Starting phenix.real_space_refine on Tue Sep 15 00:49:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mkn_23900/09_2026/7mkn_23900.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mkn_23900/09_2026/7mkn_23900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7mkn_23900/09_2026/7mkn_23900.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mkn_23900/09_2026/7mkn_23900.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mkn_23900/09_2026/7mkn_23900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mkn_23900/09_2026/7mkn_23900.map" model { file = "/net/cci-nas-00/data/ceres_data/7mkn_23900/09_2026/7mkn_23900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mkn_23900/09_2026/7mkn_23900.cif" } resolution = 3.3 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 63 5.49 5 Mg 1 5.21 5 S 133 5.16 5 C 21148 2.51 5 N 6049 2.21 5 O 6688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34084 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1794 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain: "B" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain: "C" Number of atoms: 10570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10570 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "D" Number of atoms: 10382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10382 Classifications: {'peptide': 1340} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 55, 'TRANS': 1284} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 546 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "L" Number of atoms: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7696 Classifications: {'peptide': 967} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 35, 'TRANS': 931} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "N" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "R" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 244 Classifications: {'RNAv2': 11} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna3p': 10} Chain: "T" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 583 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'2TM': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14615 SG CYS D 70 54.416 101.191 72.847 1.00 55.31 S ATOM 14629 SG CYS D 72 54.704 104.271 70.812 1.00 62.66 S ATOM 14737 SG CYS D 85 52.392 102.034 69.767 1.00 70.92 S ATOM 14761 SG CYS D 88 56.007 101.423 69.406 1.00 68.27 S ATOM 20449 SG CYS D 814 74.189 36.488 74.724 1.00 36.58 S ATOM 21014 SG CYS D 888 75.929 39.870 74.425 1.00 38.68 S ATOM 21065 SG CYS D 895 74.774 38.469 77.451 1.00 32.49 S ATOM 21086 SG CYS D 898 77.366 37.051 76.205 1.00 32.62 S Time building chain proxies: 6.78, per 1000 atoms: 0.20 Number of scatterers: 34084 At special positions: 0 Unit cell: (161.04, 163.68, 162.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 133 16.00 P 63 15.00 Mg 1 11.99 O 6688 8.00 N 6049 7.00 C 21148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 72 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 85 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 88 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 70 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 895 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 898 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 814 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 888 " Number of angles added : 12 8322 Ramachandran restraints generated. 4161 Oldfield, 0 Emsley, 4161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7750 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 49 sheets defined 42.6% alpha, 15.7% beta 19 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 4.13 Creating SS restraints... Processing helix chain 'A' and resid 34 through 51 removed outlier: 4.007A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.883A 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 159 removed outlier: 3.558A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 212 through 233 removed outlier: 3.985A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.734A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.504A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) 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 161 removed outlier: 3.987A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.755A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.515A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.552A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.785A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.655A pdb=" N ARG C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.991A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 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: 3.839A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.544A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 482 Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 Processing helix chain 'C' and resid 608 through 614 removed outlier: 3.593A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.902A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) 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 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 864 removed outlier: 3.711A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 981 removed outlier: 3.548A pdb=" N GLN C 955 " --> pdb=" O MET C 951 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.711A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 998 removed outlier: 4.008A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.624A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.520A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.563A 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 1109 through 1134 removed outlier: 3.581A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 Processing helix chain 'C' and resid 1166 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 1281 Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.693A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.626A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 113 through 119 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.580A 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 181 through 191 Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 286 removed outlier: 3.914A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 309 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 370 through 377 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 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 485 through 489 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 581 Processing helix chain 'D' and resid 588 through 593 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 613 through 636 Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.708A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.793A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.657A 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 removed outlier: 3.664A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1147 removed outlier: 3.884A pdb=" N ARG D1140 " --> pdb=" O GLY D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.868A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.554A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.394A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1293 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.823A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.873A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1373 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.518A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'L' and resid 14 through 18 Processing helix chain 'L' and resid 100 through 102 No H-bonds generated for 'chain 'L' and resid 100 through 102' Processing helix chain 'L' and resid 110 through 117 removed outlier: 4.751A pdb=" N LEU L 115 " --> pdb=" O GLN L 112 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE L 116 " --> pdb=" O ASP L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 141 removed outlier: 3.512A pdb=" N PHE L 126 " --> pdb=" O ARG L 122 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG L 141 " --> pdb=" O SER L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 155 through 167 removed outlier: 3.779A pdb=" N ARG L 167 " --> pdb=" O HIS L 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 197 Processing helix chain 'L' and resid 208 through 224 removed outlier: 4.447A pdb=" N HIS L 213 " --> pdb=" O GLU L 209 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLN L 214 " --> pdb=" O THR L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 231 through 242 removed outlier: 3.531A pdb=" N ASP L 241 " --> pdb=" O GLU L 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 248 Processing helix chain 'L' and resid 255 through 260 Processing helix chain 'L' and resid 262 through 272 Processing helix chain 'L' and resid 281 through 285 Processing helix chain 'L' and resid 293 through 303 removed outlier: 4.020A pdb=" N ALA L 298 " --> pdb=" O ARG L 294 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE L 299 " --> pdb=" O GLU L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 320 through 323 Processing helix chain 'L' and resid 324 through 332 