Starting phenix.real_space_refine on Sun Jul 5 05:36:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yrp_73373/07_2026/9yrp_73373_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yrp_73373/07_2026/9yrp_73373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yrp_73373/07_2026/9yrp_73373_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yrp_73373/07_2026/9yrp_73373_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yrp_73373/07_2026/9yrp_73373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yrp_73373/07_2026/9yrp_73373.map" } resolution = 4.13 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= 0.005 sd= 0.034 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 123 5.16 5 C 15806 2.51 5 N 4129 2.21 5 O 4619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24677 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1166 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain: "B" Number of atoms: 23511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2944, 23511 Classifications: {'peptide': 2944} Link IDs: {'PCIS': 3, 'PTRANS': 113, 'TRANS': 2827} Chain breaks: 25 Time building chain proxies: 4.68, per 1000 atoms: 0.19 Number of scatterers: 24677 At special positions: 0 Unit cell: (142.4, 121.04, 306.16, 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 123 16.00 O 4619 8.00 N 4129 7.00 C 15806 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: 1.95 Conformation dependent library (CDL) restraints added in 1.1 seconds 6076 Ramachandran restraints generated. 3038 Oldfield, 0 Emsley, 3038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5944 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 24 sheets defined 21.9% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 3.660A pdb=" N LEU A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 39 Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 66 through 77 removed outlier: 3.514A pdb=" N MET A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'A' and resid 102 through 114 Processing helix chain 'A' and resid 118 through 129 Processing helix chain 'A' and resid 138 through 148 removed outlier: 3.592A pdb=" N ALA A 148 " --> pdb=" O GLN A 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 17 removed outlier: 3.945A pdb=" N ASP B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 34 removed outlier: 3.627A pdb=" N LEU B 27 " --> pdb=" O ASN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 99 through 119 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 184 through 193 Processing helix chain 'B' and resid 270 through 280 removed outlier: 3.711A pdb=" N ILE B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 removed outlier: 3.527A pdb=" N GLU B 314 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 355 Processing helix chain 'B' and resid 356 through 361 removed outlier: 5.945A pdb=" N LYS B 359 " --> pdb=" O PRO B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 385 removed outlier: 3.889A pdb=" N LYS B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 391 removed outlier: 3.670A pdb=" N THR B 390 " --> pdb=" O ILE B 386 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 391' Processing helix chain 'B' and resid 394 through 418 Processing helix chain 'B' and resid 423 through 436 removed outlier: 4.357A pdb=" N LYS B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 637 through 648 removed outlier: 3.865A pdb=" N VAL B 641 " --> pdb=" O ASP B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 684 Processing helix chain 'B' and resid 819 through 832 removed outlier: 3.747A pdb=" N ILE B 832 " --> pdb=" O LEU B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1009 removed outlier: 4.106A pdb=" N THR B1007 " --> pdb=" O PRO B1003 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B1008 " --> pdb=" O SER B1004 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE B1009 " --> pdb=" O PHE B1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1003 through 1009' Processing helix chain 'B' and resid 1029 through 1041 Processing helix chain 'B' and resid 1193 through 1206 Processing helix chain 'B' and resid 1207 through 1233 removed outlier: 3.944A pdb=" N ALA B1233 " --> pdb=" O VAL B1229 " (cutoff:3.500A) Processing helix chain 'B' and resid 1356 through 1369 Processing helix chain 'B' and resid 1543 through 1556 Processing helix chain 'B' and resid 1682 through 1688 Processing helix chain 'B' and resid 1708 through 1715 Processing helix chain 'B' and resid 1871 through 1885 Processing helix chain 'B' and resid 2053 through 2068 Processing helix chain 'B' and resid 2162 through 2167 removed outlier: 3.953A pdb=" N GLY B2167 " --> pdb=" O ARG B2163 " (cutoff:3.500A) Processing helix chain 'B' and resid 2205 through 2219 removed outlier: 3.671A pdb=" N LEU B2219 " --> pdb=" O ILE B2215 " (cutoff:3.500A) Processing helix chain 'B' and resid 2392 through 2410 removed outlier: 3.558A pdb=" N THR B2410 " --> pdb=" O PHE B2406 " (cutoff:3.500A) Processing helix chain 'B' and resid 2582 through 2587 removed outlier: 4.216A pdb=" N ARG B2587 " --> pdb=" O LEU B2583 " (cutoff:3.500A) Processing helix chain 'B' and resid 2596 through 2600 Processing helix chain 'B' and resid 2611 through 2615 removed outlier: 3.649A pdb=" N GLU B2614 " --> pdb=" O TRP B2611 " (cutoff:3.500A) Processing helix chain 'B' and resid 3067 through 3074 Processing helix chain 'B' and resid 3131 through 3149 Processing helix chain 'B' and resid 3228 through 3233 Processing helix chain 'B' and resid 3274 through 3285 Processing helix chain 'B' and resid 3290 through 3295 removed outlier: 3.768A pdb=" N ARG B3295 " --> pdb=" O GLU B3291 " (cutoff:3.500A) Processing helix chain 'B' and resid 3300 through 3309 Processing helix chain 'B' and resid 3311 through 3315 removed outlier: 3.599A pdb=" N THR B3314 " --> pdb=" O LEU B3311 " (cutoff:3.500A) Processing helix chain 'B' and resid 3361 through 3368 removed outlier: 4.049A pdb=" N LEU B3365 " --> pdb=" O VAL B3361 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS B3366 " --> pdb=" O ASN B3362 " (cutoff:3.500A) Processing helix chain 'B' and resid 3393 through 3417 removed outlier: 3.862A pdb=" N VAL B3415 " --> pdb=" O LYS B3411 " (cutoff:3.500A) Processing helix chain 'B' and resid 3613 through 3624 removed outlier: 3.575A pdb=" N SER B3617 " --> pdb=" O GLU B3613 " (cutoff:3.500A) Processing helix chain 'B' and resid 3715 through 3729 Processing helix chain 'B' and resid 3730 through 3746 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain 'B' and resid 35 through 42 removed outlier: 6.786A pdb=" N ASP B 63 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN B 42 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN B 61 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY B 60 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU B 88 " --> pdb=" O GLY B 60 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE B 62 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU B 86 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N VAL B 80 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 10.058A pdb=" N ILE B 198 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N THR B 82 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N ASP B 200 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU B 84 " --> pdb=" O ASP B 200 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N HIS B 202 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEU B 86 " --> pdb=" O HIS B 202 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS B 204 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU