Starting phenix.real_space_refine on Fri Jun 5 22:50:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l2t_62780/06_2026/9l2t_62780.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l2t_62780/06_2026/9l2t_62780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l2t_62780/06_2026/9l2t_62780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l2t_62780/06_2026/9l2t_62780.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l2t_62780/06_2026/9l2t_62780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l2t_62780/06_2026/9l2t_62780.map" } resolution = 2.69 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= 0.001 sd= 0.086 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: 6 Type Number sf(0) Gaussians Zn 16 6.06 5 S 80 5.16 5 Cl 8 4.86 5 C 14936 2.51 5 N 4288 2.21 5 O 4536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23864 Number of models: 1 Model: "" Number of chains: 2 Chain: "G" Number of atoms: 2953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2953 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Restraints were copied for chains: A, B, C, D, E, F, H Time building chain proxies: 3.74, per 1000 atoms: 0.16 Number of scatterers: 23864 At special positions: 0 Unit cell: (122.76, 121.83, 102.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 16 29.99 Cl 8 17.00 S 80 16.00 O 4536 8.00 N 4288 7.00 C 14936 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS G 28 " - pdb=" SG CYS G 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS D 28 " - pdb=" SG CYS D 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 28 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS F 28 " - pdb=" SG CYS F 76 " distance=2.03 Simple disulfide: pdb=" SG CYS H 28 " - pdb=" SG CYS H 76 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 272 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 252 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 86 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 84 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 272 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 252 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 86 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 84 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 272 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 252 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 86 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 84 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 272 " pdb="ZN ZN D 501 " - pdb=" ND1 HIS D 252 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 86 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 84 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 272 " pdb="ZN ZN E 501 " - pdb=" ND1 HIS E 252 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 86 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 84 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 272 " pdb="ZN ZN F 501 " - pdb=" ND1 HIS F 252 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" NE2 HIS F 86 " pdb="ZN ZN F 502 " - pdb=" NE2 HIS F 84 " pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 272 " pdb="ZN ZN G 501 " - pdb=" ND1 HIS G 252 " pdb=" ZN G 502 " pdb="ZN ZN G 502 " - pdb=" NE2 HIS G 86 " pdb="ZN ZN G 502 " - pdb=" NE2 HIS G 84 " pdb=" ZN H 501 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 272 " pdb="ZN ZN H 501 " - pdb=" ND1 HIS H 252 " pdb=" ZN H 502 " pdb="ZN ZN H 502 " - pdb=" NE2 HIS H 86 " pdb="ZN ZN H 502 " - pdb=" NE2 HIS H 84 " 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5632 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 32 sheets defined 43.0% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'G' and resid 94 through 99 removed outlier: 4.076A pdb=" N GLY G 99 " --> pdb=" O SER G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 121 removed outlier: 3.988A pdb=" N GLY G 113 " --> pdb=" O PHE G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 143 removed outlier: 4.533A pdb=" N HIS G 136 " --> pdb=" O GLU G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 180 Processing helix chain 'G' and resid 191 through 205 Processing helix chain 'G' and resid 231 through 245 Processing helix chain 'G' and resid 255 through 266 Processing helix chain 'G' and resid 277 through 288 Processing helix chain 'G' and resid 294 through 306 removed outlier: 4.083A pdb=" N LYS G 306 " --> pdb=" O ALA G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 315 through 323 Processing helix chain 'G' and resid 325 through 337 Processing helix chain 'G' and resid 355 through 364 removed outlier: 3.938A pdb=" N ILE G 359 " --> pdb=" O ALA G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 384 removed outlier: 3.541A pdb=" N ALA G 375 " --> pdb=" O ALA G 371 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR G 376 " --> pdb=" O LEU G 372 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP G 378 " --> pdb=" O MET G 374 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA G 379 " --> pdb=" O ALA G 375 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA G 380 " --> pdb=" O THR G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 415 Processing helix chain 'A' and resid 94 through 99 removed outlier: 4.077A pdb=" N GLY A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 121 removed outlier: 3.988A pdb=" N GLY A 113 " --> pdb=" O PHE A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 143 removed outlier: 4.533A pdb=" N HIS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 180 Processing helix chain 'A' and resid 191 through 205 Processing helix chain 'A' and resid 231 through 245 Processing helix chain 'A' and resid 255 through 266 Processing helix chain 'A' and resid 277 through 288 Processing helix chain 'A' and resid 294 through 306 removed outlier: 4.083A pdb=" N LYS A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 323 Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.937A pdb=" N ILE A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 384 removed outlier: 3.540A pdb=" N ALA A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP A 378 " --> pdb=" O MET A 374 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ALA A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 380 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 415 Processing helix chain 'B' and resid 94 through 99 removed outlier: 4.077A pdb=" N GLY B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 121 removed outlier: 3.988A pdb=" N GLY B 113 " --> pdb=" O PHE B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 removed outlier: 4.533A pdb=" N HIS B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 180 Processing helix chain 'B' and resid 191 through 205 Processing helix chain 'B' and resid 231 through 245 Processing helix chain 'B' and resid 255 through 266 Processing helix chain 'B' and resid 277 through 288 Processing helix chain 'B' and resid 294 through 306 removed outlier: 4.083A pdb=" N LYS B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 323 Processing helix chain 'B' and resid 325 through 337 Processing helix chain 'B' and resid 355 through 364 removed outlier: 3.939A pdb=" N ILE B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 384 removed outlier: 3.541A pdb=" N ALA B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP B 378 " --> pdb=" O MET B 374 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 380 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 415 Processing helix chain 'C' and resid 94 through 99 removed outlier: 4.078A pdb=" N GLY C 99 " --> pdb=" O SER C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 121 removed outlier: 3.988A pdb=" N GLY C 113 " --> pdb=" O PHE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 removed outlier: 4.533A pdb=" N HIS C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 180 Processing helix chain 'C' and resid 191 through 205 Processing helix chain 'C' and resid 231 through 245 Processing helix chain 'C' and resid 255 through 266 Processing helix chain 'C' and resid 277 through 288 Processing helix chain 'C' and resid 294 through 306 removed outlier: 4.083A pdb=" N LYS C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 323 Processing helix chain 'C' and resid 325 through 337 Processing helix chain 'C' and resid 355 through 364 removed outlier: 3.938A pdb=" N ILE C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 384 removed outlier: 3.541A pdb=" N ALA C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C 376 " --> pdb=" O LEU C 372 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP C 378 " --> pdb=" O MET C 374 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA C 380 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 415 Processing helix chain 'D' and resid 94 through 99 removed outlier: 4.076A pdb=" N GLY D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 121 removed outlier: 3.987A pdb=" N GLY D 113 " --> pdb=" O PHE D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 143 removed outlier: 4.532A pdb=" N HIS D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 180 Processing helix chain 'D' and resid 191 through 205 Processing helix chain 'D' and resid 231 through 245 Processing helix chain 'D' and resid 255 through 266 Processing helix chain 'D' and resid 277 through 288 Processing helix chain 'D' and resid 294 through 306 removed outlier: 4.083A pdb=" N LYS D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 323 Processing helix chain 'D' and resid 325 through 337 Processing helix chain 'D' and resid 355 through 364 removed outlier: 3.938A pdb=" N ILE D 359 " --> pdb=" O ALA D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 384 removed outlier: 3.540A pdb=" N ALA D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR D 376 " --> pdb=" O LEU D 372 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP D 378 " --> pdb=" O MET D 374 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA D 380 " --> pdb=" O THR D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 415 Processing helix chain 'E' and resid 94 through 99 removed outlier: 4.077A pdb=" N GLY E 99 " --> pdb=" O SER E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 121 removed outlier: 3.988A pdb=" N GLY E 113 " --> pdb=" O PHE E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 143 removed outlier: 4.533A pdb=" N HIS E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 180 Processing helix chain 'E' and resid 191 through 205 Processing helix chain 'E' and resid 231 through 245 Processing helix chain 'E' and resid 255 through 266 Processing helix chain 'E' and resid 277 through 288 Processing helix chain 'E' and resid 294 through 306 removed outlier: 4.083A pdb=" N LYS E 306 " --> pdb=" O ALA E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 323 Processing helix chain 'E' and resid 325 through 337 Processing helix chain 'E' and resid 355 through 364 removed outlier: 3.937A