Starting phenix.real_space_refine on Fri Jun 5 23:41:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w3e_65598/06_2026/9w3e_65598.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w3e_65598/06_2026/9w3e_65598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w3e_65598/06_2026/9w3e_65598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w3e_65598/06_2026/9w3e_65598.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w3e_65598/06_2026/9w3e_65598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w3e_65598/06_2026/9w3e_65598.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 14851 2.51 5 N 4196 2.21 5 O 4536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23687 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "B" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 9499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1206, 9499 Classifications: {'peptide': 1206} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1152} Chain breaks: 2 Chain: "D" Number of atoms: 9138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9138 Classifications: {'peptide': 1166} Link IDs: {'PCIS': 2, 'PTRANS': 45, 'TRANS': 1118} Chain breaks: 1 Chain: "G" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "E" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 557 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Time building chain proxies: 5.34, per 1000 atoms: 0.23 Number of scatterers: 23687 At special positions: 0 Unit cell: (138.04, 136.85, 152.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 4536 8.00 N 4196 7.00 C 14851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 1.1 seconds 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5580 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 38 sheets defined 43.4% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 34 through 51 removed outlier: 3.727A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.770A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.655A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.132A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 212 through 228 Processing helix chain 'C' and resid 4 through 10 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.753A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 57 removed outlier: 3.726A pdb=" N ALA C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.582A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.848A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 409 Processing helix chain 'C' and resid 421 through 437 removed outlier: 3.593A 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 481 removed outlier: 3.533A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 Processing helix chain 'C' and resid 495 through 509 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.855A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.712A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 569 removed outlier: 4.084A pdb=" N ASN C 568 " --> pdb=" O GLU C 565 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE C 569 " --> pdb=" O GLY C 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 565 through 569' Processing helix chain 'C' and resid 607 through 612 removed outlier: 4.045A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 660 removed outlier: 3.561A pdb=" N GLN C 659 " --> pdb=" O SER C 656 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 656 through 660' Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.618A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.790A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 738 through 741 removed outlier: 3.799A pdb=" N MET C 741 " --> pdb=" O GLU C 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 738 through 741' Processing helix chain 'C' and resid 820 through 826 Processing helix chain 'C' and resid 858 through 864 removed outlier: 4.396A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 982 removed outlier: 3.516A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 4.179A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C1000 " --> pdb=" O TRP C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1038 Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.521A pdb=" N MET C1085 " --> pdb=" O ILE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.169A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.509A 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: 3.570A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.628A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.753A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.920A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 191 Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.711A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.883A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 309 removed outlier: 3.538A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN D 309 " --> pdb=" O ALA D 305 " (cutoff:3.500A) 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 416 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 452 through 458 removed outlier: 4.342A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 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 580 Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.607A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.650A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.569A pdb=" N SER D 655 " --> pdb=" O HIS D 651 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA D 659 " --> pdb=" O SER D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.190A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.573A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 1139 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.727A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.348A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.730A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.647A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1373 Processing helix chain 'G' and resid 12 through 17 removed outlier: 3.851A pdb=" N LEU G 17 " --> pdb=" O SER G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 29 Processing helix chain 'G' and resid 33 through 43 Processing helix chain 'G' and resid 78 through 83 Processing helix chain 'G' and resid 88 through 96 removed outlier: 3.881A pdb=" N ALA G 96 " --> pdb=" O ILE G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 109 Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.502A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 73 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 4.881A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS A 200 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL A 187 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 202 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR A 185 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU A 204 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE A 183 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU A 206 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 removed outlier: 4.240A pdb=" N THR A 101 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.083A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 16 removed outlier: 6.586A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N HIS B 23 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N THR B 207 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LYS B 25 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N MET B 205 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N THR B 27 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE B 203 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLU B 29 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU B 201 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 196 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ARG B 191 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU B 198 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ALA B 189 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 3.734A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.542A pdb=" N GLY B 108 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N HIS B 132 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.448A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 7.055A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET C 124 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU C 100 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU C 102 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LYS C 118 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ILE C 104 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.402A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 159 removed outlier: 4.712A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.529A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB7, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.521A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.111A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC1, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC2, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.535A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.820A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AC5, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.785A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.762A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AC8, first strand: chain 'C' and resid 1335 through 1338 Processing sheet with id=AC9, first strand: chain 'D' and resid 103 through 112 removed outlier: 10.302A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.785A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 159 through 160 removed outlier: 7.389A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD3, first strand: chain 'D' and resid 703 through 707 Processing sheet with id=AD4, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AD5, first strand: chain 'D' and resid 819 through 822 Processing sheet with id=AD6, first strand: chain 'D' and resid 825 through 826 removed outlier: 3.618A pdb=" N GLU D 833 " --> pdb=" O VAL D 825 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 848 through 849 Processing sheet with id=AD8, first strand: chain 'D' and resid 1186 through 1191 removed outlier: 6.681A pdb=" N LYS D1172 " --> pdb=" O GLU D1168 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU D1168 " --> pdb=" O LYS D1172 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARG D1174 " --> pdb=" O GLY D1166 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.682A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 7 through 11 Processing sheet with id=AE2, first strand: chain 'G' and resid 56 through 57 removed outlier: 3.650A pdb=" N GLY G 68 " --> pdb=" O ARG G 56 " (cutoff:3.500A) 1066 hydrogen bonds defined for protein. 