B 88 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLU B 206 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL B 90 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLN B 195 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU B 228 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS B 197 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER B 226 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR B 199 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU B 224 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU B 216 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 261 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE B 218 " --> pdb=" O TRP B 259 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP B 259 " --> pdb=" O PHE B 218 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 220 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA B 257 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU B 222 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 255 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER B 254 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE B 299 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N SER B 256 " --> pdb=" O GLN B 297 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N GLN B 297 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR B 258 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE B 295 " --> pdb=" O TYR B 258 " (cutoff:3.500A) removed outlier: 9.536A pdb=" N TYR B 294 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU B 333 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N PHE B 296 " --> pdb=" O ILE B 331 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE B 331 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE B 329 " --> pdb=" O PRO B 298 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N SER B 300 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN B 327 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU B 320 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N THR B 533 " --> pdb=" O LEU B 320 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N CYS B 322 " --> pdb=" O THR B 533 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LYS B 535 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE B 324 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL B 537 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ILE B 326 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N THR B 539 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ASN B 328 " --> pdb=" O THR B 539 " (cutoff:3.500A) removed outlier: 9.838A pdb=" N VAL B 541 " --> pdb=" O ASN B 328 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ALA B 330 " --> pdb=" O VAL B 541 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N ILE B 543 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLU B 332 " --> pdb=" O ILE B 543 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N HIS B 530 " --> pdb=" O GLN B 566 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER B 538 " --> pdb=" O ILE B 558 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE B 558 " --> pdb=" O SER B 538 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER B 540 " --> pdb=" O GLN B 556 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLN B 556 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR B 542 " --> pdb=" O LYS B 554 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS B 554 " --> pdb=" O THR B 542 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 572 through 579 current: chain 'B' and resid 595 through 599 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 595 through 599 current: chain 'B' and resid 623 through 628 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 623 through 628 current: chain 'B' and resid 713 through 717 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 713 through 717 current: chain 'B' and resid 746 through 761 removed outlier: 4.404A pdb=" N ASN B 755 " --> pdb=" O MET B 784 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N MET B 784 " --> pdb=" O ASN B 755 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU B 916 " --> pdb=" O GLY B 808 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 911 " --> pdb=" O MET B 948 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP B 952 " --> pdb=" O ARG B 949 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1014 through 1020 current: chain 'B' and resid 1084 through 1099 removed outlier: 6.822A pdb=" N ALA B1092 " --> pdb=" O GLN B1110 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN B1110 " --> pdb=" O ALA B1092 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS B1094 " --> pdb=" O LYS B1108 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS B1108 " --> pdb=" O CYS B1094 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B1096 " --> pdb=" O GLU B1106 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU B1106 " --> pdb=" O ILE B1096 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N CYS B1098 " --> pdb=" O ILE B1104 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE B1104 " --> pdb=" O CYS B1098 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE B1107 " --> pdb=" O VAL B1134 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL B1134 " --> pdb=" O ILE B1107 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE B1109 " --> pdb=" O ILE B1132 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE B1132 " --> pdb=" O ILE B1109 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLY B1111 " --> pdb=" O GLU B1130 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE B1132 " --> pdb=" O ILE B1149 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B1149 " --> pdb=" O ILE B1132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1145 through 1149 current: chain 'B' and resid 1180 through 1185 Processing sheet with id=AA3, first strand: chain 'B' and resid 813 through 818 removed outlier: 6.977A pdb=" N MET B 813 " --> pdb=" O ILE B 921 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLU B 923 " --> pdb=" O MET B 813 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL B 815 " --> pdb=" O GLU B 923 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N THR B 925 " --> pdb=" O VAL B 815 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 817 " --> pdb=" O THR B 925 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1243 through 1246 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1243 through 1246 current: chain 'B' and resid 1262 through 1265 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1262 through 1265 current: chain 'B' and resid 1288 through 1302 removed outlier: 3.673A pdb=" N LYS B1298 " --> pdb=" O ILE B1321 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE B1321 " --> pdb=" O LYS B1298 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N THR B1300 " --> pdb=" O HIS B1319 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N HIS B1319 " --> pdb=" O THR B1300 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B1318 " --> pdb=" O VAL B1353 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B1353 " --> pdb=" O LEU B1318 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N MET B1351 " --> pdb=" O PRO B1320 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN B1322 " --> pdb=" O ASP B1349 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP B1349 " --> pdb=" O ASN B1322 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU B1343 " --> pdb=" O MET B1425 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU B1427 " --> pdb=" O GLU B1343 