Starting phenix.real_space_refine on Fri Jun 5 22:47:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l6p_62861/06_2026/9l6p_62861.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l6p_62861/06_2026/9l6p_62861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l6p_62861/06_2026/9l6p_62861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l6p_62861/06_2026/9l6p_62861.map" model { file = "/net/cci-nas-00/data/ceres_data/9l6p_62861/06_2026/9l6p_62861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l6p_62861/06_2026/9l6p_62861.cif" } resolution = 2.9 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= 0.044 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: 5 Type Number sf(0) Gaussians Zn 16 6.06 5 S 80 5.16 5 C 14776 2.51 5 N 4272 2.21 5 O 4496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s 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: 23640 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2953 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 19, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 2.92, per 1000 atoms: 0.12 Number of scatterers: 23640 At special positions: 0 Unit cell: (145.35, 145.35, 102, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 16 29.99 S 80 16.00 O 4496 8.00 N 4272 7.00 C 14776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 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 G 28 " - pdb=" SG CYS G 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: 1.99 Conformation dependent library (CDL) restraints added in 911.5 milliseconds 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 84 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 86 " 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 84 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 86 " 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 84 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 86 " 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 84 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 86 " 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 84 " pdb="ZN ZN F 502 " - pdb=" NE2 HIS F 86 " 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 84 " pdb="ZN ZN G 502 " - pdb=" NE2 HIS G 86 " 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 84 " pdb="ZN ZN H 502 " - pdb=" NE2 HIS H 86 " 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: 5616 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 32 sheets defined 42.8% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.576A pdb=" N PHE A 100 " --> pdb=" O SER A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 121 removed outlier: 3.629A pdb=" N TYR A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY A 113 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 143 removed outlier: 4.636A 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: 3.591A pdb=" N GLY A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 4.138A 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: 4.119A pdb=" N ILE A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 384 removed outlier: 3.766A pdb=" N ALA A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASP A 378 " --> pdb=" O MET A 374 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 3.592A 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 97 through 101 removed outlier: 3.576A pdb=" N PHE B 100 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 121 removed outlier: 3.629A pdb=" N TYR B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY B 113 " --> pdb=" O PHE B 109 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 removed outlier: 4.636A 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: 3.592A pdb=" N GLY B 298 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 4.138A 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: 4.119A pdb=" N ILE B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 384 removed outlier: 3.766A pdb=" N ALA B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASP B 378 " --> pdb=" O MET B 374 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 3.592A 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 97 through 101 removed outlier: 3.577A pdb=" N PHE C 100 " --> pdb=" O SER C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 121 removed outlier: 3.629A pdb=" N TYR C 107 " --> pdb=" O ASP C 103 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY C 113 " --> pdb=" O PHE C 109 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 removed outlier: 4.635A 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: 3.592A pdb=" N GLY C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 4.138A 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: 4.120A pdb=" N ILE C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 384 removed outlier: 3.765A pdb=" N ALA C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR C 376 " --> pdb=" O LEU C 372 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASP C 378 " --> pdb=" O MET C 374 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 3.592A 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 97 through 101 removed outlier: 3.576A pdb=" N PHE D 100 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 121 removed outlier: 3.629A pdb=" N TYR D 107 " --> pdb=" O ASP D 103 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY D 113 " --> pdb=" O PHE D 109 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS D 116 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 143 removed outlier: 4.636A 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: 3.591A pdb=" N GLY D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 4.137A 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: 4.119A pdb=" N ILE D 359 " --> pdb=" O ALA D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 384 removed outlier: 3.766A pdb=" N ALA D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR D 376 " --> pdb=" O LEU D 372 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASP D 378 " --> pdb=" O MET D 374 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 3.592A 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 97 through 101 removed outlier: 3.576A pdb=" N PHE E 100 " --> pdb=" O SER E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 121 removed outlier: 3.628A pdb=" N TYR E 107 " --> pdb=" O ASP E 103 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY E 113 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS E 116 " --> pdb=" O VAL E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 143 removed outlier: 4.636A 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: 3.591A pdb=" N GLY E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 4.137A 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: 4.119A pdb=" N ILE E 359 " --> pdb=" O