removed outlier: 4.201A pdb=" N LEU L 330 " --> pdb=" O ALA L 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 362 removed outlier: 3.646A pdb=" N PHE L 342 " --> pdb=" O ASP L 338 " (cutoff:3.500A) Proline residue: L 351 - end of helix Processing helix chain 'L' and resid 366 through 377 removed outlier: 3.997A pdb=" N MET L 372 " --> pdb=" O ASP L 368 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU L 375 " --> pdb=" O ASN L 371 " (cutoff:3.500A) Processing helix chain 'L' and resid 381 through 392 removed outlier: 4.783A pdb=" N LEU L 385 " --> pdb=" O ASP L 381 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA L 389 " --> pdb=" O LEU L 385 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN L 390 " --> pdb=" O LEU L 386 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP L 392 " --> pdb=" O ALA L 388 " (cutoff:3.500A) Processing helix chain 'L' and resid 395 through 411 removed outlier: 3.536A pdb=" N ASP L 409 " --> pdb=" O SER L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 441 through 455 removed outlier: 3.667A pdb=" N VAL L 450 " --> pdb=" O THR L 446 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER L 451 " --> pdb=" O ALA L 447 " (cutoff:3.500A) Processing helix chain 'L' and resid 459 through 468 Processing helix chain 'L' and resid 469 through 472 Processing helix chain 'L' and resid 473 through 478 removed outlier: 3.738A pdb=" N PHE L 477 " --> pdb=" O ILE L 473 " (cutoff:3.500A) Processing helix chain 'L' and resid 483 through 487 removed outlier: 3.613A pdb=" N PHE L 487 " --> pdb=" O TRP L 484 " (cutoff:3.500A) Processing helix chain 'L' and resid 488 through 501 removed outlier: 3.782A pdb=" N GLU L 492 " --> pdb=" O ASP L 488 " (cutoff:3.500A) Processing helix chain 'L' and resid 512 through 528 Processing helix chain 'L' and resid 539 through 552 Processing helix chain 'L' and resid 586 through 596 removed outlier: 3.599A pdb=" N LEU L 590 " --> pdb=" O ASN L 586 " (cutoff:3.500A) Processing helix chain 'L' and resid 616 through 627 removed outlier: 3.539A pdb=" N ARG L 623 " --> pdb=" O SER L 619 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 656 removed outlier: 5.517A pdb=" N ASN L 648 " --> pdb=" O ASP L 644 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP L 649 " --> pdb=" O SER L 645 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN L 652 " --> pdb=" O ASN L 648 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR L 653 " --> pdb=" O ASP L 649 " (cutoff:3.500A) Processing helix chain 'L' and resid 662 through 684 Processing helix chain 'L' and resid 686 through 695 removed outlier: 3.503A pdb=" N GLY L 695 " --> pdb=" O ILE L 691 " (cutoff:3.500A) Processing helix chain 'L' and resid 695 through 710 removed outlier: 3.556A pdb=" N ALA L 699 " --> pdb=" O GLY L 695 " (cutoff:3.500A) Processing helix chain 'L' and resid 712 through 727 removed outlier: 4.105A pdb=" N ILE L 716 " --> pdb=" O ASP L 712 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN L 721 " --> pdb=" O ALA L 717 " (cutoff:3.500A) Processing helix chain 'L' and resid 764 through 771 Processing helix chain 'L' and resid 781 through 794 Processing helix chain 'L' and resid 827 through 835 removed outlier: 6.246A pdb=" N LEU L 832 " --> pdb=" O GLN L 829 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ASN L 833 " --> pdb=" O LEU L 830 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG L 834 " --> pdb=" O GLN L 831 " (cutoff:3.500A) Processing helix chain 'L' and resid 857 through 864 removed outlier: 3.546A pdb=" N PHE L 861 " --> pdb=" O GLU L 857 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN L 864 " --> pdb=" O THR L 860 " (cutoff:3.500A) Processing helix chain 'L' and resid 869 through 879 removed outlier: 3.785A pdb=" N LYS L 875 " --> pdb=" O HIS L 871 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN L 878 " --> pdb=" O SER L 874 " (cutoff:3.500A) Processing helix chain 'L' and resid 880 through 926 removed outlier: 3.677A pdb=" N HIS L 885 " --> pdb=" O GLN L 881 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA L 886 " --> pdb=" O GLN L 882 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN L 889 " --> pdb=" O HIS L 885 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU L 890 " --> pdb=" O ALA L 886 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY L 891 " --> pdb=" O ILE L 887 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA L 893 " --> pdb=" O GLN L 889 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN L 894 " --> pdb=" O LEU L 890 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU L 896 " --> pdb=" O GLU L 892 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS L 897 " --> pdb=" O ALA L 893 " (cutoff:3.500A) Processing helix chain 'L' and resid 932 through 952 removed outlier: 3.505A pdb=" N LEU L 936 " --> pdb=" O ARG L 932 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 8.615A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.691A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (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 removed outlier: 6.501A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 14 through 17 removed outlier: 6.057A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 104 removed outlier: 8.727A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (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 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.773A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.419A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.419A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB6, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.670A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB8, first strand: chain 'C' and resid 284 through 286 removed outlier: 4.596A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.774A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.974A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.612A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.928A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.618A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.731A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.698A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 887 through 888 removed outlier: 4.200A pdb=" N LYS C 914 " --> pdb=" O THR C 888 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.020A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD4, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.353A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 10.301A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 159 through 160 removed outlier: 3.818A pdb=" N TYR D 144 " --> pdb=" O LEU D 160 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 526 through 527 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 949 through 951 removed outlier: 6.810A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL D1017 " --> pdb=" O ILE D 950 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 991 through 997 removed outlier: 4.213A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 966 through 967 removed outlier: 3.518A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'D' and resid 1035 through 1038 Processing sheet with id=AE4, first strand: chain 'D' and resid 1059 through 1061 removed outlier: 3.948A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1163 through 1165 removed outlier: 4.451A pdb=" N TYR D1186 " --> pdb=" O ILE D1177 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1277 through 1279 Processing sheet with id=AE7, first strand: chain 'L' and resid 40 through 44 removed outlier: 6.832A pdb=" N THR L 29 " --> pdb=" O VAL L 25 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL L 25 " --> pdb=" O THR L 29 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR L 31 " --> pdb=" O VAL L 23 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 60 through 62 removed outlier: 7.101A pdb=" N ILE L 84 " --> pdb=" O GLU L 72 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL L 74 " --> pdb=" O THR L 82 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR L 82 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU L 76 " --> pdb=" O LEU L 80 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU L 80 " --> pdb=" O GLU L 76 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU L 81 " --> pdb=" O ARG L 98 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ARG L 98 " --> pdb=" O LEU L 81 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR L 83 " --> pdb=" O ALA L 96 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA L 96 " --> pdb=" O TYR L 83 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLY L 85 " --> pdb=" O GLY L 94 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 228 through 229 removed outlier: 6.325A pdb=" N LEU L 277 " --> pdb=" O LEU L 310 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU L 312 " --> pdb=" O LEU L 277 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL L 279 " --> pdb=" O LEU L 312 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N PHE L 418 " --> pdb=" O ARG L 172 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU L 174 " --> pdb=" O PHE L 418 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 431 through 438 removed outlier: 6.422A pdb=" N GLU L 432 " --> pdb=" O ILE L 608 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL L 610 " --> pdb=" O GLU L 432 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N HIS L 434 " --> pdb=" O VAL L 610 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N TYR L 612 " --> pdb=" O HIS L 434 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE L 436 " --> pdb=" O TYR L 612 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 531 through 532 Processing sheet with id=AF3, first strand: chain 'L' and resid 729 through 732 removed outlier: 7.177A pdb=" N THR L 760 " --> pdb=" O GLN L 775 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 839 through 845 removed outlier: 7.364A pdb=" N LEU L 815 " --> pdb=" O LEU L 962 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU L 962 " --> pdb=" O LEU L 815 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLU L 817 " --> pdb=" O LEU L 960 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU L 960 " --> pdb=" O GLU L 817 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE L 819 " --> pdb=" O ASP L 958 " (cutoff:3.500A) 1451 hydrogen bonds defined for protein. 