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS B1345 " --> pdb=" O LEU B1427 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE B1429 " --> pdb=" O LYS B1345 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N HIS B1347 " --> pdb=" O PHE B1429 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE B1431 " --> pdb=" O HIS B1347 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP B1349 " --> pdb=" O ILE B1431 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU B1433 " --> pdb=" O LEU B1455 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU B1455 " --> pdb=" O GLU B1433 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B1435 " --> pdb=" O ASN B1453 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN B1453 " --> pdb=" O VAL B1435 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR B1437 " --> pdb=" O GLU B1451 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU B1451 " --> pdb=" O THR B1437 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU B1457 " --> pdb=" O LEU B1474 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU B1474 " --> pdb=" O LEU B1457 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N MET B1459 " --> pdb=" O ALA B1472 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA B1472 " --> pdb=" O MET B1459 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA B1461 " --> pdb=" O ALA B1470 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA B1470 " --> pdb=" O ALA B1461 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL B1463 " --> pdb=" O MET B1468 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N MET B1468 " --> pdb=" O VAL B1463 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS B1481 " --> pdb=" O HIS B1493 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N HIS B1493 " --> pdb=" O CYS B1481 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1493 through 1496 current: chain 'B' and resid 1529 through 1535 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1529 through 1535 current: chain 'B' and resid 1599 through 1612 removed outlier: 6.366A pdb=" N LYS B1600 " --> pdb=" O SER B1632 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N SER B1632 " --> pdb=" O LYS B1600 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR B1602 " --> pdb=" O SER B1630 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N SER B1630 " --> pdb=" O THR B1602 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLU B1604 " --> pdb=" O ASP B1628 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP B1628 " --> pdb=" O GLU B1604 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN B1606 " --> pdb=" O GLY B1626 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA B1620 " --> pdb=" O VAL B1612 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP B1639 " --> pdb=" O SER B1632 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1638 through 1644 current: chain 'B' and resid 1660 through 1663 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1660 through 1663 current: chain 'B' and resid 1695 through 1699 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1695 through 1699 current: chain 'B' and resid 1775 through 1780 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1775 through 1780 current: chain 'B' and resid 1803 through 1820 removed outlier: 5.580A pdb=" N VAL B1836 " --> pdb=" O GLN B1813 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LYS B1815 " --> pdb=" O LYS B1834 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LYS B1834 " --> pdb=" O LYS B1815 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER B1817 " --> pdb=" O ILE B1832 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE B1832 " --> pdb=" O SER B1817 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N THR B1819 " --> pdb=" O ILE B1830 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE B1830 " --> pdb=" O THR B1819 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B1839 " --> pdb=" O LYS B1862 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS B1862 " --> pdb=" O LEU B1839 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE B1859 " --> pdb=" O ASP B1939 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N HIS B1941 " --> pdb=" O ILE B1859 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N GLY B1861 " --> pdb=" O HIS B1941 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N MET B1983 " --> pdb=" O SER B1935 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLN B1937 " --> pdb=" O GLY B1981 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY B1981 " --> pdb=" O GLN B1937 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASP B1939 " --> pdb=" O SER B1979 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER B1979 " --> pdb=" O ASP B1939 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2104 through 2109 current: chain 'B' and resid 2126 through 2139 removed outlier: 4.630A pdb=" N GLN B2133 " --> pdb=" O ASP B2153 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ASP B2153 " --> pdb=" O GLN B2133 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ASN B2135 " --> pdb=" O VAL B2151 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N VAL B2151 " --> pdb=" O ASN B2135 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER B2137 " --> pdb=" O ALA B2149 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ALA B2149 " --> pdb=" O SER B2137 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N SER B2139 " --> pdb=" O MET B2147 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N MET B2147 " --> pdb=" O SER B2139 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ALA B2158 " --> pdb=" O THR B2172 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N THR B2172 " --> pdb=" O ALA B2158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2171 through 2174 current: chain 'B' and resid 2193 through 2197 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2193 through 2197 current: chain 'B' and resid 2278 through 2289 removed outlier: 4.029A pdb=" N SER B2282 " --> pdb=" O SER B2303 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER B2303 " --> pdb=" O SER B2282 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN B2284 " --> pdb=" O ALA B2301 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ALA B2301 " --> pdb=" O GLN B2284 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR B2286 " --> pdb=" O LEU B2299 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU B2299 " --> pdb=" O THR B2286 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU B2288 " --> pdb=" O PRO B2297 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU B2298 " --> pdb=" O TYR B2329 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B2304 " --> pdb=" O THR B2323 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B2323 " --> pdb=" O LYS B2304 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER B2306 " --> pdb=" O ASP B2321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1866 through 1868 removed outlier: 3.519A pdb=" N MET B1866 " --> pdb=" O SER B1944 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1968 through 1971 current: chain 'B' and resid 1997 through 1998 Processing sheet with id=AA6, first strand: chain 'B' and resid 2442 through 2444 removed outlier: 6.269A pdb=" N THR B2425 " --> pdb=" O ILE B2539 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU B2541 " --> pdb=" O THR B2425 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS B2427 " --> pdb=" O LEU B2541 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 2454 through 2456 Processing sheet with id=AA8, first strand: chain 'B' and resid 2578 through 2580 removed