residues: 1184 sheet: -0.08 (0.24), residues: 420 loop : 0.10 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1373 TYR 0.012 0.001 TYR D 679 PHE 0.008 0.001 PHE D 35 TRP 0.007 0.001 TRP D 580 HIS 0.003 0.001 HIS C 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (23952) covalent geometry : angle 0.51211 / 0.26 (32347) hydrogen bonds : bond 0.03622 / 2.48 ( 1080) hydrogen bonds : angle 5.01698 / 3.56 ( 3108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.980 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: B 205 MET cc_start: 0.8843 (tmm) cc_final: 0.8472 (tmm) REVERT: C 369 MET cc_start: 0.9081 (ppp) cc_final: 0.8789 (ppp) REVERT: C 492 MET cc_start: 0.8974 (tmm) cc_final: 0.8536 (tmm) REVERT: C 768 MET cc_start: 0.7487 (tmm) cc_final: 0.7252 (tmm) REVERT: C 800 MET cc_start: 0.8844 (mmm) cc_final: 0.8555 (mmm) REVERT: C 805 MET cc_start: 0.8938 (ppp) cc_final: 0.8391 (ppp) REVERT: C 1066 MET cc_start: 0.8465 (tpp) cc_final: 0.8181 (mmm) REVERT: C 1119 MET cc_start: 0.9402 (mmm) cc_final: 0.9199 (mmm) REVERT: C 1230 MET cc_start: 0.8812 (tmm) cc_final: 0.8162 (tmm) REVERT: C 1231 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.7616 (t80) REVERT: C 1232 MET cc_start: 0.8491 (mmm) cc_final: 0.7950 (mmm) REVERT: D 102 MET cc_start: 0.8678 (ppp) cc_final: 0.8050 (ppp) REVERT: D 349 TYR cc_start: 0.8734 (m-10) cc_final: 0.8169 (m-10) REVERT: D 466 MET cc_start: 0.9081 (mmm) cc_final: 0.8595 (mmm) REVERT: D 622 ASP cc_start: 0.9474 (OUTLIER) cc_final: 0.9146 (t0) REVERT: D 807 LEU cc_start: 0.9446 (tp) cc_final: 0.9132 (tp) REVERT: D 821 MET cc_start: 0.9195 (mmm) cc_final: 0.8946 (mmm) REVERT: G 86 MET cc_start: 0.8517 (mpp) cc_final: 0.8115 (mpp) outliers start: 30 outliers final: 15 residues processed: 132 average time/residue: 0.1354 time to fit residues: 30.5989 Evaluate side-chains 118 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 224 PHE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1231 TYR Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 73 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 241 optimal weight: 9.9990 chunk 171 optimal weight: 0.0050 chunk 28 optimal weight: 30.0000 chunk 80 optimal weight: 20.0000 chunk 239 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 138 optimal weight: 30.0000 chunk 188 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 overall best weight: 7.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS D 712 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.030987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.022459 restraints weight = 283444.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.023111 restraints weight = 165308.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.023539 restraints weight = 116689.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.023807 restraints weight = 92963.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.023987 restraints weight = 80592.749| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 23952 Z= 0.227 Angle : 0.597 6.997 32347 Z= 0.305 Chirality : 0.042 0.232 3678 Planarity : 0.004 0.056 4245 Dihedral : 4.356 23.370 3294 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.45 % Allowed : 14.96 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.15), residues: 2986 helix: 1.09 (0.15), residues: 1207 sheet: -0.02 (0.26), residues: 385 loop : 0.17 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 26 TYR 0.019 0.001 TYR D 631 PHE 0.028 0.002 PHE D 7 TRP 0.008 0.001 TRP D 580 HIS 0.004 0.001 HIS G 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.23 (23952) covalent geometry : angle 0.59702 / 0.31 (32347) hydrogen bonds : bond 0.03798 / 2.60 ( 1080) hydrogen bonds : angle 5.07201 / 3.59 ( 3108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 101 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 205 MET cc_start: 0.8707 (tmm) cc_final: 0.8310 (tmm) REVERT: C 369 MET cc_start: 0.9142 (ppp) cc_final: 0.8899 (ppp) REVERT: C 492 MET cc_start: 0.9053 (tmm) cc_final: 0.8605 (tmm) REVERT: C 741 MET cc_start: 0.8972 (pmm) cc_final: 0.8720 (pmm) REVERT: C 768 MET cc_start: 0.7614 (tmm) cc_final: 0.7318 (tmm) REVERT: C 800 MET cc_start: 0.8753 (mmm) cc_final: 0.8449 (mmm) REVERT: C 805 MET cc_start: 0.9033 (ppp) cc_final: 0.8417 (ppp) REVERT: C 985 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7380 (pp20) REVERT: C 1230 MET cc_start: 0.8813 (tmm) cc_final: 0.8117 (tmm) REVERT: C 1232 MET cc_start: 0.8609 (mmm) cc_final: 0.8332 (mmm) REVERT: C 1297 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8088 (p0) REVERT: D 102 MET cc_start: 0.8972 (ppp) cc_final: 0.8400 (ppp) REVERT: D 139 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6494 (mm) REVERT: D 321 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8591 (mttt) REVERT: D 349 TYR cc_start: 0.8973 (m-10) cc_final: 0.8419 (m-10) REVERT: D 372 MET cc_start: 0.9264 (pmm) cc_final: 0.8997 (pmm) REVERT: D 466 MET cc_start: 0.9061 (mmm) cc_final: 0.8529 (mmm) REVERT: D 485 MET cc_start: 0.9419 (tpp) cc_final: 0.8728 (tpp) REVERT: D 622 ASP cc_start: 0.9494 (OUTLIER) cc_final: 0.9152 (t0) REVERT: D 697 MET cc_start: 0.9025 (tmm) cc_final: 0.8500 (ttp) REVERT: D 698 MET cc_start: 0.9307 (mmm) cc_final: 0.9028 (mmm) REVERT: D 747 MET cc_start: 0.8057 (mmt) cc_final: 0.7842 (mmt) REVERT: D 807 LEU cc_start: 0.9483 (tp) cc_final: 0.9162 (tp) REVERT: G 73 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8318 (tpp-160) REVERT: G 86 MET cc_start: 0.8571 (mpp) cc_final: 0.8151 (mpp) outliers start: 63 outliers final: 35 residues processed: 159 average time/residue: 0.1335 time to fit residues: 36.0638 Evaluate side-chains 137 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 96 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 224 PHE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 985 GLU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1297 ASP Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 211 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 206 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 213 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 63 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.030864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.022409 restraints weight = 281991.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.023037 restraints weight = 165851.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.023452 restraints weight = 118018.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.023722 restraints weight = 94598.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.023889 restraints weight = 82131.820| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23952 Z= 0.219 Angle : 0.583 8.075 32347 Z= 0.298 Chirality : 0.042 0.265 3678 Planarity : 0.004 0.055 4245 Dihedral : 4.348 23.204 3294 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.61 % Allowed : 15.19 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.15), residues: 2986 helix: 1.16 (0.15), residues: 1200 sheet: -0.01 (0.25), residues: 396 loop : 0.18 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1373 TYR 0.019 0.001 TYR D 631 PHE 0.026 0.001 PHE D 7 TRP 0.008 0.001 TRP D 580 HIS 0.004 0.001 HIS B 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.22 (23952) covalent geometry : angle 0.58310 / 0.30 (32347) hydrogen bonds : bond 0.03713 / 2.55 ( 1080) hydrogen bonds : angle 5.08725 / 3.60 ( 3108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 101 time to evaluate : 0.819 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: A 142 MET cc_start: 0.9217 (tpt) cc_final: 0.8760 (tpt) REVERT: B 205 MET cc_start: 0.8742 (tmm) cc_final: 0.8464 (tmm) REVERT: C 369 MET cc_start: 0.9147 (ppp) cc_final: 0.8896 (ppp) REVERT: C 405 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.8984 (t80) REVERT: C 492 MET cc_start: 0.9018 (tmm) cc_final: 0.8552 (tmm) REVERT: C 685 MET cc_start: 0.9404 (ptp) cc_final: 0.9155 (ptp) REVERT: C 768 MET cc_start: 0.7617 (tmm) cc_final: 0.7302 (tmm) REVERT: C 800 MET cc_start: 0.8794 (mmm) cc_final: 0.8490 (mmm) REVERT: C 985 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7277 (pp20) REVERT: C 1230 MET cc_start: 0.8764 (tmm) cc_final: 0.8293 (tmm) REVERT: C 1232 MET cc_start: 0.8534 (mmm) cc_final: 0.8127 (mmm) REVERT: C 1297 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8063 (p0) REVERT: D 102 MET cc_start: 0.8944 (ppp) cc_final: 0.8467 (ppp) REVERT: D 321 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8524 (mttt) REVERT: D 349 TYR cc_start: 0.8919 (m-10) cc_final: 0.8406 (m-10) REVERT: D 411 ILE cc_start: 0.9705 (OUTLIER) cc_final: 0.9444 (tt) REVERT: D 466 MET cc_start: 0.8962 (mmm) cc_final: 0.8478 (mmm) REVERT: D 485 MET cc_start: 0.9479 (tpp) cc_final: 0.9123 (tpp) REVERT: D 622 ASP cc_start: 0.9471 (OUTLIER) cc_final: 0.9150 (t0) REVERT: D 697 MET cc_start: 0.8991 (tmm) cc_final: 0.8171 (ttp) REVERT: D 698 MET cc_start: 0.9314 (mmm) cc_final: 0.9030 (mmt) REVERT: D 747 MET cc_start: 0.8309 (mmt) cc_final: 0.7991 (mmt) REVERT: D 807 LEU cc_start: 0.9451 (tp) cc_final: 0.9135 (tp) REVERT: D 1145 PHE cc_start: 0.8854 (m-80) cc_final: 0.8633 (m-80) REVERT: G 73 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8190 (tpp-160) REVERT: G 86 MET cc_start: 0.8552 (mpp) cc_final: 0.8098 (mpp) outliers start: 67 outliers final: 43 residues processed: 161 average time/residue: 0.1471 time to fit residues: 39.6813 Evaluate side-chains 146 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 96 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 224 PHE Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 985 GLU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1297 ASP Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1180 VAL Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain E residue 13 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 253 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 296 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 251 optimal weight: 9.9990 chunk 169 optimal weight: 0.2980 chunk 82 optimal weight: 9.9990 chunk 258 optimal weight: 6.9990 chunk 293 optimal weight: 20.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.031345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.022738 restraints weight = 278719.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.023403 restraints weight = 164927.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.023840 restraints weight = 115592.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.024122 restraints weight = 91943.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.024293 restraints weight = 79498.181| |-----------------------------------------------------------------------------| r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23952 Z= 0.114 Angle : 0.530 9.848 32347 Z= 0.267 Chirality : 0.042 0.287 3678 Planarity : 0.003 0.052 4245 Dihedral : 4.172 22.584 3294 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.91 % Allowed : 15.50 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.16), residues: 2986 helix: 1.36 (0.15), residues: 1201 sheet: -0.04 (0.26), residues: 392 loop : 0.31 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1373 TYR 0.011 0.001 TYR D 679 PHE 0.021 0.001 PHE D 7 TRP 0.007 0.001 TRP D 580 HIS 0.014 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (23952) covalent geometry : angle 0.52956 / 0.27 (32347) hydrogen bonds : bond 0.03363 / 2.30 ( 1080) hydrogen bonds : angle 4.88401 / 3.46 ( 3108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 100 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9297 (tp) REVERT: A 114 ASP cc_start: 0.9188 (OUTLIER) cc_final: 0.8643 (t0) REVERT: B 205 MET cc_start: 0.8734 (tmm) cc_final: 0.8461 (tmm) REVERT: C 369 MET cc_start: 0.9153 (ppp) cc_final: 0.8889 (ppp) REVERT: C 405 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8889 (t80) REVERT: C 492 MET cc_start: 0.8988 (tmm) cc_final: 0.8581 (tmm) REVERT: C 768 MET cc_start: 0.7492 (tmm) cc_final: 0.7195 (tmm) REVERT: C 800 MET cc_start: 0.8757 (mmm) cc_final: 0.8456 (mmm) REVERT: C 943 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.9107 (ptmm) REVERT: C 985 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7360 (pp20) REVERT: C 1230 MET cc_start: 0.8817 (tmm) cc_final: 0.8002 (tmm) REVERT: C 1231 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.7698 (t80) REVERT: C 1232 MET cc_start: 0.8620 (mmm) cc_final: 0.8090 (mmm) REVERT: C 1297 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8101 (p0) REVERT: D 102 MET cc_start: 0.8887 (ppp) cc_final: 0.8371 (ppp) REVERT: D 139 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6521 (mm) REVERT: D 321 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8581 (mttt) REVERT: D 349 TYR cc_start: 0.8865 (m-10) cc_final: 0.8455 (m-10) REVERT: D 466 MET cc_start: 0.8937 (mmm) cc_final: 0.8463 (mmm) REVERT: D 485 MET cc_start: 0.9474 (tpp) cc_final: 0.9093 (tpp) REVERT: D 697 MET cc_start: 0.8929 (tmm) cc_final: 0.7963 (ttp) REVERT: D 698 MET cc_start: 0.9315 (mmm) cc_final: 0.9047 (mmt) REVERT: D 747 MET cc_start: 0.8303 (mmt) cc_final: 0.7951 (mmt) REVERT: G 20 TYR cc_start: 0.8634 (t80) cc_final: 0.8422 (t80) REVERT: G 73 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8122 (tpp-160) REVERT: G 86 MET cc_start: 0.8528 (mpp) cc_final: 0.8118 (mpp) outliers start: 49 outliers final: 35 residues processed: 145 average time/residue: 0.1452 time to fit residues: 35.8653 Evaluate side-chains 142 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 97 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 224 PHE Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 985 GLU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1231 TYR Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1297 ASP Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1180 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 110 optimal weight: 20.0000 chunk 82 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 176 optimal weight: 7.9990 chunk 33 optimal weight: 30.0000 chunk 205 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.030786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.022343 restraints weight = 282197.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.022987 restraints weight = 169159.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.023401 restraints weight = 119256.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.023670 restraints weight = 95220.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.023841 restraints weight = 82660.607| |-----------------------------------------------------------------------------| r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23952 Z= 0.220 Angle : 0.610 10.317 32347 Z= 0.308 Chirality : 0.042 0.268 3678 Planarity : 0.004 0.055 4245 Dihedral : 4.305 24.768 3294 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.26 % Allowed : 15.97 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.16), residues: 2986 helix: 1.23 (0.15), residues: 1200 sheet: -0.00 (0.26), residues: 377 loop : 0.28 (0.17), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 99 TYR 0.013 0.001 TYR D 631 PHE 0.050 0.002 PHE D 7 TRP 0.010 0.001 TRP D 580 HIS 0.020 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.22 (23952) covalent geometry : angle 0.60977 / 0.31 (32347) hydrogen bonds : bond 0.03629 / 2.49 ( 1080) hydrogen bonds : angle 5.03745 / 3.58 ( 3108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 99 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 205 MET cc_start: 0.8721 (tmm) cc_final: 0.8328 (tmm) REVERT: C 491 ASP cc_start: 0.9434 (OUTLIER) cc_final: 0.9208 (p0) REVERT: C 492 MET cc_start: 0.8993 (tmm) cc_final: 0.8675 (tmm) REVERT: C 681 MET cc_start: 0.8907 (ptp) cc_final: 0.8703 (ptp) REVERT: C 768 MET cc_start: 0.7582 (tmm) cc_final: 0.7251 (tmm) REVERT: C 800 MET cc_start: 0.8751 (mmm) cc_final: 0.8478 (mmm) REVERT: C 943 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.9143 (ptmm) REVERT: C 985 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7253 (pp20) REVERT: C 1230 MET cc_start: 0.8781 (tmm) cc_final: 0.7744 (tmm) REVERT: C 1232 MET cc_start: 0.8555 (mmm) cc_final: 0.7202 (mmm) REVERT: C 1297 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8150 (p0) REVERT: D 102 MET cc_start: 0.8974 (ppp) cc_final: 0.8509 (ppp) REVERT: D 139 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6526 (mm) REVERT: D 321 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8477 (mttt) REVERT: D 349 TYR cc_start: 0.8975 (m-10) cc_final: 0.8512 (m-10) REVERT: D 466 MET cc_start: 0.8894 (mmm) cc_final: 0.8393 (mmm) REVERT: D 485 MET cc_start: 0.9513 (tpp) cc_final: 0.9060 (tpp) REVERT: D 697 MET cc_start: 0.9001 (tmm) cc_final: 0.8040 (ttp) REVERT: D 698 MET cc_start: 0.9326 (mmm) cc_final: 0.9068 (mmt) REVERT: D 743 MET cc_start: 0.8625 (tmm) cc_final: 0.8416 (tmm) REVERT: D 747 MET cc_start: 0.8332 (mmt) cc_final: 0.7997 (mmt) REVERT: G 73 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8047 (tpp-160) REVERT: G 86 MET cc_start: 0.8495 (mpp) cc_final: 0.8122 (mpp) outliers start: 58 outliers final: 47 residues processed: 152 average time/residue: 0.1442 time to fit residues: 37.1511 Evaluate side-chains 151 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 97 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 224 PHE Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 985 GLU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1297 ASP Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 1180 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 11 optimal weight: 9.9990 chunk 60 optimal weight: 30.0000 chunk 114 optimal weight: 10.0000 chunk 286 optimal weight: 8.9990 chunk 248 optimal weight: 20.0000 chunk 267 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 251 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 160 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.030741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.022327 restraints weight = 282873.