4095 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 8.75 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11288 1.34 - 1.47: 7635 1.47 - 1.60: 15509 1.60 - 1.73: 83 1.73 - 1.86: 235 Bond restraints: 34750 Sorted by residual: bond pdb=" C2 2TM T 101 " pdb=" O2 2TM T 101 " ideal model delta sigma weight residual 1.235 1.397 -0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" C4 2TM T 101 " pdb=" N4 2TM T 101 " ideal model delta sigma weight residual 1.342 1.451 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C1' 2TM T 101 " pdb=" O4' 2TM T 101 " ideal model delta sigma weight residual 1.409 1.506 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C2' 2TM T 101 " pdb=" C3' 2TM T 101 " ideal model delta sigma weight residual 1.543 1.447 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C2 2TM T 101 " pdb=" N3 2TM T 101 " ideal model delta sigma weight residual 1.354 1.440 -0.086 2.00e-02 2.50e+03 1.86e+01 ... (remaining 34745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.65: 46980 4.65 - 9.30: 246 9.30 - 13.94: 17 13.94 - 18.59: 3 18.59 - 23.24: 3 Bond angle restraints: 47249 Sorted by residual: angle pdb=" CA PRO D 758 " pdb=" N PRO D 758 " pdb=" CD PRO D 758 " ideal model delta sigma weight residual 112.00 97.25 14.75 1.40e+00 5.10e-01 1.11e+02 angle pdb=" CB ARG D 77 " pdb=" CG ARG D 77 " pdb=" CD ARG D 77 " ideal model delta sigma weight residual 111.30 88.78 22.52 2.30e+00 1.89e-01 9.59e+01 angle pdb=" N GLU L 912 " pdb=" CA GLU L 912 " pdb=" CB GLU L 912 " ideal model delta sigma weight residual 109.91 120.82 -10.91 1.46e+00 4.69e-01 5.58e+01 angle pdb=" N PRO L 156 " pdb=" CD PRO L 156 " pdb=" CG PRO L 156 " ideal model delta sigma weight residual 103.20 93.30 9.90 1.50e+00 4.44e-01 4.36e+01 angle pdb=" O4' DC T 17 " pdb=" C4' DC T 17 " pdb=" C3' DC T 17 " ideal model delta sigma weight residual 106.00 102.28 3.72 6.00e-01 2.78e+00 3.84e+01 ... (remaining 47244 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.97: 19895 27.97 - 55.94: 1114 55.94 - 83.91: 143 83.91 - 111.88: 11 111.88 - 139.85: 1 Dihedral angle restraints: 21164 sinusoidal: 9141 harmonic: 12023 Sorted by residual: dihedral pdb=" CA LEU L 560 " pdb=" C LEU L 560 " pdb=" N LEU L 561 " pdb=" CA LEU L 561 " ideal model delta harmonic sigma weight residual 180.00 122.94 57.06 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA GLU L 564 " pdb=" C GLU L 564 " pdb=" N ILE L 565 " pdb=" CA ILE L 565 " ideal model delta harmonic sigma weight residual -180.00 -123.99 -56.01 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA LYS C 236 " pdb=" C LYS C 236 " pdb=" N LEU C 237 " pdb=" CA LEU C 237 " ideal model delta harmonic sigma weight residual 180.00 138.09 41.91 0 5.00e+00 4.00e-02 7.03e+01 ... (remaining 21161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 4738 0.084 - 0.168: 565 0.168 - 0.253: 56 0.253 - 0.337: 5 0.337 - 0.421: 3 Chirality restraints: 5367 Sorted by residual: chirality pdb=" CB ILE C1076 " pdb=" CA ILE C1076 " pdb=" CG1 ILE C1076 " pdb=" CG2 ILE C1076 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CB VAL C 913 " pdb=" CA VAL C 913 " pdb=" CG1 VAL C 913 " pdb=" CG2 VAL C 913 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CA GLU L 912 " pdb=" N GLU L 912 " pdb=" C GLU L 912 " pdb=" CB GLU L 912 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 5364 not shown) Planarity restraints: 5995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 757 " -0.161 5.00e-02 4.00e+02 2.27e-01 8.23e+01 pdb=" N PRO D 758 " 0.390 5.00e-02 4.00e+02 pdb=" CA PRO D 758 " -0.138 5.00e-02 4.00e+02 pdb=" CD PRO D 758 " -0.091 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 287 " 0.072 5.00e-02 4.00e+02 1.07e-01 1.85e+01 pdb=" N PRO D 288 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO D 288 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO D 288 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C1316 " -0.063 5.00e-02 4.00e+02 9.54e-02 1.46e+01 pdb=" N PRO C1317 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO C1317 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C1317 " -0.052 5.00e-02 4.00e+02 ... (remaining 5992 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 300 2.50 - 3.10: 26277 3.10 - 3.70: 53448 3.70 - 4.30: 75638 4.30 - 4.90: 122806 Nonbonded interactions: 278469 Sorted by model distance: nonbonded pdb=" ND2 ASN D 910 " pdb=" O ASN E 15 " model vdw 1.904 3.120 nonbonded pdb=" OG SER C 522 " pdb=" O ARG C 687 " model vdw 2.007 3.040 nonbonded pdb=" OG1 THR D 816 " pdb=" OE1 GLU D 818 " model vdw 2.008 3.040 nonbonded pdb=" O GLU D 418 " pdb=" NH2 ARG D 481 " model vdw 2.014 3.120 nonbonded pdb=" OG SER D 143 " pdb=" O LEU D 160 " model vdw 2.016 3.040 ... (remaining 278464 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 235) selection = (chain 'B' and resid 7 through 235) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.040 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 37.280 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 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 : 0.006 0.374 34758 Z= 0.310 Angle : 1.022 23.238 47261 Z= 0.574 Chirality : 0.057 0.421 5367 Planarity : 0.007 0.227 5995 Dihedral : 16.408 139.847 13414 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.02 % Favored : 92.50 % Rotamer: Outliers : 0.90 % Allowed : 1.44 % Favored : 97.66 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.11), residues: 4161 helix: -1.06 (0.11), residues: 1549 sheet: -0.70 (0.21), residues: 518 loop : -2.38 (0.12), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 77 TYR 0.024 0.002 TYR D 511 PHE 0.023 0.002 PHE C 514 TRP 0.026 0.002 TRP D 115 HIS 0.028 0.002 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.29 (34750) covalent geometry : angle 1.02169 / 0.57 (47249) hydrogen bonds : bond 0.14987 / 10.01 ( 1493) hydrogen bonds : angle 7.45987 / 5.16 ( 4193) metal coordination : bond 0.20240 / 9.43 ( 8) metal coordination : angle 2.30601 / 1.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8322 Ramachandran restraints generated. 4161 Oldfield, 0 Emsley, 4161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8322 Ramachandran restraints generated. 4161 Oldfield, 0 Emsley, 4161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 492 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6764 (tm-30) REVERT: A 193 GLU cc_start: 0.7799 (tp30) cc_final: 0.7287 (pm20) REVERT: C 633 LEU cc_start: 0.6868 (tp) cc_final: 0.6577 (tp) REVERT: C 741 MET cc_start: 0.6868 (tpt) cc_final: 0.6583 (tpt) REVERT: D 460 ASP cc_start: 0.7089 (t0) cc_final: 0.6640 (t0) REVERT: L 61 ILE cc_start: 0.5913 (pt) cc_final: 0.5641 (pt) REVERT: L 302 LEU cc_start: 0.7261 (mt) cc_final: 0.6898 (mt) REVERT: L 909 GLU cc_start: 0.6046 (mm-30) cc_final: 0.5832 (mm-30) outliers start: 32 outliers final: 5 residues processed: 514 average time/residue: 0.2265 time to fit residues: 187.5344 Evaluate side-chains 344 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 339 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 1163 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 7.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 GLN B 18 GLN B 128 HIS B 137 ASN C 462 ASN C 573 ASN C 761 GLN C 965 GLN C1023 HIS C1080 ASN C1220 GLN D 276 ASN ** D 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN L 78 ASN ** L 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 411 HIS ** L 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 592 GLN L 604 HIS L 885 HIS ** L 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 968 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.170313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.138550 restraints weight = 71068.812| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.47 r_work: 0.3799 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 34758 Z= 0.204 Angle : 0.781 10.912 47261 Z= 0.402 Chirality : 0.047 0.339 5367 Planarity : 0.006 0.094 5995 Dihedral : 12.546 140.033 5284 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.00 % Favored : 94.86 % Rotamer: Outliers : 1.58 % Allowed : 9.96 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.15 % 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: -1.28 (0.12), residues: 4161 helix: 0.26 (0.12), residues: 1590 sheet: -0.58 (0.21), residues: 544 loop : -1.86 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 77 TYR 0.023 0.002 TYR D 46 PHE 0.036 0.002 PHE L 723 TRP 0.019 0.002 TRP L 955 HIS 0.014 0.002 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (34750) covalent geometry : angle 0.77831 / 0.40 (47249) hydrogen bonds : bond 0.05085 / 3.41 ( 1493) hydrogen bonds : angle 5.61925 / 3.87 ( 4193) metal coordination : bond 0.01846 / 0.85 ( 8) metal coordination : angle 4.49154 / 2.