outlier: 6.464A pdb=" N GLN B2546 " --> pdb=" O ILE B2664 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU B2666 " --> pdb=" O GLN B2546 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LYS B2548 " --> pdb=" O LEU B2666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 2567 through 2573 removed outlier: 3.664A pdb=" N GLU B2568 " --> pdb=" O LYS B2559 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE B2557 " --> pdb=" O ILE B2570 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE B2572 " --> pdb=" O PHE B2555 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE B2555 " --> pdb=" O ILE B2572 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 2698 through 2700 removed outlier: 4.117A pdb=" N VAL B2751 " --> pdb=" O PHE B2741 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 2691 through 2693 removed outlier: 3.658A pdb=" N GLU B2709 " --> pdb=" O ILE B2729 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS B2717 " --> pdb=" O LYS B2721 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LYS B2721 " --> pdb=" O LYS B2717 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 2801 through 2803 removed outlier: 3.666A pdb=" N LEU B2868 " --> pdb=" O ILE B2775 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 2791 through 2792 Processing sheet with id=AB5, first strand: chain 'B' and resid 2905 through 2908 removed outlier: 6.763A pdb=" N THR B2873 " --> pdb=" O ILE B2965 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N PHE B2967 " --> pdb=" O THR B2873 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ALA B2875 " --> pdb=" O PHE B2967 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER B2968 " --> pdb=" O LEU B2953 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU B2953 " --> pdb=" O SER B2968 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 2899 through 2900 removed outlier: 4.049A pdb=" N ILE B2887 " --> pdb=" O LYS B2917 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LYS B2917 " --> pdb=" O ILE B2887 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 3006 through 3008 removed outlier: 3.923A pdb=" N LEU B3062 " --> pdb=" O LEU B2978 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 2998 through 3001 removed outlier: 3.751A pdb=" N LEU B2988 " --> pdb=" O LEU B3001 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 3094 through 3095 removed outlier: 4.185A pdb=" N THR B3113 " --> pdb=" O TRP B3206 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TRP B3206 " --> pdb=" O THR B3113 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 3099 through 3100 Processing sheet with id=AC2, first strand: chain 'B' and resid 3128 through 3129 removed outlier: 3.638A pdb=" N SER B3177 " --> pdb=" O MET B3171 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET B3171 " --> pdb=" O SER B3177 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU B3170 " --> pdb=" O ASN B3163 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE B3160 " --> pdb=" O LEU B3156 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 3188 through 3190 removed outlier: 3.974A pdb=" N GLN B3188 " --> pdb=" O ARG B3203 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B3201 " --> pdb=" O GLU B3190 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG B3248 " --> pdb=" O PHE B3258 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N PHE B3258 " --> pdb=" O ARG B3248 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 3324 through 3325 current: chain 'B' and resid 3385 through 3387 Processing sheet with id=AC4, first strand: chain 'B' and resid 3222 through 3224 removed outlier: 3.621A pdb=" N SER B3340 " --> pdb=" O ILE B3272 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 3632 through 3637 removed outlier: 6.859A pdb=" N VAL B3648 " --> pdb=" O ARG B3633 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N HIS B3635 " --> pdb=" O LEU B3646 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B3646 " --> pdb=" O HIS B3635 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA B3637 " --> pdb=" O THR B3644 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR B3644 " --> pdb=" O ALA B3637 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG B3652 " --> pdb=" O THR B3649 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LYS B3657 " --> pdb=" O VAL B3667 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL B3667 " --> pdb=" O LYS B3657 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 3681 through 3682 887 hydrogen bonds defined for protein. 2472 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: 9.78 Time building geometry restraints manager: 2.66 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: 7973 1.34 - 1.46: 5231 1.46 - 1.58: 11711 1.58 - 1.70: 0 1.70 - 1.82: 208 Bond restraints: 25123 Sorted by residual: bond pdb=" N GLU B1212 " pdb=" CA GLU B1212 " ideal model delta sigma weight residual 1.459 1.484 -0.024 1.21e-02 6.83e+03 4.10e+00 bond pdb=" N ALA A 2 " pdb=" CA ALA A 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N VAL B 2 " pdb=" CA VAL B 2 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.72e+00 bond pdb=" N HIS B 978 " pdb=" CA HIS B 978 " ideal model delta sigma weight residual 1.455 1.474 -0.020 1.25e-02 6.40e+03 2.49e+00 bond pdb=" CG HIS B 978 " pdb=" CD2 HIS B 978 " ideal model delta sigma weight residual 1.354 1.339 0.015 1.10e-02 8.26e+03 1.76e+00 ... (remaining 25118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 32519 1.31 - 2.62: 1211 2.62 - 3.94: 206 3.94 - 5.25: 29 5.25 - 6.56: 7 Bond angle restraints: 33972 Sorted by residual: angle pdb=" N VAL B2632 " pdb=" CA VAL B2632 " pdb=" C VAL B2632 " ideal model delta sigma weight residual 112.83 109.52 3.31 9.90e-01 1.02e+00 1.12e+01 angle pdb=" C THR B 614 " pdb=" N ASN B 615 " pdb=" CA ASN B 615 " ideal model delta sigma weight residual 122.83 126.03 -3.20 1.08e+00 8.57e-01 8.78e+00 angle pdb=" C LEU B3204 " pdb=" N TYR B3205 " pdb=" CA TYR B3205 " ideal model delta sigma weight residual 122.17 117.90 4.27 1.54e+00 4.22e-01 7.69e+00 angle pdb=" N ARG B 388 " pdb=" CA ARG B 388 " pdb=" C ARG B 388 " ideal model delta sigma weight residual 113.18 110.01 3.17 1.21e+00 6.83e-01 6.86e+00 angle pdb=" CA LYS B1298 " pdb=" CB LYS B1298 " pdb=" CG LYS B1298 " ideal model delta sigma weight residual 114.10 119.22 -5.12 2.00e+00 2.50e-01 6.54e+00 ... (remaining 33967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 13960 17.85 - 35.70: 1112 35.70 - 53.56: 189 53.56 - 71.41: 66 71.41 - 89.26: 45 Dihedral angle restraints: 15372 sinusoidal: 6275 harmonic: 9097 Sorted by residual: dihedral pdb=" CA PRO B 318 " pdb=" C PRO B 318 " pdb=" N LYS B 319 " pdb=" CA LYS B 319 " ideal model delta harmonic sigma weight residual 180.00 156.99 23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA SER B3194 " pdb=" C SER B3194 " pdb=" N SER B3195 " pdb=" CA SER B3195 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA LEU B1760 " pdb=" C LEU B1760 " pdb=" N LYS B1761 " pdb=" CA LYS B1761 " ideal model delta harmonic sigma weight residual 180.00 159.46 20.54 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 15369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2659 0.037 - 0.074: 857 0.074 - 0.111: 292 0.111 - 0.149: 146 0.149 - 0.186: 7 Chirality restraints: 3961 Sorted by residual: chirality pdb=" CA ILE B 198 " pdb=" N ILE B 198 " pdb=" C ILE B 198 " pdb=" CB ILE B 198 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.61e-01 chirality pdb=" CA ILE B2539 " pdb=" N ILE B2539 " pdb=" C ILE B2539 " pdb=" CB ILE B2539 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CA