pdb=" N ILE E 359 " --> pdb=" O ALA E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 384 removed outlier: 3.540A pdb=" N ALA E 375 " --> pdb=" O ALA E 371 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR E 376 " --> pdb=" O LEU E 372 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP E 378 " --> pdb=" O MET E 374 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ALA E 379 " --> pdb=" O ALA E 375 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA E 380 " --> pdb=" O THR E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 415 Processing helix chain 'F' and resid 94 through 99 removed outlier: 4.077A pdb=" N GLY F 99 " --> pdb=" O SER F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 121 removed outlier: 3.988A pdb=" N GLY F 113 " --> pdb=" O PHE F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 143 removed outlier: 4.532A pdb=" N HIS F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 180 Processing helix chain 'F' and resid 191 through 205 Processing helix chain 'F' and resid 231 through 245 Processing helix chain 'F' and resid 255 through 266 Processing helix chain 'F' and resid 277 through 288 Processing helix chain 'F' and resid 294 through 306 removed outlier: 4.083A pdb=" N LYS F 306 " --> pdb=" O ALA F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 323 Processing helix chain 'F' and resid 325 through 337 Processing helix chain 'F' and resid 355 through 364 removed outlier: 3.939A pdb=" N ILE F 359 " --> pdb=" O ALA F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 384 removed outlier: 3.540A pdb=" N ALA F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR F 376 " --> pdb=" O LEU F 372 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP F 378 " --> pdb=" O MET F 374 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ALA F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA F 380 " --> pdb=" O THR F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 415 Processing helix chain 'H' and resid 94 through 99 removed outlier: 4.078A pdb=" N GLY H 99 " --> pdb=" O SER H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 121 removed outlier: 3.988A pdb=" N GLY H 113 " --> pdb=" O PHE H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 143 removed outlier: 4.533A pdb=" N HIS H 136 " --> pdb=" O GLU H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 180 Processing helix chain 'H' and resid 191 through 205 Processing helix chain 'H' and resid 231 through 245 Processing helix chain 'H' and resid 255 through 266 Processing helix chain 'H' and resid 277 through 288 Processing helix chain 'H' and resid 294 through 306 removed outlier: 4.082A pdb=" N LYS H 306 " --> pdb=" O ALA H 302 " (cutoff:3.500A) Processing helix chain 'H' and resid 315 through 323 Processing helix chain 'H' and resid 325 through 337 Processing helix chain 'H' and resid 355 through 364 removed outlier: 3.937A pdb=" N ILE H 359 " --> pdb=" O ALA H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 384 removed outlier: 3.541A pdb=" N ALA H 375 " --> pdb=" O ALA H 371 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR H 376 " --> pdb=" O LEU H 372 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP H 378 " --> pdb=" O MET H 374 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA H 379 " --> pdb=" O ALA H 375 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA H 380 " --> pdb=" O THR H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 409 through 415 Processing sheet with id=AA1, first strand: chain 'G' and resid 38 through 39 removed outlier: 6.518A pdb=" N THR G 44 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL G 55 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU G 46 " --> pdb=" O ALA G 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 38 through 39 removed outlier: 14.127A pdb=" N THR G 24 " --> pdb=" O ASP G 70 " (cutoff:3.500A) removed outlier: 14.402A pdb=" N SER G 72 " --> pdb=" O THR G 24 " (cutoff:3.500A) removed outlier: 12.812A pdb=" N VAL G 26 " --> pdb=" O SER G 72 " (cutoff:3.500A) removed outlier: 11.004A pdb=" N HIS G 74 " --> pdb=" O VAL G 26 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N CYS G 28 " --> pdb=" O HIS G 74 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N CYS G 76 " --> pdb=" O CYS G 28 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG G 30 " --> pdb=" O CYS G 76 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N PHE G 32 " --> pdb=" O PRO G 78 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE G 418 " --> pdb=" O ALA G 401 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL G 419 " --> pdb=" O TYR G 426 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 80 through 85 removed outlier: 6.507A pdb=" N TRP G 80 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ARG G 127 " --> pdb=" O TRP G 80 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP G 82 " --> pdb=" O ARG G 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 210 through 213 removed outlier: 6.454A pdb=" N ILE G 210 " --> pdb=" O ALA G 250 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N HIS G 252 " --> pdb=" O ILE G 210 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE G 212 " --> pdb=" O HIS G 252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 38 through 39 removed outlier: 6.519A pdb=" N THR A 44 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 55 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A 46 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 38 through 39 removed outlier: 14.128A pdb=" N THR A 24 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 14.401A pdb=" N SER A 72 " --> pdb=" O THR A 24 " (cutoff:3.500A) removed outlier: 12.812A pdb=" N VAL A 26 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 11.005A pdb=" N HIS A 74 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N CYS A 28 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N CYS A 76 " --> pdb=" O CYS A 28 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG A 30 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N PHE A 32 " --> pdb=" O PRO A 78 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE A 418 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A 419 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 80 through 85 removed outlier: 6.507A pdb=" N TRP A 80 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ARG A 127 " --> pdb=" O TRP A 80 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP A 82 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 210 through 213 removed outlier: 6.455A pdb=" N ILE A 210 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N HIS A 252 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE A 212 " --> pdb=" O HIS A 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 38 through 39 removed outlier: 6.519A pdb=" N THR B 44 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL B 55 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU B 46 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 38 through 39 removed outlier: 14.127A pdb=" N THR B 24 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 14.401A pdb=" N SER B 72 " --> pdb=" O THR B 24 " (cutoff:3.500A) removed outlier: 12.812A pdb=" N VAL B 26 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 11.005A pdb=" N HIS B 74 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N CYS B 28 " --> pdb=" O HIS B 74 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N CYS B 76 " --> pdb=" O CYS B 28 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG B 30 " --> pdb=" O CYS B 76 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N PHE B 32 " --> pdb=" O PRO B 78 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE B 418 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL B 419 " --> pdb=" O TYR B 426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 80 through 85 removed outlier: 6.507A pdb=" N TRP B 80 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ARG B 127 " --> pdb=" O TRP B 80 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP B 82 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 210 through 213 removed outlier: 6.454A pdb=" N ILE B 210 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N HIS B 252 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE B 212 " --> pdb=" O HIS B 252 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 38 through 39 removed outlier: 6.519A pdb=" N THR C 44 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL C 55 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU C 46 " --> pdb=" O ALA C 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 38 through 39 removed outlier: 14.128A pdb=" N THR C 24 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 14.402A pdb=" N SER C 72 " --> pdb=" O THR C 24 " (cutoff:3.500A) removed outlier: 12.812A pdb=" N VAL C 26 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 11.005A pdb=" N HIS C 74 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N CYS C 28 " --> pdb=" O HIS C 74 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N CYS C 76 " --> pdb=" O CYS C 28 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG C 30 " --> pdb=" O CYS C 76 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N PHE C 32 " --> pdb=" O PRO C 78 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE C 418 " --> pdb=" O ALA C 401 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL C 419 " --> pdb=" O TYR C 426 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.507A pdb=" N TRP C 80 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ARG C 127 " --> pdb=" O TRP C 80 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP C 82 " --> pdb=" O ARG C 127 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 210 through 213 removed outlier: 6.455A pdb=" N ILE C 210 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N HIS C 252 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE C 212 " --> pdb=" O HIS C 252 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 38 through 39 removed outlier: 6.519A pdb=" N THR D 44 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL D 55 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU D 46 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 38 through 39 removed outlier: 14.126A pdb=" N THR D 24 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 14.402A pdb=" N SER D 72 " --> pdb=" O THR D 24 " (cutoff:3.500A) removed outlier: 12.812A pdb=" N VAL D 26 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 11.004A pdb=" N HIS D 74 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N CYS D 28 " --> pdb=" O HIS D 74 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N CYS D 76 " --> pdb=" O CYS D 28 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG D 30 " --> pdb=" O CYS D 76 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N PHE D 32 " --> pdb=" O PRO D 78 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE D 418 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL D 419 " --> pdb=" O TYR D 426 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 80 through 85 removed outlier: 6.508A pdb=" N TRP D 80 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ARG D 127 " --> pdb=" O TRP D 80 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP D 82 " --> pdb=" O ARG D 127 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 210 through 213 removed outlier: 6.454A pdb=" N ILE D 210 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N HIS D 252 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE D 212 " --> pdb=" O HIS D 252 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 38 through 39 removed outlier: 6.519A pdb=" N THR E 44 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL E 55 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU E 46 " --> pdb=" O ALA E 53 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 38 through 39 removed outlier: 14.127A pdb=" N THR E 24 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 14.402A pdb=" N SER E 72 " --> pdb=" O THR E 24 " (cutoff:3.500A) removed outlier: 12.812A pdb=" N VAL E 26 " --> pdb=" O SER E 72 " (cutoff:3.500A) removed outlier: 11.006A pdb=" N HIS E 74 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N CYS E 28 " --> pdb=" O HIS E 74 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N CYS E 76 " --> pdb=" O CYS E 28 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG E 30 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N PHE E 32 " --> pdb=" O PRO E 78 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE E 418 " --> pdb=" O ALA E 401 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL E 419 " --> pdb=" O TYR E 426 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 80 through 85 removed outlier: 6.508A pdb=" N TRP E 80 " --> pdb=" O SER E 125 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N ARG E 127 " --> pdb=" O TRP E 80 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP E 82 " --> pdb=" O ARG E 127 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 210 through 213 removed outlier: 6.455A pdb=" N ILE E 210 " --> pdb=" O ALA E 250 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N HIS E 252 " --> pdb=" O ILE E 210 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE E 212 " --> pdb=" O HIS E 252 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 38 through 39 removed outlier: 6.519A pdb=" N THR F 44 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL F 55 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU F 46 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 38 through 39 removed outlier: 14.127A pdb=" N THR F 24 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 14.401A pdb=" N SER F 72 " --> pdb=" O THR F 24 " (cutoff:3.500A) removed outlier: 12.812A pdb=" N VAL F 26 " --> pdb=" O SER F 72 " (cutoff:3.500A) removed outlier: 11.004A pdb=" N HIS F 74 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N CYS F 28 " --> pdb=" O HIS F 74 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N CYS F 76 " --> pdb=" O CYS F 28 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG F 30 " --> pdb=" O CYS F 76 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N PHE F 32 " --> pdb=" O PRO F 78 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE F 418 " --> pdb=" O ALA F 401 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL F 419 " --> pdb=" O TYR F 426 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 80 through 85 removed outlier: 6.507A pdb=" N TRP F 80 " --> pdb=" O SER F 125 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ARG F 127 " --> pdb=" O TRP F 80 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP F 82 " --> pdb=" O ARG F 127 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 210 through 213 removed outlier: 6.454A pdb=" N ILE F 210 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N HIS F 252 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE F 212 " --> pdb=" O HIS F 252 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 38 through 39 removed outlier: 6.519A pdb=" N THR H 44 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL H 55 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU H 46 " --> pdb=" O ALA H 53 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 38 through 39 removed outlier: 14.128A pdb=" N THR H 24 " --> pdb=" O ASP H 70 " (cutoff:3.500A) removed outlier: 14.401A pdb=" N SER H 72 " --> pdb=" O THR H 24 " (cutoff:3.500A) removed outlier: 12.812A pdb=" N VAL H 26 " --> pdb=" O SER H 72 " (cutoff:3.500A) removed outlier: 11.005A pdb=" N HIS H 74 " --> pdb=" O VAL H 26 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N CYS H 28 " --> pdb=" O HIS H 74 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N CYS H 76 " --> pdb=" O CYS H 28 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG H 30 " --> pdb=" O CYS H 76 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N PHE H 32 " --> pdb=" O PRO H 78 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE H 418 " --> pdb=" O ALA H 401 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL H 419 " --> pdb=" O TYR H 426 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 80 through 85 removed outlier: 6.507A pdb=" N TRP H 80 " --> pdb=" O SER H 125 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ARG H 127 " --> pdb=" O TRP H 80 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP H 82 " --> pdb=" O ARG H 127 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 210 through 213 removed outlier: 6.455A pdb=" N ILE H 210 " --> pdb=" O ALA H 250 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N HIS H 252 " --> pdb=" O ILE H 210 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE H 212 " --> pdb=" O HIS H 252 " (cutoff:3.500A) 1080 hydrogen bonds defined for protein. 2928 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.00 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5984 1.33 - 1.45: 5017 1.45 - 1.57: 13207 1.57 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 24360 Sorted by residual: bond pdb=" CB 97U F 503 " pdb=" CG 97U F 503 " ideal model delta sigma weight residual 1.505 1.382 0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" CB 97U H 503 " pdb=" CG 97U H 503 " ideal model delta sigma weight residual 1.505 1.383 0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" CB 97U C 503 " pdb=" CG 97U C 503 " ideal model delta sigma weight residual 1.505 1.383 0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" CB 97U A 503 " pdb=" CG 97U A 503 " ideal model delta sigma weight residual 1.505 1.383 0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" CB 97U B 503 " pdb=" CG 97U B 503 " ideal model delta sigma weight residual 1.505 1.383 0.122 2.00e-02 2.50e+03 3.72e+01 ... (remaining 24355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 32404 2.54 - 5.09: 677 5.09 - 7.63: 31 7.63 - 10.17: 8 10.17 - 12.72: 8 Bond angle restraints: 33128 Sorted by residual: angle pdb=" N VAL E 348 " pdb=" CA VAL E 348 " pdb=" C VAL E 348 " ideal model delta sigma weight residual 111.90 102.94 8.96 8.10e-01 1.52e+00 1.22e+02 angle pdb=" N VAL H 348 " pdb=" CA VAL H 348 " pdb=" C VAL H 348 " ideal model delta sigma weight residual 111.90 102.94 8.96 8.10e-01 1.52e+00 1.22e+02 angle pdb=" N VAL C 348 " pdb=" CA VAL C 348 " pdb=" C VAL C 348 " ideal model delta sigma weight residual 111.90 102.96 8.94 8.10e-01 1.52e+00 1.22e+02 angle pdb=" N VAL D 348 " pdb=" CA VAL D 348 " pdb=" C VAL D 348 " ideal model delta sigma weight residual 111.90 102.96 8.94 8.10e-01 1.52e+00 1.22e+02 angle pdb=" N VAL A 348 " pdb=" CA VAL A 348 " pdb=" C VAL A 348 " ideal model delta sigma weight residual 111.90 102.96 8.94 8.10e-01 1.52e+00 1.22e+02 ... (remaining 33123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 12438 17.04 - 34.07: 1461 34.07 - 51.11: 373 51.11 - 68.15: 140 68.15 - 85.18: 52 Dihedral angle restraints: 14464 sinusoidal: 5560 harmonic: 8904 Sorted by residual: dihedral pdb=" CA GLU D 417 " pdb=" C GLU D 417 " pdb=" N PHE D 418 " pdb=" CA PHE D 418 " ideal model delta harmonic sigma weight residual 180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA GLU F 417 " pdb=" C GLU F 417 " pdb=" N PHE F 418 " pdb=" CA PHE F 418 " ideal model delta harmonic sigma weight residual -180.00 -160.47 -19.53 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA GLU G 417 " pdb=" C GLU G 417 " pdb=" N PHE G 418 " pdb=" CA PHE G 418 " ideal model delta harmonic sigma weight residual 180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 14461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3183 0.074 - 0.147: 425 0.147 - 0.221: 24 0.221 - 0.295: 16 0.295 - 0.368: 8 Chirality restraints: 3656 Sorted by residual: chirality pdb=" CA 97U G 503 " pdb=" N 97U G 503 " pdb=" C 97U G 503 " pdb=" CB 97U G 503 " both_signs ideal model delta sigma weight residual False 2.30 2.67 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA 97U H 503 " pdb=" N 97U H 503 " pdb=" C 97U H 503 " pdb=" CB 97U H 503 " both_signs ideal model delta sigma weight residual False 2.30 2.67 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA 97U C 503 " pdb=" N 97U C 503 " pdb=" C 97U C 503 " pdb=" CB 97U C 503 " both_signs ideal model delta sigma weight residual False 2.30 2.67 -0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 3653 not shown) Planarity restraints: 4392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 291 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C TYR E 291 " -0.039 2.00e-02 2.50e+03 pdb=" O TYR E 291 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE E 292 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 291 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.18e+00 pdb=" C TYR A 291 " 0.039 2.00e-02 2.50e+03 pdb=" O TYR A 291 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE A 292 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 291 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C TYR C 291 " -0.039 2.00e-02 2.50e+03 pdb=" O TYR C 291 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE C 292 " 0.013 2.00e-02 2.50e+03 ... (remaining 4389 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 75 2.17 - 2.85: 8613 2.85 - 3.54: 33450 3.54 - 4.22: 59535 4.22 - 4.90: 103669 Nonbonded interactions: 205342 Sorted by model distance: nonbonded pdb=" CE MET D 346 " pdb=" OD1 ASN D 354 " model vdw 1.491 3.460 nonbonded pdb=" CE MET A 346 " pdb=" OD1 ASN A 354 " model vdw 1.491 3.460 nonbonded pdb=" CE MET E 346 " pdb=" OD1 ASN E 354 " model vdw 1.491 3.460 nonbonded pdb=" CE MET G 346 " pdb=" OD1 ASN G 354 " model vdw 1.492 3.460 nonbonded pdb=" CE MET B 346 " pdb=" OD1 ASN B 354 " model vdw 1.492 3.460 ... (remaining 205337 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: 0.07 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 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: 0.460 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.100 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 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 : 0.008 0.268 24400 Z= 0.382 Angle : 0.794 12.717 33144 Z= 0.492 Chirality : 0.054 0.368 3656 Planarity : 0.004 0.039 4392 Dihedral : 17.073 85.185 8808 Min Nonbonded Distance : 1.491 Molprobity Statistics. All-atom Clashscore : 29.