3030 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.81 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8110 1.34 - 1.46: 4747 1.46 - 1.59: 11008 1.59 - 1.71: 0 1.71 - 1.83: 181 Bond restraints: 24046 Sorted by residual: bond pdb=" N GLU C 40 " pdb=" CA GLU C 40 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.22e-02 6.72e+03 1.14e+01 bond pdb=" N LEU G 61 " pdb=" CA LEU G 61 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.25e+00 bond pdb=" N MET C 130 " pdb=" CA MET C 130 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.21e-02 6.83e+03 6.14e+00 bond pdb=" N GLU C 813 " pdb=" CA GLU C 813 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.41e-02 5.03e+03 5.73e+00 bond pdb=" N MET C 370 " pdb=" CA MET C 370 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.28e-02 6.10e+03 5.63e+00 ... (remaining 24041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 32069 2.87 - 5.75: 333 5.75 - 8.62: 46 8.62 - 11.49: 9 11.49 - 14.37: 8 Bond angle restraints: 32465 Sorted by residual: angle pdb=" CB MET C 1 " pdb=" CG MET C 1 " pdb=" SD MET C 1 " ideal model delta sigma weight residual 112.70 127.07 -14.37 3.00e+00 1.11e-01 2.29e+01 angle pdb=" CG MET D 298 " pdb=" SD MET D 298 " pdb=" CE MET D 298 " ideal model delta sigma weight residual 100.90 111.35 -10.45 2.20e+00 2.07e-01 2.26e+01 angle pdb=" CA GLN E 62 " pdb=" CB GLN E 62 " pdb=" CG GLN E 62 " ideal model delta sigma weight residual 114.10 123.06 -8.96 2.00e+00 2.50e-01 2.01e+01 angle pdb=" CB MET C1290 " pdb=" CG MET C1290 " pdb=" SD MET C1290 " ideal model delta sigma weight residual 112.70 125.92 -13.22 3.00e+00 1.11e-01 1.94e+01 angle pdb=" CB MET C 369 " pdb=" CG MET C 369 " pdb=" SD MET C 369 " ideal model delta sigma weight residual 112.70 125.50 -12.80 3.00e+00 1.11e-01 1.82e+01 ... (remaining 32460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 13210 18.06 - 36.11: 1327 36.11 - 54.17: 231 54.17 - 72.23: 43 72.23 - 90.28: 15 Dihedral angle restraints: 14826 sinusoidal: 6153 harmonic: 8673 Sorted by residual: dihedral pdb=" CA LYS D 179 " pdb=" C LYS D 179 " pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta harmonic sigma weight residual -180.00 -155.57 -24.43 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA PRO D 288 " pdb=" C PRO D 288 " pdb=" N ASP D 289 " pdb=" CA ASP D 289 " ideal model delta harmonic sigma weight residual -180.00 -157.78 -22.22 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA SER A 49 " pdb=" C SER A 49 " pdb=" N SER A 50 " pdb=" CA SER A 50 " ideal model delta harmonic sigma weight residual -180.00 -159.38 -20.62 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 14823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2769 0.050 - 0.100: 675 0.100 - 0.150: 210 0.150 - 0.200: 24 0.200 - 0.249: 5 Chirality restraints: 3683 Sorted by residual: chirality pdb=" CA ASP C 814 " pdb=" N ASP C 814 " pdb=" C ASP C 814 " pdb=" CB ASP C 814 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CG LEU D 279 " pdb=" CB LEU D 279 " pdb=" CD1 LEU D 279 " pdb=" CD2 LEU D 279 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CG LEU B 171 " pdb=" CB LEU B 171 " pdb=" CD1 LEU B 171 " pdb=" CD2 LEU B 171 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 3680 not shown) Planarity restraints: 4268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 39 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C ILE C 39 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE C 39 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU C 40 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 189 " 0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO C 190 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 190 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 190 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 36 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.85e+00 pdb=" CG ASP E 36 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASP E 36 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP E 36 " 0.016 2.00e-02 2.50e+03 ... (remaining 4265 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5606 2.79 - 3.31: 21155 3.31 - 3.84: 41025 3.84 - 4.37: 46807 4.37 - 4.90: 79955 Nonbonded interactions: 194548 Sorted by model distance: nonbonded pdb=" O LEU D 8 " pdb=" OG1 THR D 12 " model vdw 2.257 3.040 nonbonded pdb=" O ILE C 11 " pdb=" OH TYR C1149 " model vdw 2.285 3.040 nonbonded pdb=" O THR B 116 " pdb=" OG1 THR B 116 " model vdw 2.300 3.040 nonbonded pdb=" O ARG D 214 " pdb=" OG1 THR D 218 " model vdw 2.305 3.040 nonbonded pdb=" OE2 GLU D1327 " pdb=" OG1 THR D1329 " model vdw 2.307 3.040 ... (remaining 194543 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 232) selection = (chain 'B' and resid 7 through 232) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 