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8322 Ramachandran restraints generated. 4161 Oldfield, 0 Emsley, 4161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8322 Ramachandran restraints generated. 4161 Oldfield, 0 Emsley, 4161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 365 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7164 (tm-30) REVERT: B 133 LEU cc_start: 0.5162 (OUTLIER) cc_final: 0.4925 (mm) REVERT: B 186 ASN cc_start: 0.8532 (t0) cc_final: 0.8304 (t0) REVERT: C 601 ASP cc_start: 0.7038 (t0) cc_final: 0.6774 (p0) REVERT: C 614 TYR cc_start: 0.7431 (m-10) cc_final: 0.7042 (m-80) REVERT: D 413 ASP cc_start: 0.8144 (t0) cc_final: 0.7864 (m-30) REVERT: D 725 MET cc_start: 0.8315 (mtm) cc_final: 0.8039 (mtt) REVERT: D 1095 MET cc_start: 0.2580 (tmm) cc_final: 0.1562 (tpt) REVERT: D 1334 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6526 (pp20) REVERT: L 123 MET cc_start: 0.6012 (ttt) cc_final: 0.5734 (ttt) REVERT: L 254 CYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6741 (m) REVERT: L 372 MET cc_start: 0.2593 (ptm) cc_final: 0.1850 (ttp) REVERT: L 527 GLU cc_start: 0.7256 (tp30) cc_final: 0.6943 (tp30) REVERT: L 578 MET cc_start: 0.6804 (ppp) cc_final: 0.6503 (ppp) REVERT: L 585 PHE cc_start: 0.7805 (t80) cc_final: 0.7559 (t80) REVERT: L 720 MET cc_start: 0.7211 (mtp) cc_final: 0.6991 (mtp) REVERT: L 723 PHE cc_start: 0.7772 (m-80) cc_final: 0.7412 (m-80) REVERT: L 783 LEU cc_start: 0.8454 (mt) cc_final: 0.8238 (mt) REVERT: L 903 ILE cc_start: 0.6022 (OUTLIER) cc_final: 0.5735 (mp) REVERT: L 955 TRP cc_start: 0.6229 (p90) cc_final: 0.5773 (p-90) outliers start: 56 outliers final: 26 residues processed: 403 average time/residue: 0.2036 time to fit residues: 138.0137 Evaluate side-chains 346 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 316 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 481 ARG Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 861 ASN Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 254 CYS Chi-restraints excluded: chain L residue 365 LEU Chi-restraints excluded: chain L residue 508 VAL Chi-restraints excluded: chain L residue 604 HIS Chi-restraints excluded: chain L residue 789 ASP Chi-restraints excluded: chain L residue 903 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 189 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 390 optimal weight: 6.9990 chunk 202 optimal weight: 6.9990 chunk 410 optimal weight: 6.9990 chunk 395 optimal weight: 9.9990 chunk 190 optimal weight: 0.9980 chunk 402 optimal weight: 20.0000 chunk 404 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS A 84 ASN B 128 HIS ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN C 604 HIS D 45 ASN D 232 ASN D 309 ASN ** D 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** D1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 GLN L 586 ASN L 604 HIS L 889 GLN ** L 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.166797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.134851 restraints weight = 70507.521| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.95 r_work: 0.3711 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 34758 Z= 0.229 Angle : 0.737 9.685 47261 Z= 0.380 Chirality : 0.046 0.282 5367 Planarity : 0.005 0.076 5995 Dihedral : 12.272 140.951 5281 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.72 % Favored : 94.16 % Rotamer: Outliers : 2.34 % Allowed : 13.09 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.12 % 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: -0.97 (0.12), residues: 4161 helix: 0.51 (0.13), residues: 1589 sheet: -0.37 (0.22), residues: 526 loop : -1.68 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 143 TYR 0.022 0.002 TYR D 46 PHE 0.037 0.002 PHE L 723 TRP 0.031 0.002 TRP L 624 HIS 0.015 0.002 HIS L 604 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 (34750) covalent geometry : angle 0.73437 / 0.38 (47249) hydrogen bonds : bond 0.04739 / 3.21 ( 1493) hydrogen bonds : angle 5.29185 / 3.63 ( 4193) metal coordination : bond 0.01242 / 0.59 ( 8) metal coordination : angle 3.75863 / 1.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8322 Ramachandran restraints generated. 4161 Oldfield, 0 Emsley, 4161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8322 Ramachandran restraints generated. 4161 Oldfield, 0 Emsley, 4161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 342 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 LEU cc_start: 0.5680 (OUTLIER) cc_final: 0.5469 (mm) REVERT: C 322 LEU cc_start: 0.8630 (tp) cc_final: 0.8372 (pt) REVERT: C 538 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8124 (pp) REVERT: C 1164 PHE cc_start: 0.5858 (OUTLIER) cc_final: 0.5180 (t80) REVERT: C 1167 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.5427 (pm20) REVERT: D 479 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7663 (mt-10) REVERT: D 725 MET cc_start: 0.8333 (mtm) cc_final: 0.8075 (mtt) REVERT: D 822 MET cc_start: 0.7001 (ttt) cc_final: 0.6478 (ttt) REVERT: D 1095 MET cc_start: 0.2378 (tmm) cc_final: 0.1353 (tpt) REVERT: D 1327 GLU cc_start: 0.8137 (mp0) cc_final: 0.7862 (pm20) REVERT: D 1369 ARG cc_start: 0.7866 (tmm-80) cc_final: 0.7064 (ttp80) REVERT: L 123 MET cc_start: 0.6247 (ttt) cc_final: 0.5925 (ttt) REVERT: L 219 MET cc_start: 0.8324 (mmm) cc_final: 0.8072 (mmm) REVERT: L 254 CYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6766 (m) REVERT: L 271 GLU cc_start: 0.7840 (tp30) cc_final: 0.7098 (tt0) REVERT: L 372 MET cc_start: 0.2884 (ptm) cc_final: 0.2152 (ttp) REVERT: L 624 TRP cc_start: 0.8164 (t60) cc_final: 0.7590 (t60) REVERT: L 643 TYR cc_start: 0.7343 (t80) cc_final: 0.7114 (t80) REVERT: L 720 MET cc_start: 0.7163 (mtp) cc_final: 0.6962 (mtp) REVERT: L 723 PHE cc_start: 0.7775 (m-80) cc_final: 0.7445 (m-80) REVERT: L 903 ILE cc_start: 0.5659 (OUTLIER) cc_final: 0.5374 (mp) REVERT: L 955 TRP cc_start: 0.6156 (p90) cc_final: 0.5660 (p-90) outliers start: 83 outliers final: 44 residues processed: 407 average time/residue: 0.2125 time to fit residues: 145.4837 Evaluate side-chains 358 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 308 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1167 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 1220 ILE Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain L residue 224 ASN Chi-restraints excluded: chain L residue 254 CYS Chi-restraints excluded: chain L residue 508 VAL Chi-restraints excluded: chain L residue 654 LEU Chi-restraints excluded: chain L residue 751 PHE Chi-restraints excluded: chain L residue 789 ASP Chi-restraints excluded: chain L residue 903 ILE Chi-restraints excluded: chain L residue 957 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 299 optimal weight: 0.9980 chunk 296 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 362 optimal weight: 7.9990 chunk 245 optimal weight: 10.0000 chunk 366 optimal weight: 0.6980 chunk 311 optimal weight: 1.9990 chunk 357 optimal weight: 20.0000 chunk 163 optimal weight: 2.9990 chunk 279 optimal weight: 7.9990 chunk 329 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 128 HIS C 193 ASN C 437 ASN ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 GLN C1080 ASN D 45 ASN ** D 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** D1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 604 HIS ** L 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.166584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.132756 restraints weight = 70185.495| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 3.12 r_work: 0.3690 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34758 Z= 0.184 Angle : 0.677 11.204 47261 Z= 0.349 Chirality : 0.044 0.262 5367 Planarity : 0.005 0.062 5995 Dihedral : 12.161 142.656 5281 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.43 % Favored : 94.45 % Rotamer: Outliers : 2.77 % Allowed : 14.90 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.86 (0.12), residues: 4161 helix: 0.58 (0.13), residues: 1586 sheet: -0.44 (0.22), residues: 535 loop : -1.55 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 28 TYR 0.021 0.002 TYR D 46 PHE 0.025 0.002 PHE L 723 TRP 0.012 0.001 TRP L 624 HIS 0.008 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (34750) covalent geometry : angle 0.67584 / 0.35 (47249) hydrogen bonds : bond 0.04286 / 2.92 ( 1493) hydrogen bonds : angle 5.09830 / 3.49 ( 4193) metal coordination : bond 0.00783 / 0.37 ( 8) metal coordination : angle 3.00577 / 1.