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.022969 restraints weight = 169469.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.023390 restraints weight = 119279.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.023657 restraints weight = 95260.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.023829 restraints weight = 82584.976| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 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 : 0.004 0.046 23952 Z= 0.218 Angle : 0.610 10.186 32347 Z= 0.308 Chirality : 0.042 0.279 3678 Planarity : 0.004 0.055 4245 Dihedral : 4.354 22.915 3294 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.34 % Allowed : 16.40 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.16), residues: 2986 helix: 1.20 (0.15), residues: 1200 sheet: -0.04 (0.26), residues: 380 loop : 0.29 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 26 TYR 0.014 0.001 TYR D 631 PHE 0.051 0.002 PHE D 7 TRP 0.009 0.001 TRP D 580 HIS 0.023 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.22 (23952) covalent geometry : angle 0.60968 / 0.31 (32347) hydrogen bonds : bond 0.03657 / 2.51 ( 1080) hydrogen bonds : angle 5.08940 / 3.61 ( 3108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 99 time to evaluate : 0.932 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: B 205 MET cc_start: 0.8671 (tmm) cc_final: 0.8282 (tmm) REVERT: C 492 MET cc_start: 0.9013 (tmm) cc_final: 0.8743 (tmm) REVERT: C 768 MET cc_start: 0.7589 (tmm) cc_final: 0.7247 (tmm) REVERT: C 800 MET cc_start: 0.8763 (mmm) cc_final: 0.8481 (mmm) REVERT: C 943 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9136 (ptmm) REVERT: C 985 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7307 (pp20) REVERT: C 1131 MET cc_start: 0.9250 (mtp) cc_final: 0.8991 (mtp) REVERT: C 1230 MET cc_start: 0.8772 (tmm) cc_final: 0.8002 (tmm) REVERT: C 1232 MET cc_start: 0.8579 (mmm) cc_final: 0.7245 (mmm) REVERT: C 1297 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8178 (p0) REVERT: D 102 MET cc_start: 0.8992 (ppp) cc_final: 0.8519 (ppp) REVERT: D 139 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6455 (mm) REVERT: D 321 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8485 (mttt) REVERT: D 349 TYR cc_start: 0.8975 (m-10) cc_final: 0.8557 (m-10) REVERT: D 411 ILE cc_start: 0.9697 (OUTLIER) cc_final: 0.9428 (tt) REVERT: D 466 MET cc_start: 0.8861 (mmm) cc_final: 0.8357 (mmm) REVERT: D 485 MET cc_start: 0.9506 (tpp) cc_final: 0.9083 (tpp) REVERT: D 697 MET cc_start: 0.8992 (tmm) cc_final: 0.8115 (ttp) REVERT: D 698 MET cc_start: 0.9307 (mmm) cc_final: 0.9075 (mmt) REVERT: D 747 MET cc_start: 0.8369 (mmt) cc_final: 0.8020 (mmt) REVERT: G 73 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8010 (tpp-160) REVERT: G 86 MET cc_start: 0.8487 (mpp) cc_final: 0.8050 (mpp) outliers start: 60 outliers final: 47 residues processed: 153 average time/residue: 0.1472 time to fit residues: 37.9665 Evaluate side-chains 154 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 100 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 985 GLU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1297 ASP Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 1180 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 127 optimal weight: 20.0000 chunk 293 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 267 optimal weight: 8.9990 chunk 198 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 chunk 242 optimal weight: 20.0000 chunk 226 optimal weight: 0.9980 chunk 195 optimal weight: 0.0270 overall best weight: 3.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.031209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.022676 restraints weight = 278824.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.023330 restraints weight = 162646.