24.120 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24046 Z= 0.230 Angle : 0.803 14.367 32465 Z= 0.431 Chirality : 0.049 0.249 3683 Planarity : 0.006 0.070 4268 Dihedral : 14.598 90.281 9246 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.67 % Favored : 97.27 % Rotamer: Outliers : 0.54 % Allowed : 13.57 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.14), residues: 3001 helix: -0.88 (0.13), residues: 1182 sheet: 0.26 (0.26), residues: 412 loop : -0.53 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 312 TYR 0.024 0.002 TYR G 51 PHE 0.040 0.002 PHE C1025 TRP 0.012 0.001 TRP G 81 HIS 0.006 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.23 (24046) covalent geometry : angle 0.80276 / 0.43 (32465) hydrogen bonds : bond 0.14428 / 9.73 ( 1064) hydrogen bonds : angle 6.66079 / 4.70 ( 3030) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1319 MET cc_start: 0.8412 (mmp) cc_final: 0.7912 (mmm) REVERT: D 130 MET cc_start: 0.8046 (mmm) cc_final: 0.7810 (mmp) REVERT: D 725 MET cc_start: 0.9462 (mpp) cc_final: 0.8474 (mpp) REVERT: D 743 MET cc_start: 0.8732 (tmm) cc_final: 0.8504 (tmm) outliers start: 14 outliers final: 1 residues processed: 125 average time/residue: 0.1545 time to fit residues: 31.8870 Evaluate side-chains 112 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 437 ASN C1324 ASN D 294 ASN D1259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.041023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.029473 restraints weight = 165214.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.030435 restraints weight = 83472.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.031040 restraints weight = 55579.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.031413 restraints weight = 43529.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.031635 restraints weight = 37662.296| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24046 Z= 0.196 Angle : 0.540 6.667 32465 Z= 0.280 Chirality : 0.041 0.154 3683 Planarity : 0.004 0.053 4268 Dihedral : 4.273 19.778 3316 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.17 % Allowed : 13.06 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.15), residues: 3001 helix: 0.92 (0.15), residues: 1184 sheet: 0.22 (0.26), residues: 385 loop : -0.01 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1373 TYR 0.012 0.001 TYR C 555 PHE 0.018 0.001 PHE C1025 TRP 0.009 0.001 TRP D 33 HIS 0.004 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.20 (24046) covalent geometry : angle 0.53995 / 0.28 (32465) hydrogen bonds : bond 0.03819 / 2.66 ( 1064) hydrogen bonds : angle 4.91593 / 3.51 ( 3030) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 102 MET cc_start: 0.7018 (ppp) cc_final: 0.6452 (ppp) REVERT: D 130 MET cc_start: 0.8038 (mmm) cc_final: 0.7832 (mmm) REVERT: D 298 MET cc_start: 0.8362 (mpp) cc_final: 0.8081 (mpp) REVERT: G 16 ARG cc_start: 0.8833 (tpm170) cc_final: 0.8251 (tpm170) REVERT: G 25 PHE cc_start: 0.8716 (m-10) cc_final: 0.8197 (m-80) outliers start: 30 outliers final: 15 residues processed: 135 average time/residue: 0.1580 time to fit residues: 35.7035 Evaluate side-chains 125 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 129 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 chunk 178 optimal weight: 30.0000 chunk 154 optimal weight: 8.9990 chunk 244 optimal weight: 0.9980 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.041171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.029684 restraints weight = 165453.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.030638 restraints weight = 82989.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.031245 restraints weight = 55049.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.031616 restraints weight = 43032.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.031816 restraints weight = 37265.482| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24046 Z= 0.144 Angle : 0.480 8.660 32465 Z= 0.247 Chirality : 0.040 0.147 3683 Planarity : 0.003 0.049 4268 Dihedral : 3.947 18.020 3314 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.59 % Allowed : 13.18 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.15), residues: 3001 helix: 1.51 (0.15), residues: 1185 sheet: 0.16 (0.27), residues: 369 loop : 0.16 (0.17), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1355 TYR 0.011 0.001 TYR D 631 PHE 0.036 0.001 PHE D 7 TRP 0.005 0.001 TRP C 807 HIS 0.004 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (24046) covalent geometry : angle 0.47956 / 0.25 (32465) hydrogen bonds : bond 0.03376 / 2.36 ( 1064) hydrogen bonds : angle 4.57298 / 3.28 ( 3030) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1119 MET cc_start: 0.8936 (tpt) cc_final: 0.8597 (tpp) REVERT: D 102 MET cc_start: 0.7052 (ppp) cc_final: 0.6452 (ppp) REVERT: D 298 MET cc_start: 0.8205 (mpp) cc_final: 0.7991 (mpp) REVERT: G 16 ARG cc_start: 0.8877 (tpm170) cc_final: 0.8416 (tpm170) REVERT: G 62 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8013 (ptt-90) outliers start: 41 outliers final: 23 residues processed: 151 average time/residue: 0.1648 time to fit residues: 40.7911 Evaluate side-chains 135 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1326 LEU Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 72 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 168 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 28 optimal weight: 30.0000 chunk 151 optimal weight: 0.7980 chunk 153 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 179 optimal weight: 30.0000 overall best weight: 7.