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8322 Ramachandran restraints generated. 4161 Oldfield, 0 Emsley, 4161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8322 Ramachandran restraints generated. 4161 Oldfield, 0 Emsley, 4161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 332 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6995 (tt) REVERT: B 133 LEU cc_start: 0.5742 (OUTLIER) cc_final: 0.5536 (mm) REVERT: C 322 LEU cc_start: 0.8614 (tp) cc_final: 0.8366 (pt) REVERT: D 133 ARG cc_start: 0.7340 (mmm160) cc_final: 0.6470 (tpp80) REVERT: D 725 MET cc_start: 0.8331 (mtm) cc_final: 0.8078 (mtm) REVERT: D 799 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.6609 (mtp85) REVERT: D 1095 MET cc_start: 0.2346 (tmm) cc_final: 0.1348 (tpt) REVERT: D 1325 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.6944 (p90) REVERT: D 1327 GLU cc_start: 0.8226 (mp0) cc_final: 0.7790 (pm20) REVERT: D 1334 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6659 (pp20) REVERT: D 1369 ARG cc_start: 0.8019 (tmm-80) cc_final: 0.7100 (ttp80) REVERT: L 254 CYS cc_start: 0.7005 (OUTLIER) cc_final: 0.6779 (m) REVERT: L 271 GLU cc_start: 0.7748 (tp30) cc_final: 0.6907 (tt0) REVERT: L 372 MET cc_start: 0.2841 (ptm) cc_final: 0.2335 (ttp) REVERT: L 624 TRP cc_start: 0.8096 (t60) cc_final: 0.7826 (t60) REVERT: L 720 MET cc_start: 0.7118 (mtp) cc_final: 0.6915 (mtp) REVERT: L 723 PHE cc_start: 0.7790 (m-80) cc_final: 0.7527 (m-80) REVERT: L 783 LEU cc_start: 0.8460 (mt) cc_final: 0.8248 (mt) REVERT: L 903 ILE cc_start: 0.5810 (OUTLIER) cc_final: 0.5497 (mp) outliers start: 98 outliers final: 52 residues processed: 406 average time/residue: 0.2110 time to fit residues: 144.0017 Evaluate side-chains 365 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 306 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 799 ARG Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1220 ILE Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain L residue 224 ASN Chi-restraints excluded: chain L residue 254 CYS Chi-restraints excluded: chain L residue 311 LEU Chi-restraints excluded: chain L residue 315 THR Chi-restraints excluded: chain L residue 508 VAL Chi-restraints excluded: chain L residue 654 LEU Chi-restraints excluded: chain L residue 789 ASP Chi-restraints excluded: chain L residue 903 ILE Chi-restraints excluded: chain L residue 957 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 188 optimal weight: 5.9990 chunk 403 optimal weight: 0.8980 chunk 250 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 263 optimal weight: 0.2980 chunk 175 optimal weight: 1.9990 chunk 286 optimal weight: 0.0050 chunk 412 optimal weight: 9.9990 chunk 278 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 128 HIS C 31 GLN ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN C1237 HIS D 700 ASN ** D 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** D1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1227 HIS L 119 GLN L 586 ASN ** L 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.168354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.135489 restraints weight = 70239.191| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 3.18 r_work: 0.3728 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 34758 Z= 0.129 Angle : 0.631 9.749 47261 Z= 0.324 Chirality : 0.043 0.306 5367 Planarity : 0.004 0.060 5995 Dihedral : 12.031 144.544 5281 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.17 % Favored : 94.71 % Rotamer: Outliers : 2.77 % Allowed : 16.17 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.13), residues: 4161 helix: 0.76 (0.13), residues: 1596 sheet: -0.26 (0.22), residues: 536 loop : -1.43 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 28 TYR 0.022 0.001 TYR C 62 PHE 0.027 0.001 PHE L 861 TRP 0.014 0.001 TRP L 624 HIS 0.008 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (34750) covalent geometry : angle 0.62932 / 0.32 (47249) hydrogen bonds : bond 0.03943 / 2.69 ( 1493) hydrogen bonds : angle 4.91337 / 3.37 ( 4193) metal coordination : bond 0.00407 / 0.19 ( 8) metal coordination : angle 2.51813 / 1.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8322 Ramachandran restraints generated. 4161 Oldfield, 0 Emsley, 4161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8322 Ramachandran restraints generated. 4161 Oldfield, 0 Emsley, 4161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 339 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 HIS cc_start: 0.6975 (OUTLIER) cc_final: 0.6227 (m90) REVERT: B 48 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6976 (tt) REVERT: B 145 LYS cc_start: 0.7323 (ttpt) cc_final: 0.7067 (tmmt) REVERT: B 181 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: C 322 LEU cc_start: 0.8603 (tp) cc_final: 0.8352 (pt) REVERT: C 538 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8137 (pp) REVERT: C 602 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7813 (pm20) REVERT: C 768 MET cc_start: 0.7747 (mtt) cc_final: 0.7522 (mtp) REVERT: C 1167 GLU cc_start: 0.6760 (pm20) cc_final: 0.6439 (pm20) REVERT: C 1246 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7691 (ptm160) REVERT: D 46 TYR cc_start: 0.5188 (OUTLIER) cc_final: 0.4144 (p90) REVERT: D 197 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.5183 (mp0) REVERT: D 413 ASP cc_start: 0.8305 (t0) cc_final: 0.7971 (m-30) REVERT: D 725 MET cc_start: 0.8300 (mtm) cc_final: 0.8037 (mtt) REVERT: D 799 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.6442 (mtp85) REVERT: D 1325 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.6822 (p90) REVERT: D 1327 GLU cc_start: 0.8109 (mp0) cc_final: 0.7706 (pm20) REVERT: D 1334 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6845 (pp20) REVERT: D 1366 HIS cc_start: 0.8297 (OUTLIER) cc_final: 0.7729 (m-70) REVERT: D 1369 ARG cc_start: 0.7939 (tmm-80) cc_final: 0.7158 (ttp80) REVERT: L 271 GLU cc_start: 0.7553 (tp30) cc_final: 0.6886 (tt0) REVERT: L 372 MET cc_start: 0.2897 (ptm) cc_final: 0.2406 (ttp) REVERT: L 376 MET cc_start: 0.4216 (mmp) cc_final: 0.3973 (mmt) REVERT: L 495 MET cc_start: 0.6829 (mtm) cc_final: 0.6483 (mtm) REVERT: L 585 PHE cc_start: 0.7542 (t80) cc_final: 0.6963 (t80) REVERT: L 624 TRP cc_start: 0.8179 (t60) cc_final: 0.7908 (t60) REVERT: L 720 MET cc_start: 0.7069 (mtp) cc_final: 0.6838 (mtp) REVERT: L 723 PHE cc_start: 0.7766 (m-80) cc_final: 0.7504 (m-80) REVERT: L 736 ASN cc_start: 0.6321 (m-40) cc_final: 0.6061 (m-40) REVERT: L 903 ILE cc_start: 0.5772 (OUTLIER) cc_final: 0.5472 (mp) outliers start: 98 outliers final: 54 residues processed: 420 average time/residue: 0.2093 time to fit residues: 145.9445 Evaluate side-chains 364 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 297 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 602 GLU Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1080 ASN Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1246 ARG Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 799 ARG Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1220 ILE Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 224 ASN Chi-restraints excluded: chain L residue 311 LEU Chi-restraints excluded: chain L residue 315 THR Chi-restraints excluded: chain L residue 508 VAL Chi-restraints excluded: chain L residue 604 HIS Chi-restraints excluded: chain L residue 654 LEU Chi-restraints excluded: chain L residue 751 PHE Chi-restraints excluded: chain L residue 789 ASP Chi-restraints excluded: chain L residue 903 ILE Chi-restraints excluded: chain L residue 957 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 337 optimal weight: 20.0000 chunk 231 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 242 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 179 optimal weight: 0.9990 chunk 305 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 414 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 193 ASN ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN D 45 ASN D 266 ASN D 739 GLN D 861 ASN ** D1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.165501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.131693 restraints weight = 69986.150| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 3.01 r_work: 0.3679 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.296 34758 Z= 0.197 Angle : 0.668 9.756 47261 Z= 0.345 Chirality : 0.044 0.288 5367 Planarity : 0.005 0.058 5995 Dihedral : 12.019 144.836 5280 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.84 % Favored : 94.04 % Rotamer: Outliers : 3.05 % Allowed : 16.59 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.69 (0.13), residues: 4161 helix: 0.69 (0.13), residues: 1596 sheet: -0.31 (0.23), residues: 516 loop : -1.45 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 526 TYR 0.021 0.002 TYR D 46 PHE 0.021 0.002 PHE C 506 TRP 0.015 0.002 TRP C 807 HIS 0.007 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (34750) covalent geometry : angle 0.66642 / 0.34 (47249) hydrogen bonds : bond 0.04171 / 2.84 ( 1493) hydrogen bonds : angle 4.91103 / 3.36 ( 4193) metal coordination : bond 0.00833 / 0.40 ( 8) metal coordination : angle 2.53992 / 1.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8322 Ramachandran restraints generated. 