VAL B 91 " pdb=" N VAL B 91 " pdb=" C VAL B 91 " pdb=" CB VAL B 91 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.58e-01 ... (remaining 3958 not shown) Planarity restraints: 4288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 774 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO B 775 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 775 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 775 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B2667 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO B2668 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B2668 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B2668 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B2975 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.45e+00 pdb=" N PRO B2976 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B2976 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B2976 " 0.023 5.00e-02 4.00e+02 ... (remaining 4285 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7152 2.82 - 3.34: 24173 3.34 - 3.86: 39980 3.86 - 4.38: 46481 4.38 - 4.90: 79646 Nonbonded interactions: 197432 Sorted by model distance: nonbonded pdb=" OE1 GLU B2341 " pdb=" O ASN B2388 " model vdw 2.304 3.040 nonbonded pdb=" O ALA B2501 " pdb=" OD1 ASN B2502 " model vdw 2.326 3.040 nonbonded pdb=" O SER B 340 " pdb=" OD1 ASP B 343 " model vdw 2.328 3.040 nonbonded pdb=" O ASN B 369 " pdb=" OD1 ASN B 369 " model vdw 2.358 3.040 nonbonded pdb=" O ASP B3013 " pdb=" OD1 ASP B3013 " model vdw 2.373 3.040 ... (remaining 197427 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 27.400 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 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 : 0.003 0.033 25123 Z= 0.162 Angle : 0.599 6.560 33972 Z= 0.337 Chirality : 0.046 0.186 3961 Planarity : 0.004 0.054 4288 Dihedral : 14.716 89.260 9428 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % 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: -1.69 (0.15), residues: 3038 helix: 1.00 (0.21), residues: 604 sheet: -1.31 (0.15), residues: 1184 loop : -1.89 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B2017 TYR 0.017 0.001 TYR B2837 PHE 0.021 0.002 PHE B1698 TRP 0.014 0.001 TRP B2773 HIS 0.006 0.001 HIS B 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (25123) covalent geometry : angle 0.59947 / 0.34 (33972) hydrogen bonds : bond 0.10916 / 7.27 ( 887) hydrogen bonds : angle 6.89689 / 4.84 ( 2472) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6076 Ramachandran restraints generated. 3038 Oldfield, 0 Emsley, 3038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6076 Ramachandran restraints generated. 3038 Oldfield, 0 Emsley, 3038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 392 MET cc_start: 0.7170 (mmm) cc_final: 0.6680 (mmm) REVERT: B 794 MET cc_start: 0.5062 (mtm) cc_final: 0.4724 (mtm) REVERT: B 1933 ILE cc_start: 0.6325 (mt) cc_final: 0.6095 (mt) REVERT: B 1977 MET cc_start: 0.7465 (ttp) cc_final: 0.6679 (tpp) REVERT: B 2024 ASN cc_start: 0.8129 (p0) cc_final: 0.7758 (p0) REVERT: B 2103 MET cc_start: 0.6571 (mpp) cc_final: 0.6260 (mpp) REVERT: B 2146 MET cc_start: 0.7254 (tpp) cc_final: 0.7042 (tpp) REVERT: B 3056 ASP cc_start: 0.7044 (p0) cc_final: 0.6678 (p0) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1523 time to fit residues: 54.1658 Evaluate side-chains 177 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 297 GLN B 367 HIS ** B1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1347 HIS ** B1370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1524 HIS B1543 HIS ** B1704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1827 GLN B2358 ASN ** B2529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3329 HIS B3705 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.113969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.102823 restraints weight = 69504.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.102182 restraints weight = 89817.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.101693 restraints weight = 70151.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.100982 restraints weight = 67421.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.100576 restraints weight = 73688.742| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5757 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25123 Z= 0.129 Angle : 0.582 10.350 33972 Z= 0.304 Chirality : 0.045 0.183 3961 Planarity : 0.004 0.045 4288 Dihedral : 4.821 21.876 3270 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.14 % Allowed : 3.04 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % 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: -1.35 (0.15), residues: 3038 helix: 1.28 (0.21), residues: 611 sheet: -1.20 (0.15), residues: 1192 loop : -1.59 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 127 TYR 0.022 0.001 TYR B 306 PHE 0.016 0.002 PHE B3261 TRP 0.016 0.001 TRP B 767 HIS 0.007 0.001 HIS B1709 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (25123) covalent geometry : angle 0.58208 / 0.30 (33972) hydrogen bonds : bond 0.03374 / 2.21 ( 887) hydrogen bonds : angle 5.77346 / 4.06 ( 2472) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6076 Ramachandran restraints generated. 3038 Oldfield, 0 Emsley, 3038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6076 Ramachandran restraints generated. 3038 Oldfield, 0 Emsley, 3038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 221 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.7009 (p0) cc_final: 0.6797 (p0) REVERT: B 190 VAL cc_start: 0.7544 (p) cc_final: 0.7274 (t) REVERT: B 392 MET cc_start: 0.6791 (mmm) cc_final: 0.6528 (mmm) REVERT: B 1474 LEU cc_start: 0.3973 (OUTLIER) cc_final: 0.3764 (tt) REVERT: B 1538 LEU cc_start: 0.6099 (tp) cc_final: 0.5842 (tp) REVERT: B 1933 ILE cc_start: 0.5316 (mt) cc_final: 0.5091 (mt) REVERT: B 1977 MET cc_start: 0.7467 (ttp) cc_final: 0.6809 (tpt) REVERT: B 2726 HIS cc_start: 0.6537 (m-70) cc_final: 0.6330 (m-70) REVERT: B 3056 ASP cc_start: 0.6868 (p0) cc_final: 0.6604 (p0) outliers start: 4 outliers final: 1 residues processed: 225 average time/residue: 0.1476 time to fit residues: 54.6161 Evaluate side-chains 184 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 26 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 79 optimal weight: 0.0270 chunk 146 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 367 HIS ** B1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1347 HIS ** B1370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1543 HIS ** B1704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2361 GLN ** B2529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.113502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.101615 restraints weight = 69243.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.101165 restraints weight = 93852.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.100507 restraints weight = 77877.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.099957 restraints weight = 82743.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.099482 restraints weight = 79392.174| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5830 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25123 Z= 0.140 Angle : 0.573 10.517 33972 Z= 0.298 Chirality : 0.045 0.228 3961 Planarity : 0.004 0.046 4288 Dihedral : 4.768 21.786 3270 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % 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: -1.23 (0.16), residues: 3038 helix: 1.36 (0.21), residues: 611 sheet: -1.06 (0.16), residues: 1161 loop : -1.58 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B3294 TYR 0.026 0.001 TYR B 306 PHE 0.028 0.002 PHE A 13 TRP 0.017 0.001 TRP B 767 HIS 0.006 0.001 HIS B2793 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (25123) covalent geometry : angle 0.57262 / 0.30 (33972) hydrogen bonds : bond 0.03283 / 2.14 ( 887) hydrogen bonds : angle 5.63001 / 3.97 ( 2472) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6076 Ramachandran restraints generated. 