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1336 ASN G 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.040047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.028600 restraints weight = 168982.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.029518 restraints weight = 85976.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.030100 restraints weight = 57473.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.030462 restraints weight = 45176.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.030678 restraints weight = 39105.453| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 24046 Z= 0.295 Angle : 0.621 9.944 32465 Z= 0.314 Chirality : 0.042 0.152 3683 Planarity : 0.004 0.048 4268 Dihedral : 4.263 22.181 3314 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.60 % Allowed : 13.14 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.15), residues: 3001 helix: 1.44 (0.15), residues: 1193 sheet: -0.04 (0.26), residues: 402 loop : 0.18 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 883 TYR 0.021 0.002 TYR D 679 PHE 0.024 0.002 PHE C1025 TRP 0.007 0.001 TRP D 409 HIS 0.005 0.001 HIS C 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.29 (24046) covalent geometry : angle 0.62148 / 0.31 (32465) hydrogen bonds : bond 0.03870 / 2.70 ( 1064) hydrogen bonds : angle 4.85581 / 3.46 ( 3030) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 103 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1319 MET cc_start: 0.8526 (mmp) cc_final: 0.8184 (mmm) REVERT: D 102 MET cc_start: 0.7374 (ppp) cc_final: 0.6702 (ppp) REVERT: D 298 MET cc_start: 0.8323 (mpp) cc_final: 0.7797 (mtt) REVERT: D 747 MET cc_start: 0.8450 (mmm) cc_final: 0.7919 (mmm) REVERT: D 822 MET cc_start: 0.9328 (tpp) cc_final: 0.8994 (tpp) REVERT: D 878 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7430 (t0) REVERT: G 62 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8025 (ptt-90) outliers start: 67 outliers final: 42 residues processed: 162 average time/residue: 0.1490 time to fit residues: 39.9841 Evaluate side-chains 145 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 101 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1326 LEU Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 45 MET Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 72 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 76 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 293 optimal weight: 10.0000 chunk 55 optimal weight: 30.0000 chunk 165 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 268 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.040519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.028916 restraints weight = 167755.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.029872 restraints weight = 85440.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.030470 restraints weight = 57000.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.030833 restraints weight = 44800.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.031026 restraints weight = 38900.534| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24046 Z= 0.189 Angle : 0.527 9.585 32465 Z= 0.266 Chirality : 0.041 0.145 3683 Planarity : 0.003 0.046 4268 Dihedral : 4.054 21.949 3314 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.43 % Favored : 97.53 % Rotamer: Outliers : 1.98 % Allowed : 13.72 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.16), residues: 3001 helix: 1.66 (0.15), residues: 1187 sheet: 0.05 (0.27), residues: 360 loop : 0.26 (0.17), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1373 TYR 0.023 0.001 TYR D 679 PHE 0.019 0.001 PHE C1025 TRP 0.005 0.001 TRP C 807 HIS 0.003 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (24046) covalent geometry : angle 0.52656 / 0.27 (32465) hydrogen bonds : bond 0.03446 / 2.41 ( 1064) hydrogen bonds : angle 4.62334 / 3.32 ( 3030) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 106 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1107 MET cc_start: 0.9039 (mmm) cc_final: 0.8725 (mmp) REVERT: C 1273 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8482 (mtp) REVERT: C 1319 MET cc_start: 0.8416 (mmp) cc_final: 0.8109 (mmm) REVERT: D 102 MET cc_start: 0.7358 (ppp) cc_final: 0.6713 (ppp) REVERT: D 724 MET cc_start: 0.8974 (mmt) cc_final: 0.8755 (mmt) REVERT: D 747 MET cc_start: 0.8443 (mmm) cc_final: 0.7913 (mmm) REVERT: D 822 MET cc_start: 0.9390 (tpp) cc_final: 0.9015 (tpp) REVERT: G 62 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7956 (ptt-90) outliers start: 51 outliers final: 41 residues processed: 150 average time/residue: 0.1612 time to fit residues: 40.1487 Evaluate side-chains 148 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1326 LEU Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 72 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 240 optimal weight: 9.9990 chunk 227 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 282 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1313 HIS D 157 GLN D 266 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.040359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.028806 restraints weight = 169017.