4161 Oldfield, 0 Emsley, 4161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8322 Ramachandran restraints generated. 4161 Oldfield, 0 Emsley, 4161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 311 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7137 (tt) REVERT: B 145 LYS cc_start: 0.7364 (ttpt) cc_final: 0.7044 (tmmt) REVERT: C 124 MET cc_start: 0.7363 (ptm) cc_final: 0.7069 (ttm) REVERT: C 322 LEU cc_start: 0.8600 (tp) cc_final: 0.8338 (pt) REVERT: C 538 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8199 (pp) REVERT: C 602 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7813 (pm20) REVERT: C 633 LEU cc_start: 0.7302 (tp) cc_final: 0.6948 (tp) REVERT: C 653 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.6287 (ttm) REVERT: C 1167 GLU cc_start: 0.6830 (pm20) cc_final: 0.6616 (pm20) REVERT: C 1246 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.6596 (ttm-80) REVERT: D 46 TYR cc_start: 0.4875 (OUTLIER) cc_final: 0.4087 (p90) REVERT: D 133 ARG cc_start: 0.7301 (mmm160) cc_final: 0.6451 (tpp80) REVERT: D 197 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.5266 (mp0) REVERT: D 402 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: D 725 MET cc_start: 0.8317 (mtm) cc_final: 0.8059 (mtt) REVERT: D 799 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.6487 (mtp85) REVERT: D 992 LYS cc_start: 0.7435 (mmmt) cc_final: 0.6881 (tptt) REVERT: D 1325 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.6941 (p90) REVERT: D 1334 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6907 (pp20) REVERT: D 1366 HIS cc_start: 0.8302 (OUTLIER) cc_final: 0.7797 (m-70) REVERT: D 1369 ARG cc_start: 0.8076 (tmm-80) cc_final: 0.7285 (ttp80) REVERT: L 219 MET cc_start: 0.8000 (mmm) cc_final: 0.7596 (mmm) REVERT: L 372 MET cc_start: 0.2945 (ptm) cc_final: 0.2497 (ttp) REVERT: L 376 MET cc_start: 0.4023 (mmp) cc_final: 0.3819 (mmt) REVERT: L 720 MET cc_start: 0.7187 (mtp) cc_final: 0.6980 (mtp) REVERT: L 723 PHE cc_start: 0.7803 (m-80) cc_final: 0.7599 (m-80) REVERT: L 736 ASN cc_start: 0.6451 (m-40) cc_final: 0.6186 (m-40) REVERT: L 903 ILE cc_start: 0.5779 (OUTLIER) cc_final: 0.5484 (mp) outliers start: 108 outliers final: 66 residues processed: 397 average time/residue: 0.2003 time to fit residues: 134.5293 Evaluate side-chains 371 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 292 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 602 GLU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1246 ARG Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 799 ARG Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1220 ILE Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 123 MET Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 224 ASN Chi-restraints excluded: chain L residue 311 LEU Chi-restraints excluded: chain L residue 315 THR Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 508 VAL Chi-restraints excluded: chain L residue 604 HIS Chi-restraints excluded: chain L residue 634 HIS Chi-restraints excluded: chain L residue 654 LEU Chi-restraints excluded: chain L residue 789 ASP Chi-restraints excluded: chain L residue 903 ILE Chi-restraints excluded: chain L residue 957 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 109 optimal weight: 9.9990 chunk 272 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 224 optimal weight: 0.7980 chunk 289 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 296 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 128 HIS ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 739 GLN D 861 ASN ** D1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 397 GLN ** L 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.161406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.125984 restraints weight = 69402.088| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.06 r_work: 0.3602 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 34758 Z= 0.304 Angle : 0.782 12.690 47261 Z= 0.404 Chirality : 0.048 0.257 5367 Planarity : 0.006 0.056 5995 Dihedral : 12.181 144.586 5280 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.46 % Favored : 93.46 % Rotamer: Outliers : 3.50 % Allowed : 17.72 % Favored : 78.78 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.97 (0.13), residues: 4161 helix: 0.39 (0.13), residues: 1600 sheet: -0.33 (0.23), residues: 497 loop : -1.57 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1330 TYR 0.022 0.002 TYR D 46 PHE 0.025 0.003 PHE C 506 TRP 0.046 0.002 TRP L 624 HIS 0.009 0.002 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.30 (34750) covalent geometry : angle 0.78043 / 0.40 (47249) hydrogen bonds : bond 0.04748 / 3.23 ( 1493) hydrogen bonds : angle 5.18967 / 3.54 ( 4193) metal coordination : bond 0.01386 / 0.69 ( 8) metal coordination : angle 3.11028 / 1.49 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8322 Ramachandran restraints generated. 4161 Oldfield, 0 Emsley, 4161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8322 Ramachandran restraints generated. 4161 Oldfield, 0 Emsley, 4161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 303 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.5961 (OUTLIER) cc_final: 0.5613 (mp) REVERT: C 124 MET cc_start: 0.7472 (ptm) cc_final: 0.7041 (ttm) REVERT: C 218 GLU cc_start: 0.7792 (pt0) cc_final: 0.7506 (pp20) REVERT: C 322 LEU cc_start: 0.8631 (tp) cc_final: 0.8372 (pt) REVERT: C 602 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7785 (pm20) REVERT: C 653 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.6574 (ttm) REVERT: C 739 ASP cc_start: 0.8145 (m-30) cc_final: 0.7797 (m-30) REVERT: C 912 ASP cc_start: 0.4313 (t0) cc_final: 0.4060 (t0) REVERT: C 1157 GLN cc_start: 0.6911 (OUTLIER) cc_final: 0.6422 (mm110) REVERT: C 1158 LYS cc_start: 0.7601 (mppt) cc_final: 0.7392 (tptp) REVERT: C 1246 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7416 (ptm160) REVERT: C 1265 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7657 (t80) REVERT: C 1304 MET cc_start: 0.8518 (tpt) cc_final: 0.8228 (tpt) REVERT: D 46 TYR cc_start: 0.5130 (OUTLIER) cc_final: 0.4480 (p90) REVERT: D 133 ARG cc_start: 0.7440 (mmm160) cc_final: 0.6682 (tpp80) REVERT: D 141 PHE cc_start: 0.7447 (m-80) cc_final: 0.6682 (m-80) REVERT: D 197 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.5350 (mp0) REVERT: D 402 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: D 413 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.7644 (m-30) REVERT: D 725 MET cc_start: 0.8341 (mtm) cc_final: 0.8077 (mtt) REVERT: D 799 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.6740 (mtp85) REVERT: D 992 LYS cc_start: 0.7610 (mmmt) cc_final: 0.7027 (tptt) REVERT: D 1095 MET cc_start: 0.2849 (tmm) cc_final: 0.1378 (tpt) REVERT: D 1325 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7064 (p90) REVERT: D 1366 HIS cc_start: 0.8391 (OUTLIER) cc_final: 0.7997 (m-70) REVERT: D 1369 ARG cc_start: 0.8047 (tmm-80) cc_final: 0.7280 (ttp80) REVERT: L 219 MET cc_start: 0.8097 (mmm) cc_final: 0.7657 (mmm) REVERT: L 372 MET cc_start: 0.3118 (ptm) cc_final: 0.2774 (ttp) REVERT: L 720 MET cc_start: 0.7204 (mtp) cc_final: 0.6984 (mtp) REVERT: L 736 ASN cc_start: 0.6563 (m-40) cc_final: 0.6304 (m-40) REVERT: L 790 LEU cc_start: 0.5102 (OUTLIER) cc_final: 0.4570 (mt) REVERT: L 903 ILE cc_start: 0.5790 (OUTLIER) cc_final: 0.5490 (mp) outliers start: 124 outliers final: 81 residues processed: 400 average time/residue: 0.2012 time to fit residues: 135.5233 Evaluate side-chains 388 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 292 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 602 GLU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1246 ARG Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 799 ARG Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 861 ASN Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1220 ILE Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 123 MET Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain L residue 224 ASN Chi-restraints excluded: chain L residue 311 LEU Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 315 THR Chi-restraints excluded: chain L residue 356 VAL Chi-restraints excluded: chain L residue 365 LEU Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 508 VAL Chi-restraints excluded: chain L residue 604 HIS Chi-restraints excluded: chain L residue 654 LEU Chi-restraints excluded: chain L residue 789 ASP Chi-restraints excluded: chain L residue 790 LEU Chi-restraints excluded: chain L residue 903 ILE Chi-restraints excluded: chain L residue 957 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 57 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 181 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 chunk 362 optimal weight: 20.0000 chunk 346 optimal weight: 9.9990 chunk 294 optimal weight: 10.0000 chunk 312 optimal weight: 0.8980 chunk 210 optimal weight: 10.0000 chunk 276 optimal weight: 9.9990 chunk 237 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** D1086 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 ASN ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 829 GLN ** L 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.165799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.132235 restraints weight = 69994.654| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.84 r_work: 0.3700 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34758 Z= 0.132 Angle : 0.654 13.940 47261 Z= 0.337 Chirality : 0.043 0.265 5367 Planarity : 0.004 0.078 5995 Dihedral : 12.006 147.356 5278 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.14 % Favored : 94.78 % Rotamer: Outliers : 2.37 % Allowed : 19.38 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.65 (0.13), residues: 4161 helix: 0.66 (0.13), residues: 1604 sheet: -0.23 (0.23), residues: 506 loop : -1.38 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 860 TYR 0.020 0.002 TYR C 62 PHE 0.038 0.001 PHE L 861 TRP 0.058 0.002 TRP L 624 HIS 0.009 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (34750) covalent geometry : angle 0.65290 / 0.34 (47249) hydrogen bonds : bond 0.03984 / 2.74 ( 1493) hydrogen bonds : angle 4.89624 / 3.34 ( 4193) metal coordination : bond 0.00407 / 0.20 ( 8) metal coordination : angle 2.40336 / 1.