3038 Oldfield, 0 Emsley, 3038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6076 Ramachandran restraints generated. 3038 Oldfield, 0 Emsley, 3038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 LYS cc_start: 0.8307 (mptt) cc_final: 0.7594 (mmmt) REVERT: B 190 VAL cc_start: 0.7650 (p) cc_final: 0.7312 (t) REVERT: B 1538 LEU cc_start: 0.6236 (tp) cc_final: 0.5903 (tp) REVERT: B 1933 ILE cc_start: 0.5625 (mt) cc_final: 0.5421 (mt) REVERT: B 1977 MET cc_start: 0.7321 (ttp) cc_final: 0.6560 (tpt) REVERT: B 3056 ASP cc_start: 0.6830 (p0) cc_final: 0.6577 (p0) outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.1540 time to fit residues: 56.3724 Evaluate side-chains 181 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 38 optimal weight: 0.8980 chunk 251 optimal weight: 0.3980 chunk 148 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 216 optimal weight: 0.4980 chunk 2 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 263 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 233 HIS B 367 HIS B1194 HIS B1347 HIS B1543 HIS ** B1704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1822 GLN B2024 ASN ** B2529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2756 HIS ** B2992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.113937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.102499 restraints weight = 69481.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.101376 restraints weight = 91174.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.100643 restraints weight = 85546.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.100288 restraints weight = 88115.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.099761 restraints weight = 88580.673| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25123 Z= 0.122 Angle : 0.557 8.256 33972 Z= 0.287 Chirality : 0.045 0.171 3961 Planarity : 0.004 0.070 4288 Dihedral : 4.666 20.963 3270 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.04 % Allowed : 2.75 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % 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: -1.16 (0.16), residues: 3038 helix: 1.43 (0.21), residues: 610 sheet: -1.06 (0.15), residues: 1177 loop : -1.49 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B3294 TYR 0.026 0.001 TYR B 306 PHE 0.016 0.001 PHE B1670 TRP 0.017 0.001 TRP B 767 HIS 0.005 0.001 HIS B3196 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (25123) covalent geometry : angle 0.55657 / 0.29 (33972) hydrogen bonds : bond 0.03086 / 2.02 ( 887) hydrogen bonds : angle 5.46272 / 3.85 ( 2472) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6076 Ramachandran restraints generated. 3038 Oldfield, 0 Emsley, 3038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6076 Ramachandran restraints generated. 3038 Oldfield, 0 Emsley, 3038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 LYS cc_start: 0.8333 (mptt) cc_final: 0.7729 (mmmt) REVERT: B 190 VAL cc_start: 0.7437 (p) cc_final: 0.7168 (t) REVERT: B 1538 LEU cc_start: 0.5966 (tp) cc_final: 0.5713 (tp) REVERT: B 1933 ILE cc_start: 0.5414 (mt) cc_final: 0.5209 (mt) REVERT: B 1977 MET cc_start: 0.7223 (ttp) cc_final: 0.6574 (tpt) REVERT: B 2147 MET cc_start: 0.7726 (tmm) cc_final: 0.7507 (tmm) REVERT: B 3056 ASP cc_start: 0.6780 (p0) cc_final: 0.6540 (p0) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.1464 time to fit residues: 51.8453 Evaluate side-chains 180 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 110 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 296 optimal weight: 9.9990 chunk 127 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 102 optimal weight: 1.9990 chunk 265 optimal weight: 0.0970 chunk 300 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 367 HIS ** B1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1347 HIS ** B1370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1543 HIS ** B1704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3082 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.113493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.102156 restraints weight = 69644.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.100956 restraints weight = 95617.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.099867 restraints weight = 94139.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.099536 restraints weight = 93594.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.099338 restraints weight = 85457.883| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5853 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25123 Z= 0.130 Angle : 0.565 11.105 33972 Z= 0.291 Chirality : 0.045 0.169 3961 Planarity : 0.004 0.054 4288 Dihedral : 4.652 24.535 3270 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.04 % Allowed : 2.11 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % 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: -1.15 (0.16), residues: 3038 helix: 1.41 (0.21), residues: 611 sheet: -1.06 (0.16), residues: 1178 loop : -1.45 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B3294 TYR 0.017 0.001 TYR B3085 PHE 0.021 0.002 PHE B3240 TRP 0.021 0.001 TRP B 767 HIS 0.006 0.001 HIS B1319 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (25123) covalent geometry : angle 0.56481 / 0.29 (33972) hydrogen bonds : bond 0.03066 / 2.00 ( 887) hydrogen bonds : angle 5.41398 / 3.81 ( 2472) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6076 Ramachandran restraints generated. 3038 Oldfield, 0 Emsley, 3038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6076 Ramachandran restraints generated. 3038 Oldfield, 0 Emsley, 3038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 LYS cc_start: 0.8300 (mptt) cc_final: 0.7685 (mmmt) REVERT: B 190 VAL cc_start: 0.7479 (p) cc_final: 0.7216 (t) REVERT: B 392 MET cc_start: 0.6937 (mmm) cc_final: 0.6462 (mmm) REVERT: B 1538 LEU cc_start: 0.6233 (tp) cc_final: 0.5960 (tp) REVERT: B 1933 ILE cc_start: 0.5578 (mt) cc_final: 0.5370 (mt) REVERT: B 1977 MET cc_start: 0.7059 (ttp) cc_final: 0.6438 (tpt) REVERT: B 2147 MET cc_start: 0.8047 (tmm) cc_final: 0.7517 (tmm) REVERT: B 3056 ASP cc_start: 0.6795 (p0) cc_final: 0.6555 (p0) outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 0.1502 time to fit residues: 53.7859 Evaluate side-chains 181 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 281 optimal weight: 0.4980 chunk 221 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 56 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1319 HIS B1347 HIS ** B1370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3076 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.113358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.101873 restraints weight = 69640.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.101252 restraints weight = 92547.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.100904 restraints weight = 78347.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.100590 restraints weight = 76621.