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.38 % Allowed : 19.69 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.15), residues: 3104 helix: 0.58 (0.15), residues: 1288 sheet: 0.41 (0.27), residues: 384 loop : -0.77 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 248 TYR 0.026 0.002 TYR D 291 PHE 0.026 0.003 PHE C 418 TRP 0.012 0.001 TRP E 152 HIS 0.009 0.001 HIS D 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.34 (24360) covalent geometry : angle 0.79376 / 0.49 (33128) SS BOND : bond 0.00112 / 0.07 ( 8) SS BOND : angle 0.64751 / 0.40 ( 16) hydrogen bonds : bond 0.15365 / 10.67 ( 1064) hydrogen bonds : angle 6.12166 / 4.43 ( 2928) metal coordination : bond 0.13923 / 9.22 ( 32) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 334 time to evaluate : 0.854 Fit side-chains REVERT: G 374 MET cc_start: 0.6461 (ttt) cc_final: 0.5750 (ttt) REVERT: A 117 GLN cc_start: 0.7413 (mt0) cc_final: 0.7150 (mp10) REVERT: A 374 MET cc_start: 0.7211 (ttt) cc_final: 0.6856 (ttt) REVERT: C 117 GLN cc_start: 0.7473 (mt0) cc_final: 0.6843 (mp10) REVERT: C 259 MET cc_start: 0.7721 (mtp) cc_final: 0.7425 (mtp) REVERT: C 316 ARG cc_start: 0.7083 (ttt180) cc_final: 0.5903 (ttp80) REVERT: C 374 MET cc_start: 0.7563 (ttt) cc_final: 0.7144 (ttt) REVERT: D 168 THR cc_start: 0.8331 (m) cc_final: 0.8090 (m) REVERT: E 252 HIS cc_start: 0.7761 (OUTLIER) cc_final: 0.7397 (t70) REVERT: F 340 MET cc_start: 0.5904 (tpt) cc_final: 0.5559 (tpt) REVERT: H 252 HIS cc_start: 0.7546 (OUTLIER) cc_final: 0.7274 (t70) REVERT: H 373 GLN cc_start: 0.6739 (mt0) cc_final: 0.6426 (mt0) outliers start: 9 outliers final: 6 residues processed: 341 average time/residue: 0.5273 time to fit residues: 211.5599 Evaluate side-chains 236 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 228 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 252 HIS Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain E residue 252 HIS Chi-restraints excluded: chain F residue 252 HIS Chi-restraints excluded: chain H residue 252 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 5.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 229 GLN G 327 GLN G 351 HIS A 136 HIS B 229 GLN B 327 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 HIS ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN C 201 GLN C 354 ASN D 136 HIS D 229 GLN D 327 GLN ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 HIS E 327 GLN ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 GLN F 327 GLN ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 HIS H 169 ASN H 201 GLN H 327 GLN ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.212715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.171663 restraints weight = 18888.753| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.12 r_work: 0.3561 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24400 Z= 0.202 Angle : 0.629 6.689 33144 Z= 0.328 Chirality : 0.047 0.231 3656 Planarity : 0.005 0.078 4392 Dihedral : 8.651 58.733 3744 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.93 % Allowed : 18.96 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.15), residues: 3104 helix: 0.54 (0.14), residues: 1312 sheet: 0.77 (0.28), residues: 368 loop : -0.35 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 101 TYR 0.025 0.002 TYR D 245 PHE 0.030 0.003 PHE G 123 TRP 0.008 0.001 TRP G 152 HIS 0.007 0.001 HIS E 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (24360) covalent geometry : angle 0.62911 / 0.33 (33128) SS BOND : bond 0.00223 / 0.12 ( 8) SS BOND : angle 0.87584 / 0.54 ( 16) hydrogen bonds : bond 0.03248 / 2.22 ( 1064) hydrogen bonds : angle 4.33006 / 3.14 ( 2928) metal coordination : bond 0.00767 / 0.54 ( 32) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 315 time to evaluate : 0.865 Fit side-chains REVERT: G 338 VAL cc_start: 0.6384 (t) cc_final: 0.6171 (t) REVERT: A 256 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7880 (tm-30) REVERT: A 316 ARG cc_start: 0.7122 (ttt180) cc_final: 0.5976 (ttp80) REVERT: A 381 ARG cc_start: 0.8079 (mtp180) cc_final: 0.7800 (mtm-85) REVERT: B 420 MET cc_start: 0.2761 (OUTLIER) cc_final: 0.1932 (mmm) REVERT: C 316 ARG cc_start: 0.7675 (ttt180) cc_final: 0.6480 (ttp80) REVERT: C 381 ARG cc_start: 0.8017 (mtp180) cc_final: 0.7788 (mtm-85) REVERT: D 94 ASP cc_start: 0.7140 (OUTLIER) cc_final: 0.6896 (m-30) REVERT: D 156 LYS cc_start: 0.8574 (mttt) cc_final: 0.7568 (tptm) REVERT: E 156 LYS cc_start: 0.8511 (mttt) cc_final: 0.7513 (tptm) REVERT: E 281 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.5349 (mtp) REVERT: E 316 ARG cc_start: 0.6461 (ttt180) cc_final: 0.5846 (ttp80) REVERT: E 373 GLN cc_start: 0.8267 (mt0) cc_final: 0.8016 (mt0) REVERT: F 94 ASP cc_start: 0.7143 (OUTLIER) cc_final: 0.6901 (m-30) REVERT: F 156 LYS cc_start: 0.8559 (mttt) cc_final: 0.7533 (tptm) REVERT: F 299 ARG cc_start: 0.7968 (mtp180) cc_final: 0.7668 (mmm-85) REVERT: H 156 LYS cc_start: 0.8505 (mttt) cc_final: 0.7533 (tptm) REVERT: H 286 ARG cc_start: 0.7585 (ttm170) cc_final: 0.6982 (mtp180) REVERT: H 373 GLN cc_start: 0.8301 (mt0) cc_final: 0.8064 (mt0) REVERT: H 390 ARG cc_start: 0.6740 (mtm180) cc_final: 0.6410 (mtm-85) outliers start: 69 outliers final: 14 residues processed: 358 average time/residue: 0.6662 time to fit residues: 272.4027 Evaluate side-chains 268 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 250 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 281 MET Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 95 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 229 optimal weight: 6.9990 chunk 275 optimal weight: 20.0000 chunk 114 optimal weight: 0.5980 chunk 267 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 251 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 210 optimal weight: 0.0770 chunk 175 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 overall best weight: 3.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 43 HIS G 327 GLN ** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN B 327 GLN ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS D 90 GLN E 43 HIS E 90 GLN ** E 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 HIS F 90 GLN H 43 HIS ** H 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.174415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.140250 restraints weight = 18790.211| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 0.96 r_work: 0.3218 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.7757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 24400 Z= 0.292 Angle : 0.735 7.732 33144 Z= 0.380 Chirality : 0.050 0.241 3656 Planarity : 0.006 0.078 4392 Dihedral : 9.345 73.233 3728 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 4.46 % Allowed : 17.90 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.14), residues: 3104 helix: 0.24 (0.14), residues: 1304 sheet: 0.44 (0.30), residues: 328 loop : -0.45 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 248 TYR 0.028 0.003 TYR D 89 PHE 0.038 0.003 PHE D 418 TRP 0.009 0.001 TRP B 80 HIS 0.007 0.001 HIS H 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.29 (24360) covalent geometry : angle 0.73412 / 0.38 (33128) SS BOND : bond 0.00499 / 0.22 ( 8) SS BOND : angle 1.30889 / 0.75 ( 16) hydrogen bonds : bond 0.04933 / 3.38 ( 1064) hydrogen bonds : angle 4.57858 / 3.35 ( 2928) metal coordination : bond 0.00830 / 0.57 ( 32) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 347 time to evaluate : 0.856 Fit side-chains REVERT: G 193 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8111 (m-30) REVERT: G 279 GLU cc_start: 0.7338 (mp0) cc_final: 0.6925 (tm-30) REVERT: G 303 ASP cc_start: 0.6956 (m-30) cc_final: 0.6496 (t70) REVERT: G 316 ARG cc_start: 0.7752 (ttt180) cc_final: 0.6476 (ttp80) REVERT: G 328 ASP cc_start: 0.7665 (t70) cc_final: 0.7380 (t0) REVERT: G 390 ARG cc_start: 0.7184 (mtm180) cc_final: 0.6793 (mtm-85) REVERT: A 279 GLU cc_start: 0.7395 (mp0) cc_final: 0.6842 (tm-30) REVERT: A 304 LYS cc_start: 0.8026 (tppt) cc_final: 0.7529 (tppt) REVERT: A 316 ARG cc_start: 0.7772 (ttt180) cc_final: 0.6551 (ttp80) REVERT: A 328 ASP cc_start: 0.7954 (t70) cc_final: 0.7685 (t0) REVERT: A 354 ASN cc_start: 0.9068 (OUTLIER) cc_final: 0.8866 (m-40) REVERT: A 381 ARG cc_start: 0.8173 (mtp180) cc_final: 0.7823 (mtm-85) REVERT: A 390 ARG cc_start: 0.7471 (mtm180) cc_final: 0.7120 (mtm-85) REVERT: B 117 GLN cc_start: 0.8420 (mt0) cc_final: 0.8211 (mm-40) REVERT: B 303 ASP cc_start: 0.6761 (m-30) cc_final: 0.6203 (t0) REVERT: B 316 ARG cc_start: 0.7457 (ttt180) cc_final: 0.6341 (ttp80) REVERT: B 381 ARG cc_start: 0.8333 (mtp180) cc_final: 0.7926 (mtm-85) REVERT: C 279 GLU cc_start: 0.7331 (mp0) cc_final: 0.6832 (tm-30) REVERT: C 304 LYS cc_start: 0.8035 (tppt) cc_final: 0.7528 (tppt) REVERT: C 316 ARG cc_start: 0.7755 (ttt180) cc_final: 0.6540 (ttp80) REVERT: C 328 ASP cc_start: 0.7954 (t70) cc_final: 0.7664 (t0) REVERT: C 381 ARG cc_start: 0.8185 (mtp180) cc_final: 0.7841 (mtm-85) REVERT: C 390 ARG cc_start: 0.7389 (mtm180) cc_final: 0.7176 (mtm110) REVERT: D 94 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.7084 (m-30) REVERT: D 104 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7312 (tt0) REVERT: D 156 LYS cc_start: 0.8504 (mttt) cc_final: 0.7410 (tptm) REVERT: D 264 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7305 (pt0) REVERT: D 294 THR cc_start: 0.8192 (p) cc_final: 0.7984 (p) REVERT: D 313 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6908 (mm-30) REVERT: D 316 ARG cc_start: 0.6987 (ttt180) cc_final: 0.6613 (ttt-90) REVERT: D 427 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7336 (mtm180) REVERT: E 98 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7258 (pt0) REVERT: E 156 LYS cc_start: 0.8548 (mttt) cc_final: 0.7445 (tptm) REVERT: E 264 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7166 (mm-30) REVERT: E 279 GLU cc_start: 0.7178 (mp0) cc_final: 0.6841 (pt0) REVERT: E 316 ARG cc_start: 0.6865 (ttt180) cc_final: 0.6588 (ttt-90) REVERT: F 94 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7135 (m-30) REVERT: F 156 LYS cc_start: 0.8521 (mttt) cc_final: 0.7420 (tptm) REVERT: F 256 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7523 (tm-30) REVERT: F 264 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7268 (pt0) REVERT: F 294 THR cc_start: 0.8145 (p) cc_final: 0.7942 (p) REVERT: F 313 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7015 (mm-30) REVERT: F 316 ARG cc_start: 0.6748 (ttt180) cc_final: 0.6515 (ttt-90) REVERT: H 30 ARG cc_start: 0.6355 (mtm180) cc_final: 0.5960 (mtm-85) REVERT: H 156 LYS cc_start: 0.8555 (mttt) cc_final: 0.7421 (tptm) REVERT: H 264 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7333 (pt0) REVERT: H 279 GLU cc_start: 0.7234 (mp0) cc_final: 0.6876 (pt0) outliers start: 105 outliers final: 24 residues processed: 397 average time/residue: 0.8261 time to fit residues: 365.9798 Evaluate side-chains 322 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 292 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 427 ARG Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 85 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 288 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 199 optimal weight: 9.9990 chunk 293 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 chunk 223 optimal weight: 9.9990 chunk 156 optimal weight: 30.