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8322 Ramachandran restraints generated. 4161 Oldfield, 0 Emsley, 4161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8322 Ramachandran restraints generated. 4161 Oldfield, 0 Emsley, 4161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 339 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 LYS cc_start: 0.6899 (tmmt) cc_final: 0.6542 (tmmt) REVERT: C 218 GLU cc_start: 0.7776 (pt0) cc_final: 0.7452 (pp20) REVERT: C 322 LEU cc_start: 0.8577 (tp) cc_final: 0.8304 (pt) REVERT: C 602 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7846 (pm20) REVERT: C 633 LEU cc_start: 0.7308 (tp) cc_final: 0.6918 (tp) REVERT: C 653 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6098 (ttm) REVERT: C 942 ASP cc_start: 0.5333 (t0) cc_final: 0.4797 (t0) REVERT: C 1164 PHE cc_start: 0.6462 (OUTLIER) cc_final: 0.5879 (t80) REVERT: C 1246 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.6407 (ttm-80) REVERT: C 1265 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.7291 (t80) REVERT: D 46 TYR cc_start: 0.5115 (OUTLIER) cc_final: 0.4646 (p90) REVERT: D 133 ARG cc_start: 0.7266 (mmm160) cc_final: 0.6727 (tpp80) REVERT: D 141 PHE cc_start: 0.7367 (m-80) cc_final: 0.6612 (m-80) REVERT: D 197 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.5559 (mp0) REVERT: D 402 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: D 413 ASP cc_start: 0.8273 (t0) cc_final: 0.7933 (m-30) REVERT: D 543 SER cc_start: 0.8746 (t) cc_final: 0.8503 (p) REVERT: D 725 MET cc_start: 0.8322 (mtm) cc_final: 0.8091 (mtt) REVERT: D 799 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.6538 (mtp85) REVERT: D 992 LYS cc_start: 0.7659 (mmmt) cc_final: 0.7077 (tptm) REVERT: D 1040 MET cc_start: -0.1810 (tpt) cc_final: -0.2242 (mmm) REVERT: D 1095 MET cc_start: 0.2958 (tmm) cc_final: 0.1623 (tpt) REVERT: D 1325 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.6826 (p90) REVERT: D 1334 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6836 (pp20) REVERT: D 1366 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.7831 (m-70) REVERT: D 1369 ARG cc_start: 0.8020 (tmm-80) cc_final: 0.7301 (ttp80) REVERT: L 142 MET cc_start: 0.6235 (tmm) cc_final: 0.5827 (tmm) REVERT: L 218 GLU cc_start: 0.7710 (pp20) cc_final: 0.7469 (pp20) REVERT: L 219 MET cc_start: 0.8158 (mmm) cc_final: 0.7711 (mmm) REVERT: L 265 ARG cc_start: 0.6925 (ttm-80) cc_final: 0.6432 (ttm-80) REVERT: L 271 GLU cc_start: 0.8116 (tp30) cc_final: 0.7163 (tt0) REVERT: L 349 TYR cc_start: 0.6187 (t80) cc_final: 0.5957 (t80) REVERT: L 372 MET cc_start: 0.3054 (ptm) cc_final: 0.2697 (ttp) REVERT: L 578 MET cc_start: 0.6627 (ppp) cc_final: 0.6361 (ppp) REVERT: L 720 MET cc_start: 0.6953 (mtp) cc_final: 0.6748 (mtp) REVERT: L 736 ASN cc_start: 0.6610 (m-40) cc_final: 0.6342 (m-40) REVERT: L 903 ILE cc_start: 0.5776 (OUTLIER) cc_final: 0.5475 (mp) outliers start: 84 outliers final: 53 residues processed: 404 average time/residue: 0.2074 time to fit residues: 140.4562 Evaluate side-chains 383 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 317 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 602 GLU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1246 ARG Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 799 ARG Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1220 ILE Chi-restraints excluded: chain D residue 1272 SER Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain L residue 224 ASN Chi-restraints excluded: chain L residue 311 LEU Chi-restraints excluded: chain L residue 315 THR Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 604 HIS Chi-restraints excluded: chain L residue 634 HIS Chi-restraints excluded: chain L residue 654 LEU Chi-restraints excluded: chain L residue 789 ASP Chi-restraints excluded: chain L residue 903 ILE Chi-restraints excluded: chain L residue 957 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 163 optimal weight: 0.7980 chunk 265 optimal weight: 0.0980 chunk 365 optimal weight: 5.9990 chunk 356 optimal weight: 20.0000 chunk 97 optimal weight: 0.9990 chunk 388 optimal weight: 30.0000 chunk 399 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 194 optimal weight: 6.9990 chunk 232 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 227 GLN ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN D 861 ASN ** D1086 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 324 HIS L 721 ASN L 829 GLN ** L 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.164933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.129903 restraints weight = 69248.192| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.79 r_work: 0.3679 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 34758 Z= 0.154 Angle : 0.661 13.873 47261 Z= 0.338 Chirality : 0.043 0.268 5367 Planarity : 0.004 0.064 5995 Dihedral : 11.918 147.596 5278 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.58 % Favored : 94.35 % Rotamer: Outliers : 2.43 % Allowed : 19.41 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.61 (0.13), residues: 4161 helix: 0.68 (0.13), residues: 1614 sheet: -0.16 (0.23), residues: 504 loop : -1.37 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D1330 TYR 0.025 0.001 TYR C 62 PHE 0.048 0.001 PHE L 723 TRP 0.081 0.002 TRP L 624 HIS 0.008 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (34750) covalent geometry : angle 0.66041 / 0.34 (47249) hydrogen bonds : bond 0.03986 / 2.73 ( 1493) hydrogen bonds : angle 4.88239 / 3.34 ( 4193) metal coordination : bond 0.00532 / 0.25 ( 8) metal coordination : angle 2.28427 / 1.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8322 Ramachandran restraints generated. 4161 Oldfield, 0 Emsley, 4161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8322 Ramachandran restraints generated. 4161 Oldfield, 0 Emsley, 4161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 325 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 MET cc_start: 0.7213 (tmm) cc_final: 0.6579 (tmm) REVERT: C 218 GLU cc_start: 0.7783 (pt0) cc_final: 0.7468 (pp20) REVERT: C 322 LEU cc_start: 0.8579 (tp) cc_final: 0.8314 (pt) REVERT: C 379 GLU cc_start: 0.6991 (pm20) cc_final: 0.6673 (pm20) REVERT: C 602 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7897 (pm20) REVERT: C 633 LEU cc_start: 0.7293 (tp) cc_final: 0.6900 (tp) REVERT: C 653 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6084 (ttm) REVERT: C 739 ASP cc_start: 0.8082 (m-30) cc_final: 0.7767 (m-30) REVERT: C 1164 PHE cc_start: 0.6508 (OUTLIER) cc_final: 0.5978 (t80) REVERT: C 1167 GLU cc_start: 0.7051 (pm20) cc_final: 0.6353 (pm20) REVERT: C 1246 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.6513 (ttm-80) REVERT: C 1265 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7459 (t80) REVERT: C 1296 ASP cc_start: 0.7899 (t0) cc_final: 0.7677 (m-30) REVERT: C 1304 MET cc_start: 0.8716 (tpt) cc_final: 0.8425 (tpt) REVERT: D 46 TYR cc_start: 0.5110 (OUTLIER) cc_final: 0.4706 (p90) REVERT: D 133 ARG cc_start: 0.7338 (mmm160) cc_final: 0.6747 (tpp80) REVERT: D 141 PHE cc_start: 0.7409 (m-80) cc_final: 0.6665 (m-80) REVERT: D 197 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.5583 (mp0) REVERT: D 402 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: D 413 ASP cc_start: 0.8317 (t0) cc_final: 0.7973 (m-30) REVERT: D 481 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.8021 (ptm160) REVERT: D 543 SER cc_start: 0.8759 (t) cc_final: 0.8555 (p) REVERT: D 725 MET cc_start: 0.8306 (mtm) cc_final: 0.8075 (mtt) REVERT: D 799 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.6536 (mtp85) REVERT: D 992 LYS cc_start: 0.7574 (mmmt) cc_final: 0.7018 (tptp) REVERT: D 1040 MET cc_start: -0.1862 (tpt) cc_final: -0.2346 (mmm) REVERT: D 1095 MET cc_start: 0.2949 (tmm) cc_final: 0.1607 (tpt) REVERT: D 1325 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.6907 (p90) REVERT: D 1334 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6875 (pp20) REVERT: D 1366 HIS cc_start: 0.8297 (OUTLIER) cc_final: 0.7847 (m-70) REVERT: D 1369 ARG cc_start: 0.8038 (tmm-80) cc_final: 0.7295 (ttp80) REVERT: L 142 MET cc_start: 0.6442 (tmm) cc_final: 0.6129 (tmm) REVERT: L 219 MET cc_start: 0.8071 (mmm) cc_final: 0.7628 (mmm) REVERT: L 265 ARG cc_start: 0.6870 (ttm-80) cc_final: 