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.023766 restraints weight = 115079.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.024038 restraints weight = 91814.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.024225 restraints weight = 79808.791| |-----------------------------------------------------------------------------| r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23952 Z= 0.128 Angle : 0.568 11.454 32347 Z= 0.281 Chirality : 0.042 0.303 3678 Planarity : 0.003 0.053 4245 Dihedral : 4.163 23.837 3294 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.91 % Allowed : 16.91 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.16), residues: 2986 helix: 1.38 (0.15), residues: 1199 sheet: 0.00 (0.26), residues: 392 loop : 0.38 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 81 TYR 0.011 0.001 TYR D 679 PHE 0.051 0.001 PHE D 7 TRP 0.006 0.001 TRP D 236 HIS 0.022 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (23952) covalent geometry : angle 0.56840 / 0.28 (32347) hydrogen bonds : bond 0.03341 / 2.29 ( 1080) hydrogen bonds : angle 4.88004 / 3.46 ( 3108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 99 time to evaluate : 0.987 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: A 102 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9338 (tp) REVERT: A 114 ASP cc_start: 0.9218 (OUTLIER) cc_final: 0.8634 (t0) REVERT: C 41 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8545 (mm-40) REVERT: C 459 MET cc_start: 0.9029 (ptp) cc_final: 0.8764 (mpp) REVERT: C 492 MET cc_start: 0.9009 (tmm) cc_final: 0.8802 (tmm) REVERT: C 768 MET cc_start: 0.7536 (tmm) cc_final: 0.7254 (tmm) REVERT: C 800 MET cc_start: 0.8736 (mmm) cc_final: 0.8462 (mmm) REVERT: C 943 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.9141 (ptmm) REVERT: C 1085 MET cc_start: 0.9265 (mtp) cc_final: 0.8971 (mtt) REVERT: C 1131 MET cc_start: 0.9257 (mtp) cc_final: 0.9004 (mtp) REVERT: C 1230 MET cc_start: 0.8766 (tmm) cc_final: 0.8502 (tmm) REVERT: C 1297 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8212 (p0) REVERT: D 102 MET cc_start: 0.8941 (ppp) cc_final: 0.8456 (ppp) REVERT: D 139 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6486 (mm) REVERT: D 321 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8563 (mttt) REVERT: D 349 TYR cc_start: 0.8920 (m-10) cc_final: 0.8607 (m-10) REVERT: D 466 MET cc_start: 0.8816 (mmm) cc_final: 0.8259 (mmm) REVERT: D 485 MET cc_start: 0.9489 (tpp) cc_final: 0.8999 (tpp) REVERT: D 697 MET cc_start: 0.8920 (tmm) cc_final: 0.7913 (ttp) REVERT: D 698 MET cc_start: 0.9287 (mmm) cc_final: 0.9054 (mmt) REVERT: D 747 MET cc_start: 0.8243 (mmt) cc_final: 0.7900 (mmt) REVERT: G 86 MET cc_start: 0.8420 (mpp) cc_final: 0.7998 (mpp) outliers start: 49 outliers final: 35 residues processed: 143 average time/residue: 0.1461 time to fit residues: 35.4342 Evaluate side-chains 140 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 98 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1297 ASP Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 1180 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 224 optimal weight: 5.9990 chunk 145 optimal weight: 20.0000 chunk 219 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 217 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 119 optimal weight: 0.0070 chunk 75 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 149 optimal weight: 20.0000 overall best weight: 4.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.031108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.022581 restraints weight = 279139.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.023241 restraints weight = 165805.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.023670 restraints weight = 116479.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.023948 restraints weight = 92870.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.024120 restraints weight = 80274.228| |-----------------------------------------------------------------------------| r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23952 Z= 0.154 Angle : 0.592 11.470 32347 Z= 0.292 Chirality : 0.042 0.320 3678 Planarity : 0.004 0.053 4245 Dihedral : 4.167 23.001 3294 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.87 % Allowed : 16.83 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.16), residues: 2986 helix: 1.38 (0.15), residues: 1199 sheet: 0.13 (0.26), residues: 377 loop : 0.42 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 81 TYR 0.013 0.001 TYR D 631 PHE 0.050 0.001 PHE D 7 TRP 0.005 0.001 TRP D 236 HIS 0.008 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (23952) covalent geometry : angle 0.59159 / 0.29 (32347) hydrogen bonds : bond 0.03381 / 2.33 ( 1080) hydrogen bonds : angle 4.89018 / 3.47 ( 3108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5972 Ramachandran restraints generated. 