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.029761 restraints weight = 86040.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.030362 restraints weight = 57331.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.030722 restraints weight = 44928.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.030939 restraints weight = 38967.623| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 24046 Z= 0.210 Angle : 0.545 9.634 32465 Z= 0.275 Chirality : 0.041 0.148 3683 Planarity : 0.004 0.047 4268 Dihedral : 4.040 23.196 3314 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.87 % Rotamer: Outliers : 2.37 % Allowed : 13.84 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.16), residues: 3001 helix: 1.65 (0.15), residues: 1199 sheet: 0.05 (0.27), residues: 378 loop : 0.27 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1373 TYR 0.022 0.001 TYR D 679 PHE 0.020 0.001 PHE C1025 TRP 0.005 0.001 TRP D 409 HIS 0.004 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (24046) covalent geometry : angle 0.54483 / 0.28 (32465) hydrogen bonds : bond 0.03467 / 2.43 ( 1064) hydrogen bonds : angle 4.64532 / 3.33 ( 3030) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 104 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 189 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7598 (p0) REVERT: C 1273 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8463 (mtp) REVERT: D 47 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8884 (mtp-110) REVERT: D 102 MET cc_start: 0.7429 (ppp) cc_final: 0.6742 (ppp) REVERT: D 724 MET cc_start: 0.9033 (mmt) cc_final: 0.8742 (mmt) REVERT: D 747 MET cc_start: 0.8442 (mmm) cc_final: 0.7918 (mmm) REVERT: D 878 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7453 (t0) outliers start: 61 outliers final: 47 residues processed: 157 average time/residue: 0.1609 time to fit residues: 41.6500 Evaluate side-chains 153 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 102 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1326 LEU Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 45 MET Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 72 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 37 optimal weight: 5.9990 chunk 229 optimal weight: 20.0000 chunk 136 optimal weight: 7.9990 chunk 225 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 296 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.040469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.028907 restraints weight = 167353.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.029859 restraints weight = 85263.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.030459 restraints weight = 56974.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.030826 restraints weight = 44759.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.031038 restraints weight = 38790.807| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24046 Z= 0.190 Angle : 0.542 10.554 32465 Z= 0.272 Chirality : 0.041 0.153 3683 Planarity : 0.004 0.047 4268 Dihedral : 3.995 23.370 3314 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.73 % Favored : 97.23 % Rotamer: Outliers : 2.41 % Allowed : 14.31 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.16), residues: 3001 helix: 1.72 (0.15), residues: 1199 sheet: 0.16 (0.28), residues: 350 loop : 0.28 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 62 TYR 0.021 0.001 TYR D 679 PHE 0.019 0.001 PHE C1025 TRP 0.005 0.001 TRP D 409 HIS 0.003 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 (24046) covalent geometry : angle 0.54171 / 0.27 (32465) hydrogen bonds : bond 0.03374 / 2.36 ( 1064) hydrogen bonds : angle 4.59487 / 3.30 ( 3030) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 105 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 189 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7594 (p0) REVERT: C 1107 MET cc_start: 0.9013 (mmm) cc_final: 0.8727 (mmp) REVERT: C 1243 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7535 (tpp) REVERT: C 1273 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8478 (mtp) REVERT: C 1319 MET cc_start: 0.8508 (mmp) cc_final: 0.8199 (mmm) REVERT: D 47 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8884 (mtp-110) REVERT: D 102 MET cc_start: 0.7493 (ppp) cc_final: 0.6844 (ppp) REVERT: D 747 MET cc_start: 0.8431 (mmm) cc_final: 0.7938 (mmm) REVERT: D 878 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7451 (t0) outliers start: 62 outliers final: 51 residues processed: 159 average time/residue: 0.1601 time to fit residues: 42.4563 Evaluate side-chains 158 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 102 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1326 LEU Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 45 MET Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 59 ARG Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 72 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 124 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 180 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 274 optimal weight: 7.9990 chunk 71 optimal weight: 30.0000 chunk 186 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 235 optimal weight: 1.