0.6381 (ttm-80) REVERT: L 271 GLU cc_start: 0.8101 (tp30) cc_final: 0.7124 (tt0) REVERT: L 302 LEU cc_start: 0.8492 (mt) cc_final: 0.8285 (mt) REVERT: L 372 MET cc_start: 0.3249 (ptm) cc_final: 0.2743 (ttp) REVERT: L 578 MET cc_start: 0.6671 (ppp) cc_final: 0.6368 (ppp) REVERT: L 736 ASN cc_start: 0.6624 (m-40) cc_final: 0.6298 (m-40) REVERT: L 894 GLN cc_start: 0.5771 (mt0) cc_final: 0.5529 (mp10) REVERT: L 903 ILE cc_start: 0.5794 (OUTLIER) cc_final: 0.5496 (mp) outliers start: 86 outliers final: 64 residues processed: 391 average time/residue: 0.2121 time to fit residues: 137.6414 Evaluate side-chains 393 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 315 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 602 GLU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1246 ARG Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 481 ARG Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 799 ARG Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 861 ASN Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1220 ILE Chi-restraints excluded: chain D residue 1272 SER Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain L residue 224 ASN Chi-restraints excluded: chain L residue 311 LEU Chi-restraints excluded: chain L residue 315 THR Chi-restraints excluded: chain L residue 508 VAL Chi-restraints excluded: chain L residue 604 HIS Chi-restraints excluded: chain L residue 654 LEU Chi-restraints excluded: chain L residue 789 ASP Chi-restraints excluded: chain L residue 903 ILE Chi-restraints excluded: chain L residue 957 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 339 optimal weight: 10.0000 chunk 217 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 395 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 196 optimal weight: 20.0000 chunk 332 optimal weight: 9.9990 chunk 187 optimal weight: 0.0970 chunk 130 optimal weight: 1.9990 chunk 270 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN D 861 ASN ** D1086 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1279 GLN ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 324 HIS L 387 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.165641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.131049 restraints weight = 70394.272| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.93 r_work: 0.3690 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34758 Z= 0.143 Angle : 0.656 13.894 47261 Z= 0.336 Chirality : 0.043 0.268 5367 Planarity : 0.004 0.057 5995 Dihedral : 11.888 147.907 5278 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.67 % Favored : 94.26 % Rotamer: Outliers : 2.34 % Allowed : 19.78 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.13), residues: 4161 helix: 0.68 (0.13), residues: 1614 sheet: -0.16 (0.24), residues: 502 loop : -1.33 (0.13), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C1033 TYR 0.028 0.001 TYR L 349 PHE 0.027 0.001 PHE D1274 TRP 0.064 0.002 TRP L 624 HIS 0.008 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (34750) covalent geometry : angle 0.65523 / 0.34 (47249) hydrogen bonds : bond 0.03916 / 2.68 ( 1493) hydrogen bonds : angle 4.88229 / 3.34 ( 4193) metal coordination : bond 0.00446 / 0.21 ( 8) metal coordination : angle 2.24563 / 1.06 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8322 Ramachandran restraints generated. 4161 Oldfield, 0 Emsley, 4161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8322 Ramachandran restraints generated. 4161 Oldfield, 0 Emsley, 4161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 323 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 MET cc_start: 0.7194 (tmm) cc_final: 0.6575 (tmm) REVERT: B 145 LYS cc_start: 0.6893 (tmmt) cc_final: 0.6571 (tmmt) REVERT: C 218 GLU cc_start: 0.7814 (pt0) cc_final: 0.7471 (pp20) REVERT: C 322 LEU cc_start: 0.8576 (tp) cc_final: 0.8306 (pt) REVERT: C 379 GLU cc_start: 0.7033 (pm20) cc_final: 0.6757 (pm20) REVERT: C 542 ARG cc_start: 0.7887 (mmp80) cc_final: 0.6990 (mmp80) REVERT: C 602 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7850 (pm20) REVERT: C 633 LEU cc_start: 0.7290 (tp) cc_final: 0.6894 (tp) REVERT: C 653 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.6051 (ttm) REVERT: C 739 ASP cc_start: 0.8103 (m-30) cc_final: 0.7777 (m-30) REVERT: C 942 ASP cc_start: 0.5554 (t0) cc_final: 0.5334 (t0) REVERT: C 1164 PHE cc_start: 0.6492 (OUTLIER) cc_final: 0.5994 (t80) REVERT: C 1167 GLU cc_start: 0.7070 (pm20) cc_final: 0.6410 (pm20) REVERT: C 1265 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7448 (t80) REVERT: C 1296 ASP cc_start: 0.7923 (t0) cc_final: 0.7661 (m-30) REVERT: C 1304 MET cc_start: 0.8755 (tpt) cc_final: 0.8408 (tpt) REVERT: D 46 TYR cc_start: 0.5112 (OUTLIER) cc_final: 0.4702 (p90) REVERT: D 133 ARG cc_start: 0.7342 (mmm160) cc_final: 0.6676 (tpp80) REVERT: D 141 PHE cc_start: 0.7430 (m-80) cc_final: 0.6736 (m-80) REVERT: D 197 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.5573 (mp0) REVERT: D 402 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: D 413 ASP cc_start: 0.8327 (t0) cc_final: 0.7984 (m-30) REVERT: D 481 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7918 (ptm160) REVERT: D 543 SER cc_start: 0.8839 (t) cc_final: 0.8560 (p) REVERT: D 725 MET cc_start: 0.8311 (mtm) cc_final: 0.8080 (mtt) REVERT: D 799 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.6516 (mtp85) REVERT: D 992 LYS cc_start: 0.7527 (mmmt) cc_final: 0.6960 (tptm) REVERT: D 1040 MET cc_start: -0.1844 (tpt) cc_final: -0.2293 (mmm) REVERT: D 1095 MET cc_start: 0.3169 (tmm) cc_final: 0.1931 (tpt) REVERT: D 1325 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.6895 (p90) REVERT: D 1334 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6849 (pp20) REVERT: D 1366 HIS cc_start: 0.8306 (OUTLIER) cc_final: 0.7854 (m-70) REVERT: D 1369 ARG cc_start: 0.8058 (tmm-80) cc_final: 0.7301 (ttp80) REVERT: L 142 MET cc_start: 0.6590 (tmm) cc_final: 0.6262 (tmm) REVERT: L 219 MET cc_start: 0.8059 (mmm) cc_final: 0.7612 (mmm) REVERT: L 265 ARG cc_start: 0.6721 (ttm-80) cc_final: 0.6237 (ttm-80) REVERT: L 271 GLU cc_start: 0.8089 (tp30) cc_final: 0.7124 (tt0) REVERT: L 302 LEU cc_start: 0.8506 (mt) cc_final: 0.8299 (mt) REVERT: L 372 MET cc_start: 0.3139 (ptm) cc_final: 0.2660 (ttp) REVERT: L 376 MET cc_start: 0.4532 (mmm) cc_final: 0.3981 (mtm) REVERT: L 578 MET cc_start: 0.6650 (ppp) cc_final: 0.6355 (ppp) REVERT: L 736 ASN cc_start: 0.6635 (m-40) cc_final: 0.6313 (m-40) REVERT: L 894 GLN cc_start: 0.5748 (mt0) cc_final: 0.5511 (mp10) REVERT: L 903 ILE cc_start: 0.5761 (OUTLIER) cc_final: 0.5468 (mp) outliers start: 83 outliers final: 65 residues processed: 387 average time/residue: 0.2023 time to fit residues: 131.1317 Evaluate side-chains 393 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 315 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 602 GLU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 481 ARG Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 799 ARG Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1220 ILE Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1272 SER Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain L residue 224 ASN Chi-restraints excluded: chain L residue 311 LEU Chi-restraints excluded: chain L residue 315 THR Chi-restraints excluded: chain L residue 508 VAL Chi-restraints excluded: chain L residue 604 HIS Chi-restraints excluded: chain L residue 634 HIS Chi-restraints excluded: chain L residue 654 LEU Chi-restraints excluded: chain L residue 789 ASP Chi-restraints excluded: chain L residue 903 ILE Chi-restraints excluded: chain L residue 957 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 279 optimal weight: 0.0040 chunk 31 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 392 optimal weight: 0.0980 chunk 344 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 397 optimal weight: 0.9990 chunk 399 optimal weight: 8.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** D1086 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 324 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.165098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.130198 restraints weight = 70091.875| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.95 r_work: 0.3678 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34758 Z= 0.159 Angle : 0.659 13.670 47261 Z= 0.339 Chirality : 0.043 0.268 5367 Planarity : 0.004 0.058 5995 Dihedral : 11.846 148.263 5278 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 2.40 % Allowed : 19.92 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.55 (0.13), residues: 4161 helix: 0.68 (0.13), residues: 1620 sheet: -0.04 (0.24), residues: 486 loop : -1.31 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C1246 TYR 0.021 0.001 TYR C 62 PHE 0.013 0.001 PHE C 506 TRP 0.057 0.002 TRP L 624 HIS 0.008 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (34750) covalent geometry : angle 0.65856 / 0.34 (47249) hydrogen bonds : bond 0.03923 / 2.68 ( 1493) hydrogen bonds : angle 4.88602 / 3.34 ( 4193) metal coordination : bond 0.00587 / 0.28 ( 8) metal coordination : angle 2.28583 / 1.08 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8800.86 seconds wall clock time: 151 minutes 34.08 seconds (9094.08 seconds total)