2986 Oldfield, 0 Emsley, 2986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 98 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9295 (tp) REVERT: A 114 ASP cc_start: 0.9230 (OUTLIER) cc_final: 0.8635 (t0) REVERT: C 41 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8522 (mm-40) REVERT: C 459 MET cc_start: 0.9078 (ptp) cc_final: 0.8778 (mpp) REVERT: C 492 MET cc_start: 0.9007 (tmm) cc_final: 0.8799 (tmm) REVERT: C 768 MET cc_start: 0.7548 (tmm) cc_final: 0.7266 (tmm) REVERT: C 800 MET cc_start: 0.8733 (mmm) cc_final: 0.8456 (mmm) REVERT: C 943 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9137 (ptmm) REVERT: C 1131 MET cc_start: 0.9261 (mtp) cc_final: 0.9012 (mtp) REVERT: C 1180 MET cc_start: 0.9481 (tpp) cc_final: 0.9241 (tpp) REVERT: C 1230 MET cc_start: 0.8761 (tmm) cc_final: 0.7934 (tmm) REVERT: C 1232 MET cc_start: 0.8668 (mmm) cc_final: 0.7472 (mmm) REVERT: C 1297 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8247 (p0) REVERT: D 102 MET cc_start: 0.8902 (ppp) cc_final: 0.8455 (ppp) REVERT: D 139 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6419 (mm) REVERT: D 321 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8566 (mttt) REVERT: D 349 TYR cc_start: 0.8965 (m-10) cc_final: 0.8660 (m-10) REVERT: D 466 MET cc_start: 0.8800 (mmm) cc_final: 0.8246 (mmm) REVERT: D 485 MET cc_start: 0.9496 (tpp) cc_final: 0.9010 (tpp) REVERT: D 697 MET cc_start: 0.8924 (tmm) cc_final: 0.8444 (ttp) REVERT: D 698 MET cc_start: 0.9297 (mmm) cc_final: 0.8996 (mmm) REVERT: D 747 MET cc_start: 0.8246 (mmt) cc_final: 0.7913 (mmt) REVERT: G 86 MET cc_start: 0.8427 (mpp) cc_final: 0.8040 (mpp) outliers start: 48 outliers final: 38 residues processed: 141 average time/residue: 0.1465 time to fit residues: 35.3902 Evaluate side-chains 142 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 97 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1297 ASP Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 1180 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 51 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 265 optimal weight: 7.9990 chunk 122 optimal weight: 0.0470 chunk 79 optimal weight: 7.9990 chunk 286 optimal weight: 4.9990 chunk 238 optimal weight: 40.0000 chunk 162 optimal weight: 0.7980 chunk 5 optimal weight: 20.0000 chunk 246 optimal weight: 6.9990 chunk 270 optimal weight: 0.1980 chunk 194 optimal weight: 6.9990 chunk 296 optimal weight: 5.9990 overall best weight: 2.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.031450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.022924 restraints weight = 277029.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.023599 restraints weight = 164028.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.024035 restraints weight = 114820.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.024320 restraints weight = 91293.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.024501 restraints weight = 78884.415| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23952 Z= 0.108 Angle : 0.569 11.466 32347 Z= 0.279 Chirality : 0.042 0.311 3678 Planarity : 0.003 0.052 4245 Dihedral : 4.054 23.588 3294 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.60 % Allowed : 17.02 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.16), residues: 2986 helix: 1.46 (0.15), residues: 1198 sheet: 0.16 (0.26), residues: 380 loop : 0.45 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 81 TYR 0.011 0.001 TYR D 679 PHE 0.050 0.001 PHE D 7 TRP 0.006 0.001 TRP D 33 HIS 0.005 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (23952) covalent geometry : angle 0.56888 / 0.28 (32347) hydrogen bonds : bond 0.03198 / 2.20 ( 1080) hydrogen bonds : angle 4.77928 / 3.39 ( 3108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3499.50 seconds wall clock time: 61 minutes 46.52 seconds (3706.52 seconds total)