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 354 ASN B 90 GLN B 229 GLN ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN E 90 GLN F 90 GLN H 90 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.178321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.134198 restraints weight = 18595.048| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.88 r_work: 0.3287 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.7793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24400 Z= 0.126 Angle : 0.532 6.599 33144 Z= 0.270 Chirality : 0.044 0.222 3656 Planarity : 0.004 0.064 4392 Dihedral : 7.917 64.898 3728 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.02 % Allowed : 20.37 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.15), residues: 3104 helix: 0.90 (0.14), residues: 1304 sheet: 0.44 (0.30), residues: 328 loop : -0.21 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 248 TYR 0.013 0.001 TYR B 245 PHE 0.027 0.002 PHE B 418 TRP 0.003 0.001 TRP F 290 HIS 0.003 0.001 HIS E 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (24360) covalent geometry : angle 0.53230 / 0.27 (33128) SS BOND : bond 0.00200 / 0.09 ( 8) SS BOND : angle 0.52005 / 0.29 ( 16) hydrogen bonds : bond 0.03086 / 2.12 ( 1064) hydrogen bonds : angle 4.10582 / 3.01 ( 2928) metal coordination : bond 0.00278 / 0.17 ( 32) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 322 time to evaluate : 0.915 Fit side-chains REVERT: G 104 GLU cc_start: 0.7915 (mp0) cc_final: 0.7428 (tt0) REVERT: G 193 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8057 (m-30) REVERT: G 303 ASP cc_start: 0.6772 (m-30) cc_final: 0.6306 (t70) REVERT: G 316 ARG cc_start: 0.7634 (ttt180) cc_final: 0.6260 (ttp80) REVERT: G 328 ASP cc_start: 0.7775 (t70) cc_final: 0.7477 (t0) REVERT: G 390 ARG cc_start: 0.6999 (mtm180) cc_final: 0.6744 (mtm110) REVERT: A 104 GLU cc_start: 0.7894 (mp0) cc_final: 0.7394 (tt0) REVERT: A 193 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8057 (m-30) REVERT: A 316 ARG cc_start: 0.7702 (ttt180) cc_final: 0.6356 (ttp80) REVERT: A 328 ASP cc_start: 0.7876 (t70) cc_final: 0.7547 (t0) REVERT: A 381 ARG cc_start: 0.7988 (mtp180) cc_final: 0.7574 (mtm-85) REVERT: A 390 ARG cc_start: 0.7142 (mtm180) cc_final: 0.6899 (mtm110) REVERT: B 110 ARG cc_start: 0.8718 (mtt180) cc_final: 0.8479 (mtt180) REVERT: B 117 GLN cc_start: 0.8207 (mt0) cc_final: 0.7993 (mm110) REVERT: B 193 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8104 (m-30) REVERT: B 281 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7036 (mtt) REVERT: B 303 ASP cc_start: 0.6570 (m-30) cc_final: 0.6025 (t70) REVERT: B 316 ARG cc_start: 0.7336 (ttt180) cc_final: 0.6084 (ttp80) REVERT: B 381 ARG cc_start: 0.8118 (mtp180) cc_final: 0.7611 (mtm-85) REVERT: B 390 ARG cc_start: 0.6856 (mtm180) cc_final: 0.6471 (mtm110) REVERT: B 420 MET cc_start: 0.5889 (mpt) cc_final: 0.5666 (ttm) REVERT: C 193 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8106 (m-30) REVERT: C 316 ARG cc_start: 0.7672 (ttt180) cc_final: 0.6346 (ttp80) REVERT: C 328 ASP cc_start: 0.7865 (t70) cc_final: 0.7520 (t0) REVERT: C 381 ARG cc_start: 0.7999 (mtp180) cc_final: 0.7578 (mtm-85) REVERT: C 390 ARG cc_start: 0.7188 (mtm180) cc_final: 0.6894 (mtm110) REVERT: D 94 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6779 (m-30) REVERT: D 156 LYS cc_start: 0.8508 (mttt) cc_final: 0.7373 (tptm) REVERT: D 316 ARG cc_start: 0.6842 (ttt180) cc_final: 0.6560 (ttt-90) REVERT: E 30 ARG cc_start: 0.6347 (mtm180) cc_final: 0.5897 (mtm-85) REVERT: E 156 LYS cc_start: 0.8514 (mttt) cc_final: 0.7369 (tptm) REVERT: E 264 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6977 (mm-30) REVERT: E 286 ARG cc_start: 0.7941 (ttp-110) cc_final: 0.7107 (mtp180) REVERT: E 316 ARG cc_start: 0.6706 (ttt180) cc_final: 0.6407 (ttt-90) REVERT: F 89 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.6441 (p90) REVERT: F 94 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6795 (m-30) REVERT: F 156 LYS cc_start: 0.8451 (mttt) cc_final: 0.7328 (tptm) REVERT: F 264 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7024 (pt0) REVERT: F 286 ARG cc_start: 0.7525 (ttp-110) cc_final: 0.7051 (ptp-110) REVERT: F 316 ARG cc_start: 0.6628 (ttt180) cc_final: 0.6411 (ttt-90) REVERT: H 30 ARG cc_start: 0.6428 (mtm180) cc_final: 0.5903 (mtm-85) REVERT: H 264 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7076 (pt0) REVERT: H 316 ARG cc_start: 0.6391 (ttt-90) cc_final: 0.5604 (ttp80) outliers start: 71 outliers final: 24 residues processed: 358 average time/residue: 0.7807 time to fit residues: 313.1008 Evaluate side-chains 327 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 295 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 89 TYR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 322 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 187 optimal weight: 3.9990 chunk 250 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 298 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.0020 chunk 9 optimal weight: 2.9990 chunk 195 optimal weight: 30.0000 chunk 113 optimal weight: 0.9990 chunk 224 optimal weight: 9.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 172 ASN A 90 GLN B 395 GLN C 90 GLN ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN F 327 GLN F 373 GLN H 90 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.173161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.131164 restraints weight = 18635.532| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.78 r_work: 0.3220 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.8189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24400 Z= 0.162 Angle : 0.548 6.131 33144 Z= 0.281 Chirality : 0.045 0.228 3656 Planarity : 0.005 0.060 4392 Dihedral : 8.127 88.054 3728 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.57 % Allowed : 19.81 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 3104 helix: 0.94 (0.14), residues: 1312 sheet: 0.45 (0.30), residues: 328 loop : -0.14 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 248 TYR 0.015 0.002 TYR B 245 PHE 0.027 0.002 PHE B 418 TRP 0.003 0.001 TRP G 80 HIS 0.003 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (24360) covalent geometry : angle 0.54783 / 0.28 (33128) SS BOND : bond 0.00292 / 0.16 ( 8) SS BOND : angle 0.58877 / 0.35 ( 16) hydrogen bonds : bond 0.03484 / 2.38 ( 1064) hydrogen bonds : angle 4.05982 / 2.98 ( 2928) metal coordination : bond 0.00354 / 0.24 ( 32) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 314 time to evaluate : 0.897 Fit side-chains REVERT: G 104 GLU cc_start: 0.7976 (mp0) cc_final: 0.7477 (tt0) REVERT: G 193 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8108 (m-30) REVERT: G 303 ASP cc_start: 0.6834 (m-30) cc_final: 0.6328 (t70) REVERT: G 316 ARG cc_start: 0.7643 (ttt180) cc_final: 0.6246 (ttp80) REVERT: G 328 ASP cc_start: 0.7812 (t70) cc_final: 0.7493 (t0) REVERT: G 390 ARG cc_start: 0.6974 (mtm180) cc_final: 0.6711 (mtm110) REVERT: A 104 GLU cc_start: 0.7880 (mp0) cc_final: 0.7424 (tt0) REVERT: A 193 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8094 (m-30) REVERT: A 279 GLU cc_start: 0.7107 (mp0) cc_final: 0.6530 (pt0) REVERT: A 313 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7092 (mm-30) REVERT: A 316 ARG cc_start: 0.7691 (ttt180) cc_final: 0.6356 (ttp80) REVERT: A 328 ASP cc_start: 0.7917 (t70) cc_final: 0.7609 (t0) REVERT: A 381 ARG cc_start: 0.8035 (mtp180) cc_final: 0.7574 (mtm-85) REVERT: A 390 ARG cc_start: 0.7146 (mtm180) cc_final: 0.6827 (mtp-110) REVERT: B 104 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7259 (mm-30) REVERT: B 117 GLN cc_start: 0.8288 (mt0) cc_final: 0.7992 (mm-40) REVERT: B 193 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8098 (m-30) REVERT: B 303 ASP cc_start: 0.6636 (m-30) cc_final: 0.6204 (t70) REVERT: B 316 ARG cc_start: 0.7509 (ttt180) cc_final: 0.6164 (ttp80) REVERT: B 328 ASP cc_start: 0.7787 (t70) cc_final: 0.7444 (t0) REVERT: B 357 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: B 381 ARG cc_start: 0.8110 (mtp180) cc_final: 0.7606 (mtm-85) REVERT: B 390 ARG cc_start: 0.7137 (mtm180) cc_final: 0.6786 (mtm110) REVERT: C 104 GLU cc_start: 0.7970 (mp0) cc_final: 0.7437 (tt0) REVERT: C 193 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8054 (m-30) REVERT: C 279 GLU cc_start: 0.7115 (mp0) cc_final: 0.6520 (pt0) REVERT: C 313 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6999 (mm-30) REVERT: C 316 ARG cc_start: 0.7708 (ttt180) cc_final: 0.6384 (ttp80) REVERT: C 328 ASP cc_start: 0.7914 (t70) cc_final: 0.7594 (t0) REVERT: C 357 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.5933 (tt0) REVERT: C 381 ARG cc_start: 0.8031 (mtp180) cc_final: 0.7540 (mtm-85) REVERT: C 390 ARG cc_start: 0.7171 (mtm180) cc_final: 0.6816 (mtp-110) REVERT: D 89 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.6671 (p90) REVERT: D 94 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6812 (m-30) REVERT: D 256 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7314 (tm-30) REVERT: D 264 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7067 (pt0) REVERT: D 281 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7761 (mtt) REVERT: D 316 ARG cc_start: 0.7016 (ttt180) cc_final: 0.6720 (ttt-90) REVERT: E 30 ARG cc_start: 0.6410 (mtm180) cc_final: 0.5658 (mtm-85) REVERT: E 98 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7036 (pt0) REVERT: E 156 LYS cc_start: 0.8499 (mttt) cc_final: 0.7357 (tptm) REVERT: E 256 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7298 (tm-30) REVERT: E 264 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7081 (mm-30) REVERT: E 286 ARG cc_start: 0.7796 (ttp-110) cc_final: 0.7073 (mtp180) REVERT: E 316 ARG cc_start: 0.6715 (ttt180) cc_final: 0.6449 (ttt-90) REVERT: F 89 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.6676 (p90) REVERT: F 94 ASP cc_start: 0.7150 (OUTLIER) cc_final: 0.6804 (m-30) REVERT: F 156 LYS cc_start: 0.8512 (mttt) cc_final: 0.7366 (tptm) REVERT: F 256 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7323 (tm-30) REVERT: F 264 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7087 (pt0) REVERT: F 316 ARG cc_start: 0.6650 (ttt180) cc_final: 0.6410 (ttt-90) REVERT: H 30 ARG cc_start: 0.6506 (mtm180) cc_final: 0.5998 (mtm-85) REVERT: H 256 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7386 (tm-30) REVERT: H 264 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7104 (pt0) REVERT: H 286 ARG cc_start: 0.7824 (ttp-110) cc_final: 0.7104 (mtp180) outliers start: 84 outliers final: 31 residues processed: 360 average time/residue: 0.7651 time to fit residues: 308.9145 Evaluate side-chains 341 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 297 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 89 TYR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 89 TYR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain H residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 277 optimal weight: 0.0870 chunk 5 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 222 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 245 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 43 HIS B 90 GLN ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 HIS E 351 HIS F 351 HIS H 351 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.169334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.124595 restraints weight = 18930.584| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.44 r_work: 0.3207 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.8887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24400 Z= 0.234 Angle : 0.630 6.899 33144 Z= 0.324 Chirality : 0.048 0.227 3656 Planarity : 0.005 0.063 4392 Dihedral : 9.085 88.905 3728 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.21 % Allowed : 20.07 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 3104 helix: 0.66 (0.14), residues: 1312 sheet: 0.30 (0.30), residues: 328 loop : -0.20 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 316 TYR 0.020 0.002 TYR B 245 PHE 0.029 0.003 PHE F 418 TRP 0.003 0.001 TRP F 290 HIS 0.005 0.001 HIS G 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.23 (24360) covalent geometry : angle 0.62973 / 0.32 (33128) SS BOND : bond 0.00476 / 0.29 ( 8) SS BOND : angle 1.08427 / 0.69 ( 16) hydrogen bonds : bond 0.04101 / 2.80 ( 1064) hydrogen bonds : angle 4.29690 / 3.15 ( 2928) metal coordination : bond 0.00635 / 0.44 ( 32) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 330 time to evaluate : 0.688 Fit side-chains REVERT: G 104 GLU cc_start: 0.7971 (mp0) cc_final: 0.7423 (tt0) REVERT: G 279 GLU cc_start: 0.7127 (mp0) cc_final: 0.6519 (pt0) REVERT: G 303 ASP cc_start: 0.6850 (m-30) cc_final: 0.6397 (t0) REVERT: G 316 ARG cc_start: 0.7588 (ttt180) cc_final: 0.6258 (ttp80) REVERT: G 328 ASP cc_start: 0.7913 (t70) cc_final: 0.7571 (t0) REVERT: G 427 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7214 (ttm170) REVERT: A 104 GLU cc_start: 0.7877 (mp0) cc_final: 0.7337 (tt0) REVERT: A 281 MET cc_start: 0.8207 (mtt) cc_final: 0.7897 (mtt) REVERT: A 313 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6955 (mm-30) REVERT: A 316 ARG cc_start: 0.7587 (ttt180) cc_final: 0.6254 (ttp80) REVERT: A 328 ASP cc_start: 0.7971 (t70) cc_final: 0.7639 (t0) REVERT: A 381 ARG cc_start: 0.7934 (mtp180) cc_final: 0.7463 (mtm-85) REVERT: A 390 ARG cc_start: 0.7155 (mtm180) cc_final: 0.6909 (mtm110) REVERT: B 104 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7309 (mm-30) REVERT: B 117 GLN cc_start: 0.8216 (mt0) cc_final: 0.7916 (mm-40) REVERT: B 279 GLU cc_start: 0.7085 (mp0) cc_final: 0.6465 (pp20) REVERT: B 303 ASP cc_start: 0.6803 (m-30) cc_final: 0.6359 (t70) REVERT: B 316 ARG cc_start: 0.7581 (ttt180) cc_final: 0.6219 (ttp80) REVERT: B 328 ASP cc_start: 0.7912 (t70) cc_final: 0.7578 (t0) REVERT: B 381 ARG cc_start: 0.8003 (mtp180) cc_final: 0.7506 (mtm-85) REVERT: B 390 ARG cc_start: 0.7122 (mtm180) cc_final: 0.6848 (mtm110) REVERT: C 104 GLU cc_start: 0.7988 (mp0) cc_final: 0.7345 (tt0) REVERT: C 281 MET cc_start: 0.8220 (mtt) cc_final: 0.7865 (mtt) REVERT: C 313 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6956 (mm-30) REVERT: C 316 ARG cc_start: 0.7603 (ttt180) cc_final: 0.6235 (ttp80) REVERT: C 328 ASP cc_start: 0.7908 (t70) cc_final: 0.7572 (t0) REVERT: C 357 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6063 (tt0) REVERT: C 381 ARG cc_start: 0.7936 (mtp180) cc_final: 0.7469 (mtm-85) REVERT: C 390 ARG cc_start: 0.7138 (mtm180) cc_final: 0.6906 (mtm110) REVERT: D 30 ARG cc_start: 0.6131 (mtm180) cc_final: 0.5611 (mtm-85) REVERT: D 89 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.6450 (p90) REVERT: D 94 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.6970 (m-30) REVERT: D 256 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7401 (tm-30) REVERT: D 264 GLU cc_start: 0.7527 (mm-30) cc_final: 0.6976 (pt0) REVERT: D 316 ARG cc_start: 0.6961 (ttt180) cc_final: 0.6637 (ttt-90) REVERT: E 30 ARG cc_start: 0.6479 (mtm180) cc_final: 0.5838 (mtm-85) REVERT: E 156 LYS cc_start: 0.8461 (mttt) cc_final: 0.7239 (tptm) REVERT: E 256 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7406 (tm-30) REVERT: E 257 GLU cc_start: 0.8009 (tp30) cc_final: 0.7720 (tp30) REVERT: E 264 GLU cc_start: 0.7420 (mm-30) cc_final: 0.6994 (mm-30) REVERT: E 285 LYS cc_start: 0.7821 (tttt) cc_final: 0.7595 (ttmp) REVERT: E 316 ARG cc_start: 0.6706 (ttt180) cc_final: 0.6377 (ttt-90) REVERT: F 30 ARG cc_start: 0.6216 (mtm180) cc_final: 0.5497 (mtm-85) REVERT: F 89 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.6501 (p90) REVERT: F 94 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.6919 (m-30) REVERT: F 156 LYS cc_start: 0.8548 (mttt) cc_final: 0.7256 (tptm) REVERT: F 256 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7135 (tm-30) REVERT: F 264 GLU cc_start: 0.7516 (mm-30) cc_final: 0.6968 (pt0) REVERT: F 316 ARG cc_start: 0.6758 (ttt180) cc_final: 0.6429 (ttt-90) REVERT: F 428 GLN cc_start: 0.6773 (mm-40) cc_final: 0.6448 (mm-40) REVERT: H 30 ARG cc_start: 0.6446 (mtm180) cc_final: 0.5688 (mtm-85) REVERT: H 94 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6935 (m-30) REVERT: H 256 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7313 (tm-30) REVERT: H 264 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7003 (pt0) REVERT: H 286 ARG cc_start: 0.7589 (ttp-110) cc_final: 0.6856 (mtp180) outliers start: 99 outliers final: 48 residues processed: 377 average time/residue: 0.7538 time to fit residues: 319.6389 Evaluate side-chains 374 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 317 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 304 LYS Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 400 VAL Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 427 ARG Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 89 TYR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 89 TYR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 322 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 52 optimal weight: 0.0870 chunk 63 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 237 optimal weight: 0.7980 chunk 253 optimal weight: 7.9990 chunk 283 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 196 optimal weight: 7.9990 chunk 225 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 172 ASN B 428 GLN C 90 GLN ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.176383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.133895 restraints weight = 19045.821| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.38 r_work: 0.3328 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.8789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24400 Z= 0.106 Angle : 0.503 6.339 33144 Z= 0.253 Chirality : 0.044 0.232 3656 Planarity : 0.004 0.051 4392 Dihedral : 7.641 89.556 3728 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.85 % Allowed : 21.56 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.15), residues: 3104 helix: 1.14 (0.14), residues: 1312 sheet: 0.37 (0.30), residues: 328 loop : -0.11 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 248 TYR 0.011 0.001 TYR F 291 PHE 0.016 0.001 PHE G 123 TRP 0.004 0.001 TRP B 152 HIS 0.003 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (24360) covalent geometry : angle 0.50353 / 0.25 (33128) SS BOND : bond 0.00224 / 0.14 ( 8) SS BOND : angle 0.40163 / 0.25 ( 16) hydrogen bonds : bond 0.02861 / 1.97 ( 1064) hydrogen bonds : angle 4.02578 / 2.95 ( 2928) metal coordination : bond 0.00349 / 0.19 ( 32) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 329 time to evaluate : 0.880 Fit side-chains REVERT: G 104 GLU cc_start: 0.7839 (mp0) cc_final: 0.7420 (tt0) REVERT: G 193 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: G 279 GLU cc_start: 0.7081 (mp0) cc_final: 0.6570 (pt0) REVERT: G 303 ASP cc_start: 0.6911 (m-30) cc_final: 0.6477 (t70) REVERT: G 316 ARG cc_start: 0.7615 (ttt180) cc_final: 0.6277 (ttp80) REVERT: G 328 ASP cc_start: 0.7823 (t70) cc_final: 0.7497 (t0) REVERT: G 390 ARG cc_start: 0.7595 (mtm-85) cc_final: 0.7216 (mtm110) REVERT: A 104 GLU cc_start: 0.7870 (mp0) cc_final: 0.7409 (tt0) REVERT: A 193 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8016 (m-30) REVERT: A 279 GLU cc_start: 0.7086 (mp0) cc_final: 0.6518 (pp20) REVERT: A 316 ARG cc_start: 0.7608 (ttt180) cc_final: 0.6249 (ttp80) REVERT: A 328 ASP cc_start: 0.7928 (t70) cc_final: 0.7614 (t0) REVERT: A 381 ARG cc_start: 0.7921 (mtp180) cc_final: 0.7579 (mtm-85) REVERT: A 390 ARG cc_start: 0.7133 (mtm180) cc_final: 0.6797 (mtp-110) REVERT: A 411 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6811 (mp10) REVERT: B 104 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7369 (mm-30) REVERT: B 110 ARG cc_start: 0.8657 (mtt180) cc_final: 0.8410 (mtt180) REVERT: B 117 GLN cc_start: 0.8211 (mt0) cc_final: 0.7959 (mm110) REVERT: B 193 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8066 (m-30) REVERT: B 279 GLU cc_start: 0.7053 (mp0) cc_final: 0.6532 (pp20) REVERT: B 303 ASP cc_start: 0.6875 (m-30) cc_final: 0.6432 (t70) REVERT: B 316 ARG cc_start: 0.7574 (ttt180) cc_final: 0.6196 (ttp80) REVERT: B 328 ASP cc_start: 0.7816 (t70) cc_final: 0.7492 (t0) REVERT: B 363 GLU cc_start: 0.7565 (pt0) cc_final: 0.7297 (pt0) REVERT: B 381 ARG cc_start: 0.8009 (mtp180) cc_final: 0.7676 (mtm-85) REVERT: B 390 ARG cc_start: 0.7077 (mtm180) cc_final: 0.6815 (mtm110) REVERT: C 186 GLU cc_start: 0.8600 (mp0) cc_final: 0.8380 (mp0) REVERT: C 193 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8051 (m-30) REVERT: C 279 GLU cc_start: 0.7146 (mp0) cc_final: 0.6593 (pp20) REVERT: C 316 ARG cc_start: 0.7622 (ttt180) cc_final: 0.6258 (ttp80) REVERT: C 328 ASP cc_start: 0.7881 (t70) cc_final: 0.7568 (t0) REVERT: C 381 ARG cc_start: 0.7933 (mtp180) cc_final: 0.7582 (mtm-85) REVERT: C 390 ARG cc_start: 0.7149 (mtm180) cc_final: 0.6826 (mtp-110) REVERT: C 411 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6832 (mp10) REVERT: D 30 ARG cc_start: 0.6282 (mtm180) cc_final: 0.5697 (mtm-85) REVERT: D 89 TYR cc_start: 0.7246 (OUTLIER) cc_final: 0.6507 (p90) REVERT: D 94 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6816 (m-30) REVERT: D 256 GLU cc_start: 0.7391 (tm-30) cc_final: 0.7163 (tm-30) REVERT: D 264 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7070 (pt0) REVERT: D 286 ARG cc_start: 0.7744 (ttp-110) cc_final: 0.7194 (mtp180) REVERT: D 316 ARG cc_start: 0.6883 (ttt180) cc_final: 0.6605 (ttt-90) REVERT: E 30 ARG cc_start: 0.6594 (mtm180) cc_final: 0.6016 (mtm-85) REVERT: E 156 LYS cc_start: 0.8411 (mttt) cc_final: 0.7340 (tptm) REVERT: E 256 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7222 (tm-30) REVERT: E 264 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7037 (mm-30) REVERT: E 286 ARG cc_start: 0.7825 (ttp-110) cc_final: 0.7201 (mtp180) REVERT: E 316 ARG cc_start: 0.6739 (ttt180) cc_final: 0.6507 (ttt-90) REVERT: F 30 ARG cc_start: 0.6362 (mtm180) cc_final: 0.5768 (mtm-85) REVERT: F 89 TYR cc_start: 0.7262 (OUTLIER) cc_final: 0.6545 (p90) REVERT: F 94 ASP cc_start: 0.7177 (OUTLIER) cc_final: 0.6791 (m-30) REVERT: F 156 LYS cc_start: 0.8515 (mttt) cc_final: 0.7374 (tptm) REVERT: F 256 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7102 (tm-30) REVERT: F 264 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7031 (pt0) REVERT: F 316 ARG cc_start: 0.6735 (ttt180) cc_final: 0.6482 (ttt-90) REVERT: H 30 ARG cc_start: 0.6643 (mtm180) cc_final: 0.6076 (mtm-85) REVERT: H 256 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7233 (tm-30) REVERT: H 264 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7245 (pt0) REVERT: H 286 ARG cc_start: 0.7643 (ttp-110) cc_final: 0.7052 (mtp180) outliers start: 67 outliers final: 33 residues processed: 363 average time/residue: 0.7694 time to fit residues: 313.6399 Evaluate side-chains 353 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 310 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 400 VAL Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 411 GLN Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 89 TYR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 89 TYR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain H residue 85 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 68 optimal weight: 3.9990 chunk 216 optimal weight: 7.9990 chunk 196 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 199 optimal weight: 20.0000 chunk 296 optimal weight: 5.9990 chunk 240 optimal weight: 7.9990 chunk 220 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 ASN ** C 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 ASN F 345 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.167071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.122805 restraints weight = 19029.928| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.42 r_work: 0.3176 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.9155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 24400 Z= 0.288 Angle : 0.675 7.424 33144 Z= 0.346 Chirality : 0.051 0.227 3656 Planarity : 0.005 0.059 4392 Dihedral : 9.524 83.881 3728 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.53 % Allowed : 21.09 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 3104 helix: 0.66 (0.14), residues: 1312 sheet: 0.32 (0.31), residues: 328 loop : -0.25 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 427 TYR 0.024 0.003 TYR D 245 PHE 0.020 0.003 PHE A 123 TRP 0.004 0.001 TRP D 290 HIS 0.006 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.29 (24360) covalent geometry : angle 0.67497 / 0.35 (33128) SS BOND : bond 0.00578 / 0.35 ( 8) SS BOND : angle 1.31326 / 0.83 ( 16) hydrogen bonds : bond 0.04457 / 3.04 ( 1064) hydrogen bonds : angle 4.33824 / 3.17 ( 2928) metal coordination : bond 0.00759 / 0.51 ( 32) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 340 time to evaluate : 0.839 Fit side-chains REVERT: G 104 GLU cc_start: 0.7861 (mp0) cc_final: 0.7329 (tt0) REVERT: G 281 MET cc_start: 0.8312 (mtt) cc_final: 0.7939 (mtt) REVERT: G 303 ASP cc_start: 0.6903 (m-30) cc_final: 0.6429 (t0) REVERT: G 316 ARG cc_start: 0.7605 (ttt180) cc_final: 0.6274 (ttp80) REVERT: G 328 ASP cc_start: 0.7936 (t70) cc_final: 0.7607 (t0) REVERT: G 390 ARG cc_start: 0.7622 (mtm-85) cc_final: 0.7251 (mtm110) REVERT: A 104 GLU cc_start: 0.7905 (mp0) cc_final: 0.7354 (tt0) REVERT: A 316 ARG cc_start: 0.7590 (ttt180) cc_final: 0.6273 (ttp80) REVERT: A 328 ASP cc_start: 0.7957 (t70) cc_final: 0.7626 (t0) REVERT: A 381 ARG cc_start: 0.7984 (mtp180) cc_final: 0.7523 (mtm-85) REVERT: A 390 ARG cc_start: 0.7169 (mtm180) cc_final: 0.6887 (mtm110) REVERT: A 411 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6551 (mp10) REVERT: B 104 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7350 (mm-30) REVERT: B 117 GLN cc_start: 0.8275 (mt0) cc_final: 0.7978 (mm110) REVERT: B 193 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8102 (m-30) REVERT: B 303 ASP cc_start: 0.6873 (m-30) cc_final: 0.6452 (t70) REVERT: B 316 ARG cc_start: 0.7610 (ttt180) cc_final: 0.6268 (ttp80) REVERT: B 328 ASP cc_start: 0.7950 (t70) cc_final: 0.7613 (t0) REVERT: B 381 ARG cc_start: 0.8056 (mtp180) cc_final: 0.7571 (mtm-85) REVERT: C 316 ARG cc_start: 0.7620 (ttt180) cc_final: 0.6254 (ttp80) REVERT: C 328 ASP cc_start: 0.7942 (t70) cc_final: 0.7611 (t0) REVERT: C 357 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6005 (tt0) REVERT: C 381 ARG cc_start: 0.7961 (mtp180) cc_final: 0.7487 (mtm-85) REVERT: C 390 ARG cc_start: 0.7225 (mtm180) cc_final: 0.6892 (mtm110) REVERT: C 411 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6591 (mp10) REVERT: D 30 ARG cc_start: 0.6318 (mtm180) cc_final: 0.5675 (mtm-85) REVERT: D 89 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.6597 (p90) REVERT: D 94 ASP cc_start: 0.7323 (OUTLIER) cc_final: 0.6931 (m-30) REVERT: D 256 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7439 (tm-30) REVERT: D 264 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7069 (pt0) REVERT: D 281 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.6352 (mpp) REVERT: D 316 ARG cc_start: 0.6959 (ttt180) cc_final: 0.6632 (ttt-90) REVERT: E 30 ARG cc_start: 0.6444 (mtm180) cc_final: 0.5800 (mtm-85) REVERT: E 156 LYS cc_start: 0.8501 (mttt) cc_final: 0.7265 (tptm) REVERT: E 256 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7374 (tm-30) REVERT: E 257 GLU cc_start: 0.8018 (tp30) cc_final: 0.7723 (tp30) REVERT: E 264 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7080 (mm-30) REVERT: E 285 LYS cc_start: 0.7869 (tttt) cc_final: 0.7633 (ttmp) REVERT: E 316 ARG cc_start: 0.6688 (ttt180) cc_final: 0.6346 (ttt-90) REVERT: F 30 ARG cc_start: 0.6463 (mtm180) cc_final: 0.5822 (mtm-85) REVERT: F 89 TYR cc_start: 0.7877 (OUTLIER) cc_final: 0.6526 (p90) REVERT: F 94 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.6873 (m-30) REVERT: F 156 LYS cc_start: 0.8544 (mttt) cc_final: 0.7260 (tptm) REVERT: F 256 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7291 (tm-30) REVERT: F 264 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7072 (pt0) REVERT: F 281 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.6409 (mpp) REVERT: F 316 ARG cc_start: 0.6816 (ttt180) cc_final: 0.6500 (ttt-90) REVERT: F 428 GLN cc_start: 0.6954 (mm-40) cc_final: 0.6587 (mm-40) REVERT: H 30 ARG cc_start: 0.6522 (mtm180) cc_final: 0.5888 (mtm-85) REVERT: H 173 SER cc_start: 0.8451 (m) cc_final: 0.8245 (p) REVERT: H 256 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7369 (tm-30) REVERT: H 257 GLU cc_start: 0.8006 (tp30) cc_final: 0.7746 (tp30) REVERT: H 264 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7080 (pt0) outliers start: 83 outliers final: 43 residues processed: 382 average time/residue: 0.7426 time to fit residues: 319.7773 Evaluate side-chains 384 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 331 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 400 VAL Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 411 GLN Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 89 TYR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 89 TYR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 285 LYS Chi-restraints excluded: chain H residue 322 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 87 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 226 optimal weight: 0.8980 chunk 250 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 92 optimal weight: 0.0980 chunk 263 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 306 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 172 ASN A 90 GLN B 90 GLN B 351 HIS B 428 GLN C 90 GLN C 351 HIS F 86 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.174273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.132962 restraints weight = 19157.278| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.57 r_work: 0.3286 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.9037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 24400 Z= 0.115 Angle : 0.518 6.373 33144 Z= 0.260 Chirality : 0.044 0.229 3656 Planarity : 0.004 0.055 4392 Dihedral : 7.886 81.646 3728 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.47 % Allowed : 22.49 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.15), residues: 3104 helix: 1.32 (0.15), residues: 1264 sheet: 0.36 (0.31), residues: 328 loop : -0.13 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 248 TYR 0.011 0.001 TYR B 245 PHE 0.017 0.001 PHE F 123 TRP 0.003 0.000 TRP G 290 HIS 0.003 0.001 HIS B 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (24360) covalent geometry : angle 0.51753 / 0.26 (33128) SS BOND : bond 0.00182 / 0.11 ( 8) SS BOND : angle 0.50615 / 0.32 ( 16) hydrogen bonds : bond 0.02983 / 2.06 ( 1064) hydrogen bonds : angle 4.06849 / 2.98 ( 2928) metal coordination : bond 0.02032 / 1.58 ( 32) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 325 time to evaluate : 0.954 Fit side-chains REVERT: G 104 GLU cc_start: 0.7931 (mp0) cc_final: 0.7435 (tt0) REVERT: G 193 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8065 (m-30) REVERT: G 279 GLU cc_start: 0.7221 (mp0) cc_final: 0.6603 (pp20) REVERT: G 303 ASP cc_start: 0.6797 (m-30) cc_final: 0.6301 (t70) REVERT: G 316 ARG cc_start: 0.7510 (ttt180) cc_final: 0.6171 (ttp80) REVERT: G 328 ASP cc_start: 0.7848 (t70) cc_final: 0.7511 (t0) REVERT: G 390 ARG cc_start: 0.7532 (mtm-85) cc_final: 0.7090 (mtm110) REVERT: A 104 GLU cc_start: 0.7878 (mp0) cc_final: 0.7348 (tt0) REVERT: A 279 GLU cc_start: 0.7248 (mp0) cc_final: 0.6532 (pp20) REVERT: A 316 ARG cc_start: 0.7534 (ttt180) cc_final: 0.6145 (ttp80) REVERT: A 328 ASP cc_start: 0.7886 (t70) cc_final: 0.7556 (t0) REVERT: A 381 ARG cc_start: 0.7883 (mtp180) cc_final: 0.7468 (mtm-85) REVERT: A 390 ARG cc_start: 0.7040 (mtm180) cc_final: 0.6688 (mtp-110) REVERT: A 411 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6617 (mp10) REVERT: B 104 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7338 (mm-30) REVERT: B 110 ARG cc_start: 0.8644 (mtt180) cc_final: 0.8410 (mtt180) REVERT: B 117 GLN cc_start: 0.8190 (mt0) cc_final: 0.7887 (mm110) REVERT: B 193 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: B 279 GLU cc_start: 0.7244 (mp0) cc_final: 0.6599 (pp20) REVERT: B 303 ASP cc_start: 0.6773 (m-30) cc_final: 0.6366 (t70) REVERT: B 316 ARG cc_start: 0.7486 (ttt180) cc_final: 0.6102 (ttp80) REVERT: B 328 ASP cc_start: 0.7842 (t70) cc_final: 0.7505 (t0) REVERT: B 381 ARG cc_start: 0.7970 (mtp180) cc_final: 0.7458 (mtm-85) REVERT: C 279 GLU cc_start: 0.7225 (mp0) cc_final: 0.6570 (pt0) REVERT: C 285 LYS cc_start: 0.7705 (tttt) cc_final: 0.7398 (mtpp) REVERT: C 316 ARG cc_start: 0.7546 (ttt180) cc_final: 0.6162 (ttp80) REVERT: C 328 ASP cc_start: 0.7892 (t70) cc_final: 0.7558 (t0) REVERT: C 381 ARG cc_start: 0.7875 (mtp180) cc_final: 0.7446 (mtm-85) REVERT: C 390 ARG cc_start: 0.7088 (mtm180) cc_final: 0.6696 (mtp-110) REVERT: C 411 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6643 (mp10) REVERT: D 30 ARG cc_start: 0.6340 (mtm180) cc_final: 0.5671 (mtm-85) REVERT: D 89 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.6543 (p90) REVERT: D 94 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6760 (m-30) REVERT: D 256 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7147 (tm-30) REVERT: D 264 GLU cc_start: 0.7459 (mm-30) cc_final: 0.6934 (pt0) REVERT: D 286 ARG cc_start: 0.7718 (ttp-110) cc_final: 0.7073 (mtp180) REVERT: D 316 ARG cc_start: 0.6831 (ttt180) cc_final: 0.6531 (ttt-90) REVERT: E 30 ARG cc_start: 0.6434 (mtm180) cc_final: 0.5809 (mtm-85) REVERT: E 156 LYS cc_start: 0.8447 (mttt) cc_final: 0.7288 (tptm) REVERT: E 256 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7256 (tm-30) REVERT: E 264 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7017 (mm-30) REVERT: E 286 ARG cc_start: 0.7764 (ttp-110) cc_final: 0.7089 (mtp180) REVERT: E 316 ARG cc_start: 0.6677 (ttt180) cc_final: 0.6390 (ttt-90) REVERT: F 30 ARG cc_start: 0.6372 (mtm180) cc_final: 0.5738 (mtm-85) REVERT: F 89 TYR cc_start: 0.7369 (OUTLIER) cc_final: 0.6545 (p90) REVERT: F 94 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6781 (m-30) REVERT: F 156 LYS cc_start: 0.8518 (mttt) cc_final: 0.7298 (tptm) REVERT: F 256 GLU cc_start: 0.7380 (tm-30) cc_final: 0.7136 (tm-30) REVERT: F 264 GLU cc_start: 0.7464 (mm-30) cc_final: 0.6909 (pt0) REVERT: F 281 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.6773 (mpp) REVERT: F 316 ARG cc_start: 0.6687 (ttt180) cc_final: 0.6405 (ttt-90) REVERT: H 30 ARG cc_start: 0.6486 (mtm180) cc_final: 0.5859 (mtm-85) REVERT: H 173 SER cc_start: 0.8367 (m) cc_final: 0.8144 (p) REVERT: H 256 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7241 (tm-30) REVERT: H 264 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7066 (pt0) REVERT: H 286 ARG cc_start: 0.7669 (ttp-110) cc_final: 0.7035 (mtp180) REVERT: H 316 ARG cc_start: 0.6880 (mtp180) cc_final: 0.6676 (mtp180) outliers start: 58 outliers final: 37 residues processed: 358 average time/residue: 0.7574 time to fit residues: 305.6603 Evaluate side-chains 359 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 313 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 400 VAL Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 411 GLN Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 89 TYR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 89 TYR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 322 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 31 optimal weight: 2.9990 chunk 239 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 232 optimal weight: 6.9990 chunk 270 optimal weight: 7.9990 chunk 300 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 308 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.166226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.122141 restraints weight = 19210.350| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.43 r_work: 0.3168 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.9284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 24400 Z= 0.287 Angle : 0.682 7.981 33144 Z= 0.349 Chirality : 0.052 0.228 3656 Planarity : 0.006 0.058 4392 Dihedral : 9.549 79.231 3728 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.47 % Allowed : 22.41 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3104 helix: 0.64 (0.14), residues: 1312 sheet: 0.26 (0.31), residues: 328 loop : -0.31 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 427 TYR 0.023 0.003 TYR F 245 PHE 0.033 0.003 PHE B 418 TRP 0.005 0.001 TRP F 290 HIS 0.006 0.001 HIS F 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.29 (24360) covalent geometry : angle 0.68106 / 0.35 (33128) SS BOND : bond 0.00599 / 0.35 ( 8) SS BOND : angle 1.41269 / 0.87 ( 16) hydrogen bonds : bond 0.04488 / 3.05 ( 1064) hydrogen bonds : angle 4.35869 / 3.19 ( 2928) metal coordination : bond 0.00760 / 0.52 ( 32) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 337 time to evaluate : 0.968 Fit side-chains REVERT: G 104 GLU cc_start: 0.7859 (mp0) cc_final: 0.7320 (tt0) REVERT: G 303 ASP cc_start: 0.6855 (m-30) cc_final: 0.6407 (t0) REVERT: G 316 ARG cc_start: 0.7596 (ttt180) cc_final: 0.6263 (ttp80) REVERT: G 328 ASP cc_start: 0.7962 (t70) cc_final: 0.7629 (t0) REVERT: G 390 ARG cc_start: 0.7590 (mtm-85) cc_final: 0.7252 (mtm110) REVERT: A 104 GLU cc_start: 0.7890 (mp0) cc_final: 0.7319 (tt0) REVERT: A 316 ARG cc_start: 0.7565 (ttt180) cc_final: 0.6245 (ttp80) REVERT: A 328 ASP cc_start: 0.7957 (t70) cc_final: 0.7620 (t0) REVERT: A 381 ARG cc_start: 0.7955 (mtp180) cc_final: 0.7568 (mtm-85) REVERT: A 390 ARG cc_start: 0.7131 (mtm180) cc_final: 0.6804 (mtm110) REVERT: A 411 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6522 (mp10) REVERT: B 104 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7327 (mm-30) REVERT: B 117 GLN cc_start: 0.8262 (mt0) cc_final: 0.7921 (mm-40) REVERT: B 303 ASP cc_start: 0.6813 (m-30) cc_final: 0.6379 (t70) REVERT: B 316 ARG cc_start: 0.7566 (ttt180) cc_final: 0.6234 (ttp80) REVERT: B 328 ASP cc_start: 0.7928 (t70) cc_final: 0.7593 (t0) REVERT: B 381 ARG cc_start: 0.8019 (mtp180) cc_final: 0.7516 (mtm-85) REVERT: B 411 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.6865 (mp10) REVERT: C 281 MET cc_start: 0.8291 (mtt) cc_final: 0.7947 (mtt) REVERT: C 316 ARG cc_start: 0.7612 (ttt180) cc_final: 0.6250 (ttp80) REVERT: C 328 ASP cc_start: 0.7938 (t70) cc_final: 0.7604 (t0) REVERT: C 381 ARG cc_start: 0.7976 (mtp180) cc_final: 0.7493 (mtm-85) REVERT: C 390 ARG cc_start: 0.7192 (mtm180) cc_final: 0.6908 (mtm110) REVERT: C 411 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6571 (mp10) REVERT: D 30 ARG cc_start: 0.6392 (mtm180) cc_final: 0.5642 (mtm-85) REVERT: D 89 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.6496 (p90) REVERT: D 94 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6862 (m-30) REVERT: D 256 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7373 (tm-30) REVERT: D 264 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7049 (pt0) REVERT: D 316 ARG cc_start: 0.6965 (ttt180) cc_final: 0.6647 (ttt-90) REVERT: E 30 ARG cc_start: 0.6523 (mtm180) cc_final: 0.5816 (mtm-85) REVERT: E 156 LYS cc_start: 0.8482 (mttt) cc_final: 0.7245 (tptm) REVERT: E 256 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7434 (tm-30) REVERT: E 264 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7066 (mm-30) REVERT: E 285 LYS cc_start: 0.7871 (tttt) cc_final: 0.7638 (ttmp) REVERT: E 316 ARG cc_start: 0.6736 (ttt180) cc_final: 0.6447 (ttt-90) REVERT: F 30 ARG cc_start: 0.6467 (mtm180) cc_final: 0.5735 (mtm-85) REVERT: F 89 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.6448 (p90) REVERT: F 94 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.6841 (m-30) REVERT: F 156 LYS cc_start: 0.8543 (mttt) cc_final: 0.7245 (tptm) REVERT: F 264 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7026 (pt0) REVERT: F 316 ARG cc_start: 0.6831 (ttt180) cc_final: 0.6538 (ttt-90) REVERT: F 428 GLN cc_start: 0.6829 (mm-40) cc_final: 0.6448 (mm-40) REVERT: H 30 ARG cc_start: 0.6637 (mtm180) cc_final: 0.5956 (mtm110) REVERT: H 54 GLN cc_start: 0.6590 (OUTLIER) cc_final: 0.6296 (tm-30) REVERT: H 256 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7329 (tm-30) REVERT: H 257 GLU cc_start: 0.7967 (tp30) cc_final: 0.7689 (tp30) REVERT: H 264 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7072 (pt0) REVERT: H 286 ARG cc_start: 0.7628 (ttp-110) cc_final: 0.6952 (mtp180) outliers start: 58 outliers final: 36 residues processed: 367 average time/residue: 0.7617 time to fit residues: 315.0251 Evaluate side-chains 369 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 325 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 400 VAL Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 411 GLN Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 89 TYR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 89 TYR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 54 GLN Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 322 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 232 optimal weight: 8.9990 chunk 257 optimal weight: 9.9990 chunk 18 optimal weight: 0.0670 chunk 296 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 268 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 251 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 351 HIS B 90 GLN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 GLN ** C 90 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 = 0.3902 r_free = 0.3902 target = 0.174348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.133286 restraints weight = 19226.196| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.67 r_work: 0.3288 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.9139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24400 Z= 0.111 Angle : 0.522 6.808 33144 Z= 0.262 Chirality : 0.045 0.239 3656 Planarity : 0.004 0.053 4392 Dihedral : 7.881 78.083 3728 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.08 % Allowed : 22.70 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.15), residues: 3104 helix: 1.29 (0.15), residues: 1264 sheet: 0.24 (0.30), residues: 328 loop : -0.20 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 101 TYR 0.012 0.001 TYR B 245 PHE 0.015 0.001 PHE F 123 TRP 0.004 0.001 TRP G 290 HIS 0.003 0.001 HIS B 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (24360) covalent geometry : angle 0.52210 / 0.26 (33128) SS BOND : bond 0.00227 / 0.13 ( 8) SS BOND : angle 0.49549 / 0.30 ( 16) hydrogen bonds : bond 0.02948 / 2.03 ( 1064) hydrogen bonds : angle 4.08336 / 3.00 ( 2928) metal coordination : bond 0.00304 / 0.19 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8833.66 seconds wall clock time: 150 minutes 55.99 seconds (9055.99 seconds total)