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.039916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.028454 restraints weight = 169213.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.029384 restraints weight = 86335.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.029975 restraints weight = 57782.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.030327 restraints weight = 45383.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.030541 restraints weight = 39424.108| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 24046 Z= 0.273 Angle : 0.626 11.211 32465 Z= 0.313 Chirality : 0.042 0.186 3683 Planarity : 0.004 0.046 4268 Dihedral : 4.223 26.127 3314 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 2.68 % Allowed : 14.35 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.16), residues: 3001 helix: 1.50 (0.15), residues: 1204 sheet: -0.03 (0.27), residues: 372 loop : 0.25 (0.17), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 59 TYR 0.021 0.001 TYR D 679 PHE 0.024 0.001 PHE C1025 TRP 0.008 0.001 TRP D 409 HIS 0.004 0.001 HIS C 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.27 (24046) covalent geometry : angle 0.62581 / 0.31 (32465) hydrogen bonds : bond 0.03687 / 2.58 ( 1064) hydrogen bonds : angle 4.81012 / 3.44 ( 3030) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 102 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 189 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7616 (p0) REVERT: C 405 PHE cc_start: 0.9293 (t80) cc_final: 0.9068 (t80) REVERT: C 1243 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7557 (tpp) REVERT: C 1273 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8448 (mtp) REVERT: C 1319 MET cc_start: 0.8411 (mmp) cc_final: 0.8112 (mmm) REVERT: D 47 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8884 (mtp-110) REVERT: D 102 MET cc_start: 0.7635 (ppp) cc_final: 0.6943 (ppp) REVERT: D 724 MET cc_start: 0.9028 (mmt) cc_final: 0.8819 (mmt) REVERT: D 743 MET cc_start: 0.8828 (tmm) cc_final: 0.8618 (tmm) REVERT: D 747 MET cc_start: 0.8412 (mmm) cc_final: 0.7927 (mmm) REVERT: D 878 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7436 (t0) outliers start: 69 outliers final: 54 residues processed: 162 average time/residue: 0.1573 time to fit residues: 42.8039 Evaluate side-chains 160 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 101 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1326 LEU Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 45 MET Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 59 ARG Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 72 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 145 optimal weight: 3.9990 chunk 178 optimal weight: 20.0000 chunk 137 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 191 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 206 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.040352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.028847 restraints weight = 167427.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.029796 restraints weight = 85192.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.030390 restraints weight = 56798.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.030748 restraints weight = 44616.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.030959 restraints weight = 38694.629| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24046 Z= 0.196 Angle : 0.566 11.727 32465 Z= 0.283 Chirality : 0.041 0.178 3683 Planarity : 0.004 0.046 4268 Dihedral : 4.091 25.251 3314 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.73 % Favored : 97.23 % Rotamer: Outliers : 2.33 % Allowed : 15.01 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.16), residues: 3001 helix: 1.65 (0.15), residues: 1198 sheet: -0.00 (0.27), residues: 359 loop : 0.27 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 59 TYR 0.021 0.001 TYR D 679 PHE 0.019 0.001 PHE C1025 TRP 0.005 0.001 TRP C 183 HIS 0.003 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (24046) covalent geometry : angle 0.56598 / 0.28 (32465) hydrogen bonds : bond 0.03439 / 2.41 ( 1064) hydrogen bonds : angle 4.67282 / 3.36 ( 3030) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 101 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.9061 (ttmm) REVERT: C 189 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7599 (p0) REVERT: C 1107 MET cc_start: 0.9010 (mmm) cc_final: 0.8659 (mmp) REVERT: C 1243 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7517 (tpp) REVERT: C 1273 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8479 (mtp) REVERT: C 1319 MET cc_start: 0.8374 (mmp) cc_final: 0.7822 (mmm) REVERT: D 47 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8908 (mtp-110) REVERT: D 102 MET cc_start: 0.7535 (ppp) cc_final: 0.6929 (ppp) REVERT: D 724 MET cc_start: 0.9034 (mmt) cc_final: 0.8393 (mmt) REVERT: D 747 MET cc_start: 0.8408 (mmm) cc_final: 0.7929 (mmm) REVERT: D 878 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7472 (t0) outliers start: 60 outliers final: 52 residues processed: 152 average time/residue: 0.1670 time to fit residues: 41.9018 Evaluate side-chains 157 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 99 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1326 LEU Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 45 MET Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 59 ARG Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 72 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 232 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 283 optimal weight: 9.9990 chunk 218 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 197 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.040026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.028564 restraints weight = 169276.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.029489 restraints weight = 86155.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.030078 restraints weight = 57591.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.030436 restraints weight = 45277.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.030651 restraints weight = 39312.339| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24046 Z= 0.252 Angle : 0.613 12.081 32465 Z= 0.306 Chirality : 0.042 0.178 3683 Planarity : 0.004 0.048 4268 Dihedral : 4.202 26.922 3314 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.60 % Favored : 96.37 % Rotamer: Outliers : 2.33 % Allowed : 14.97 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.16), residues: 3001 helix: 1.51 (0.15), residues: 1198 sheet: -0.02 (0.27), residues: 384 loop : 0.23 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 25 TYR 0.020 0.001 TYR D 679 PHE 0.023 0.001 PHE C1025 TRP 0.008 0.001 TRP D 409 HIS 0.004 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.25 (24046) covalent geometry : angle 0.61272 / 0.31 (32465) hydrogen bonds : bond 0.03620 / 2.54 ( 1064) hydrogen bonds : angle 4.78874 / 3.43 ( 3030) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 99 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 189 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7620 (p0) REVERT: C 405 PHE cc_start: 0.9289 (t80) cc_final: 0.9063 (t80) REVERT: C 1243 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7537 (tpp) REVERT: C 1273 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8433 (mtp) REVERT: C 1319 MET cc_start: 0.8381 (mmp) cc_final: 0.7829 (mmm) REVERT: D 47 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8936 (mtp-110) REVERT: D 102 MET cc_start: 0.7612 (ppp) cc_final: 0.6990 (ppp) REVERT: D 298 MET cc_start: 0.8529 (mpp) cc_final: 0.8142 (pmm) REVERT: D 747 MET cc_start: 0.8425 (mmm) cc_final: 0.7944 (mmm) REVERT: D 878 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7501 (t0) REVERT: E 69 ARG cc_start: 0.9452 (mtt180) cc_final: 0.8769 (ptp-110) outliers start: 60 outliers final: 52 residues processed: 150 average time/residue: 0.1547 time to fit residues: 39.0931 Evaluate side-chains 156 residues out of total 2572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 99 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1326 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 28 TYR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 45 MET Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 59 ARG Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 72 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 119 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 217 optimal weight: 0.9980 chunk 273 optimal weight: 9.9990 chunk 246 optimal weight: 4.9990 chunk 177 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 184 optimal weight: 10.0000 chunk 275 optimal weight: 7.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.040598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.029090 restraints weight = 165766.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.030041 restraints weight = 84200.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.030635 restraints weight = 55972.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.030994 restraints weight = 43933.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.031209 restraints weight = 38080.440| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24046 Z= 0.163 Angle : 0.548 12.070 32465 Z= 0.274 Chirality : 0.041 0.181 3683 Planarity : 0.003 0.046 4268 Dihedral : 4.012 25.345 3314 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.63 % Favored : 97.33 % Rotamer: Outliers : 2.37 % Allowed : 14.97 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.16), residues: 3001 helix: 1.73 (0.15), residues: 1199 sheet: 0.03 (0.28), residues: 344 loop : 0.29 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1373 TYR 0.021 0.001 TYR D 679 PHE 0.018 0.001 PHE C1025 TRP 0.006 0.001 TRP C 807 HIS 0.003 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (24046) covalent geometry : angle 0.54774 / 0.27 (32465) hydrogen bonds : bond 0.03301 / 2.32 ( 1064) hydrogen bonds : angle 4.59073 / 3.31 ( 3030) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3873.28 seconds wall clock time: 68 minutes 2.42 seconds (4082.42 seconds total)