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.100051 restraints weight = 78147.302| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5819 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25123 Z= 0.129 Angle : 0.566 10.324 33972 Z= 0.290 Chirality : 0.045 0.227 3961 Planarity : 0.004 0.051 4288 Dihedral : 4.631 22.996 3270 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % 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: -1.16 (0.16), residues: 3038 helix: 1.35 (0.21), residues: 617 sheet: -1.06 (0.16), residues: 1180 loop : -1.46 (0.17), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 87 TYR 0.016 0.001 TYR B3085 PHE 0.021 0.002 PHE B3222 TRP 0.022 0.001 TRP B 767 HIS 0.005 0.001 HIS B 530 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (25123) covalent geometry : angle 0.56585 / 0.29 (33972) hydrogen bonds : bond 0.03020 / 1.97 ( 887) hydrogen bonds : angle 5.37596 / 3.79 ( 2472) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6076 Ramachandran restraints generated. 3038 Oldfield, 0 Emsley, 3038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6076 Ramachandran restraints generated. 3038 Oldfield, 0 Emsley, 3038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 LYS cc_start: 0.8358 (mptt) cc_final: 0.7742 (mmmt) REVERT: B 190 VAL cc_start: 0.7467 (p) cc_final: 0.7251 (t) REVERT: B 216 LEU cc_start: 0.6411 (mm) cc_final: 0.6126 (mm) REVERT: B 307 MET cc_start: 0.7472 (mtt) cc_final: 0.7048 (mtm) REVERT: B 392 MET cc_start: 0.7044 (mmm) cc_final: 0.6516 (mmm) REVERT: B 1150 MET cc_start: 0.6543 (mtt) cc_final: 0.6250 (mmt) REVERT: B 1439 MET cc_start: 0.1944 (tmm) cc_final: 0.1372 (ttp) REVERT: B 1538 LEU cc_start: 0.6057 (tp) cc_final: 0.5827 (tp) REVERT: B 2147 MET cc_start: 0.7808 (tmm) cc_final: 0.7581 (tmm) REVERT: B 2695 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7119 (mm-30) REVERT: B 3056 ASP cc_start: 0.6733 (p0) cc_final: 0.6531 (p0) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1570 time to fit residues: 55.4588 Evaluate side-chains 183 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 264 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 250 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 212 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 225 optimal weight: 0.0970 chunk 95 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 367 HIS B1014 GLN ** B1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1347 HIS ** B1370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2401 ASN ** B2992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3050 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.113424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.101818 restraints weight = 69207.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.100082 restraints weight = 90429.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.099345 restraints weight = 94401.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.099112 restraints weight = 95986.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.098799 restraints weight = 86123.463| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5859 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25123 Z= 0.122 Angle : 0.560 9.835 33972 Z= 0.287 Chirality : 0.044 0.179 3961 Planarity : 0.004 0.049 4288 Dihedral : 4.610 25.208 3270 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.04 % Allowed : 1.29 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.16), residues: 3038 helix: 1.36 (0.21), residues: 624 sheet: -1.07 (0.16), residues: 1179 loop : -1.42 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B3294 TYR 0.016 0.001 TYR B3385 PHE 0.025 0.002 PHE B2200 TRP 0.024 0.001 TRP B 767 HIS 0.006 0.001 HIS B3196 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (25123) covalent geometry : angle 0.56004 / 0.29 (33972) hydrogen bonds : bond 0.02951 / 1.93 ( 887) hydrogen bonds : angle 5.31759 / 3.75 ( 2472) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6076 Ramachandran restraints generated. 3038 Oldfield, 0 Emsley, 3038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6076 Ramachandran restraints generated. 3038 Oldfield, 0 Emsley, 3038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 PHE cc_start: 0.7096 (t80) cc_final: 0.6882 (t80) REVERT: B 105 LYS cc_start: 0.8385 (mptt) cc_final: 0.7751 (mmmt) REVERT: B 190 VAL cc_start: 0.7505 (p) cc_final: 0.7279 (t) REVERT: B 265 MET cc_start: 0.2573 (tpt) cc_final: 0.1912 (tmm) REVERT: B 307 MET cc_start: 0.7578 (mtt) cc_final: 0.7154 (mtm) REVERT: B 392 MET cc_start: 0.7125 (mmm) cc_final: 0.6536 (mmm) REVERT: B 1150 MET cc_start: 0.6644 (mtt) cc_final: 0.6315 (mmt) REVERT: B 1538 LEU cc_start: 0.6149 (tp) cc_final: 0.5927 (tp) REVERT: B 3056 ASP cc_start: 0.6730 (p0) cc_final: 0.6525 (p0) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.1583 time to fit residues: 56.0125 Evaluate side-chains 181 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 29 optimal weight: 3.9990 chunk 178 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 131 optimal weight: 8.9990 chunk 258 optimal weight: 5.9990 chunk 253 optimal weight: 0.3980 chunk 208 optimal weight: 0.7980 chunk 179 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 418 GLN ** B1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1347 HIS ** B1370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3050 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.113294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.101797 restraints weight = 68786.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.100009 restraints weight = 93193.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.099509 restraints weight = 93504.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.099407 restraints weight = 87151.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.099131 restraints weight = 85271.112| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25123 Z= 0.126 Angle : 0.565 12.595 33972 Z= 0.290 Chirality : 0.045 0.166 3961 Planarity : 0.004 0.050 4288 Dihedral : 4.597 23.654 3270 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % 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: -1.08 (0.16), residues: 3038 helix: 1.44 (0.21), residues: 619 sheet: -1.05 (0.16), residues: 1185 loop : -1.38 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 87 TYR 0.016 0.001 TYR B3085 PHE 0.023 0.002 PHE B2555 TRP 0.027 0.001 TRP B 767 HIS 0.006 0.001 HIS B 530 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (25123) covalent geometry : angle 0.56525 / 0.29 (33972) hydrogen bonds : bond 0.02964 / 1.93 ( 887) hydrogen bonds : angle 5.30307 / 3.74 ( 2472) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6076 Ramachandran restraints generated. 3038 Oldfield, 0 Emsley, 3038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6076 Ramachandran restraints generated. 3038 Oldfield, 0 Emsley, 3038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 PHE cc_start: 0.7107 (t80) cc_final: 0.6886 (t80) REVERT: B 105 LYS cc_start: 0.8396 (mptt) cc_final: 0.7757 (mmmt) REVERT: B 190 VAL cc_start: 0.7491 (p) cc_final: 0.7262 (t) REVERT: B 265 MET cc_start: 0.2367 (tpt) cc_final: 0.1838 (tmm) REVERT: B 307 MET cc_start: 0.7588 (mtt) cc_final: 0.7099 (mtm) REVERT: B 392 MET cc_start: 0.7180 (mmm) cc_final: 0.6482 (mmm) REVERT: B 1150 MET cc_start: 0.6665 (mtt) cc_final: 0.6351 (mmt) REVERT: B 1538 LEU cc_start: 0.6173 (tp) cc_final: 0.5962 (tp) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1561 time to fit residues: 54.8623 Evaluate side-chains 180 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 217 optimal weight: 0.1980 chunk 120 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 288 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 233 HIS B 367 HIS B 447 GLN ** B1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1347 HIS ** B1370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2135 ASN B2210 ASN ** B2327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3050 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.111233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.100055 restraints weight = 70271.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.098658 restraints weight = 97966.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.098167 restraints weight = 97373.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.098012 restraints weight = 87889.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.097759 restraints weight = 79226.478| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25123 Z= 0.199 Angle : 0.659 13.522 33972 Z= 0.337 Chirality : 0.047 0.262 3961 Planarity : 0.005 0.088 4288 Dihedral : 4.970 24.234 3270 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 0.04 % Allowed : 0.50 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % 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: -1.30 (0.16), residues: 3038 helix: 1.28 (0.21), residues: 617 sheet: -1.19 (0.16), residues: 1167 loop : -1.52 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B3633 TYR 0.024 0.002 TYR B3385 PHE 0.040 0.002 PHE B2551 TRP 0.030 0.002 TRP B 767 HIS 0.009 0.001 HIS B 530 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (25123) covalent geometry : angle 0.65879 / 0.34 (33972) hydrogen bonds : bond 0.03398 / 2.23 ( 887) hydrogen bonds : angle 5.60798 / 3.96 ( 2472) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6076 Ramachandran restraints generated. 3038 Oldfield, 0 Emsley, 3038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6076 Ramachandran restraints generated. 3038 Oldfield, 0 Emsley, 3038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 14 PHE cc_start: 0.7191 (t80) cc_final: 0.6941 (t80) REVERT: B 86 LEU cc_start: 0.7070 (tt) cc_final: 0.6747 (tt) REVERT: B 101 VAL cc_start: 0.8576 (t) cc_final: 0.8093 (p) REVERT: B 105 LYS cc_start: 0.8433 (mptt) cc_final: 0.7804 (mmmt) REVERT: B 190 VAL cc_start: 0.7744 (p) cc_final: 0.7441 (t) REVERT: B 265 MET cc_start: 0.2479 (tpt) cc_final: 0.1875 (tmm) REVERT: B 307 MET cc_start: 0.7385 (mtt) cc_final: 0.7075 (mtm) REVERT: B 742 MET cc_start: 0.5124 (pmm) cc_final: 0.4868 (pmm) REVERT: B 1150 MET cc_start: 0.6520 (mtt) cc_final: 0.6082 (mmt) REVERT: B 1538 LEU cc_start: 0.6336 (tp) cc_final: 0.6087 (tp) REVERT: B 2014 MET cc_start: 0.7272 (mmm) cc_final: 0.6958 (mmm) outliers start: 1 outliers final: 0 residues processed: 208 average time/residue: 0.1568 time to fit residues: 54.3072 Evaluate side-chains 185 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 176 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 33 optimal weight: 0.1980 chunk 196 optimal weight: 0.8980 chunk 264 optimal weight: 0.1980 chunk 193 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 220 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1347 HIS ** B1370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1543 HIS ** B1704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3050 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.112895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.102084 restraints weight = 69043.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.101349 restraints weight = 90758.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.100681 restraints weight = 73701.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.099775 restraints weight = 79966.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.098962 restraints weight = 86069.351| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5845 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25123 Z= 0.113 Angle : 0.580 11.590 33972 Z= 0.296 Chirality : 0.045 0.193 3961 Planarity : 0.004 0.051 4288 Dihedral : 4.702 23.012 3270 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % 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: -1.17 (0.16), residues: 3038 helix: 1.38 (0.21), residues: 618 sheet: -1.18 (0.16), residues: 1184 loop : -1.35 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B3633 TYR 0.016 0.001 TYR B3085 PHE 0.037 0.002 PHE A 66 TRP 0.031 0.001 TRP B 767 HIS 0.007 0.001 HIS B2982 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (25123) covalent geometry : angle 0.57969 / 0.30 (33972) hydrogen bonds : bond 0.02978 / 1.95 ( 887) hydrogen bonds : angle 5.34821 / 3.78 ( 2472) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6076 Ramachandran restraints generated. 3038 Oldfield, 0 Emsley, 3038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6076 Ramachandran restraints generated. 3038 Oldfield, 0 Emsley, 3038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.4802 (ptt) cc_final: 0.4568 (ptt) REVERT: B 86 LEU cc_start: 0.6897 (tt) cc_final: 0.6666 (tt) REVERT: B 101 VAL cc_start: 0.8489 (t) cc_final: 0.8026 (p) REVERT: B 105 LYS cc_start: 0.8367 (mptt) cc_final: 0.7743 (mmmt) REVERT: B 190 VAL cc_start: 0.7637 (p) cc_final: 0.7341 (t) REVERT: B 265 MET cc_start: 0.2334 (tpt) cc_final: 0.1853 (tmm) REVERT: B 392 MET cc_start: 0.7103 (mmm) cc_final: 0.6820 (mmt) REVERT: B 742 MET cc_start: 0.4762 (pmm) cc_final: 0.4322 (pmm) REVERT: B 1150 MET cc_start: 0.6479 (mtt) cc_final: 0.6024 (mmt) REVERT: B 1155 PHE cc_start: 0.5964 (p90) cc_final: 0.5729 (p90) REVERT: B 3217 MET cc_start: 0.7227 (pmm) cc_final: 0.6985 (pmm) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1551 time to fit residues: 53.2007 Evaluate side-chains 175 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 5 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 267 optimal weight: 7.9990 chunk 170 optimal weight: 0.8980 chunk 301 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 216 optimal weight: 0.2980 chunk 277 optimal weight: 0.0010 chunk 83 optimal weight: 0.3980 chunk 162 optimal weight: 0.9990 chunk 282 optimal weight: 0.2980 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1347 HIS ** B1370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3050 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3059 GLN ** B3404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.112806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.097312 restraints weight = 68942.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.091356 restraints weight = 90549.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.090998 restraints weight = 97333.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.090662 restraints weight = 100527.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.090792 restraints weight = 86281.204| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25123 Z= 0.104 Angle : 0.569 10.834 33972 Z= 0.290 Chirality : 0.044 0.190 3961 Planarity : 0.004 0.050 4288 Dihedral : 4.584 21.315 3270 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.16), residues: 3038 helix: 1.52 (0.21), residues: 612 sheet: -1.08 (0.16), residues: 1173 loop : -1.34 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B2730 TYR 0.014 0.001 TYR B 995 PHE 0.031 0.001 PHE B2551 TRP 0.031 0.001 TRP B 767 HIS 0.006 0.001 HIS B2982 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (25123) covalent geometry : angle 0.56872 / 0.29 (33972) hydrogen bonds : bond 0.02884 / 1.90 ( 887) hydrogen bonds : angle 5.22373 / 3.68 ( 2472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3940.99 seconds wall clock time: 69 minutes 26.31 seconds (4166.31 seconds total)