ALA E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 384 removed outlier: 3.767A pdb=" N ALA E 375 " --> pdb=" O ALA E 371 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR E 376 " --> pdb=" O LEU E 372 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASP E 378 " --> pdb=" O MET E 374 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA E 379 " --> pdb=" O ALA E 375 " (cutoff:3.500A) removed outlier: 3.592A 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 97 through 101 removed outlier: 3.577A pdb=" N PHE F 100 " --> pdb=" O SER F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 121 removed outlier: 3.630A pdb=" N TYR F 107 " --> pdb=" O ASP F 103 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY F 113 " --> pdb=" O PHE F 109 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS F 116 " --> pdb=" O VAL F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 143 removed outlier: 4.636A 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: 3.592A pdb=" N GLY F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 4.137A 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: 4.121A pdb=" N ILE F 359 " --> pdb=" O ALA F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 384 removed outlier: 3.765A pdb=" N ALA F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR F 376 " --> pdb=" O LEU F 372 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASP F 378 " --> pdb=" O MET F 374 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) removed outlier: 3.591A 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 'G' and resid 97 through 101 removed outlier: 3.577A pdb=" N PHE G 100 " --> pdb=" O SER G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 121 removed outlier: 3.630A pdb=" N TYR G 107 " --> pdb=" O ASP G 103 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY G 113 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS G 116 " --> pdb=" O VAL G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 143 removed outlier: 4.635A 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: 3.591A pdb=" N GLY G 298 " --> pdb=" O THR G 294 " (cutoff:3.500A) removed outlier: 4.137A 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: 4.119A pdb=" N ILE G 359 " --> pdb=" O ALA G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 384 removed outlier: 3.766A pdb=" N ALA G 375 " --> pdb=" O ALA G 371 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR G 376 " --> pdb=" O LEU G 372 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP G 378 " --> pdb=" O MET G 374 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA G 379 " --> pdb=" O ALA G 375 " (cutoff:3.500A) removed outlier: 3.592A 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 'H' and resid 97 through 101 removed outlier: 3.577A pdb=" N PHE H 100 " --> pdb=" O SER H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 121 removed outlier: 3.629A pdb=" N TYR H 107 " --> pdb=" O ASP H 103 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY H 113 " --> pdb=" O PHE H 109 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS H 116 " --> pdb=" O VAL H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 143 removed outlier: 4.636A 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: 3.592A pdb=" N GLY H 298 " --> pdb=" O THR H 294 " (cutoff:3.500A) removed outlier: 4.137A 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: 4.118A pdb=" N ILE H 359 " --> pdb=" O ALA H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 384 removed outlier: 3.765A pdb=" N ALA H 375 " --> pdb=" O ALA H 371 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR H 376 " --> pdb=" O LEU H 372 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASP H 378 " --> pdb=" O MET H 374 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA H 379 " --> pdb=" O ALA H 375 " (cutoff:3.500A) removed outlier: 3.592A 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 'A' and resid 38 through 39 removed outlier: 6.690A pdb=" N THR A 44 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 55 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU A 46 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 14.166A pdb=" N THR A 24 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 14.166A pdb=" N SER A 72 " --> pdb=" O THR A 24 " (cutoff:3.500A) removed outlier: 12.615A pdb=" N VAL A 26 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 10.859A pdb=" N HIS A 74 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N CYS A 28 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N CYS A 76 " --> pdb=" O CYS A 28 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG A 30 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N PHE A 32 " --> pdb=" O PRO A 78 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 418 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL A 419 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 85 removed outlier: 6.317A pdb=" N TRP A 80 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ARG A 127 " --> pdb=" O TRP A 80 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ASP A 82 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 210 through 213 removed outlier: 6.546A pdb=" N ILE A 210 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N HIS A 252 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE A 212 " --> pdb=" O HIS A 252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 38 through 39 removed outlier: 6.690A pdb=" N THR B 44 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL B 55 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU B 46 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 38 through 39 removed outlier: 14.166A pdb=" N THR B 24 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 14.166A pdb=" N SER B 72 " --> pdb=" O THR B 24 " (cutoff:3.500A) removed outlier: 12.616A pdb=" N VAL B 26 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 10.859A pdb=" N HIS B 74 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N CYS B 28 " --> pdb=" O HIS B 74 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N CYS B 76 " --> pdb=" O CYS B 28 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG B 30 " --> pdb=" O CYS B 76 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N PHE B 32 " --> pdb=" O PRO B 78 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE B 418 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 419 " --> pdb=" O TYR B 426 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 80 through 85 removed outlier: 6.318A pdb=" N TRP B 80 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ARG B 127 " --> pdb=" O TRP B 80 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP B 82 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 210 through 213 removed outlier: 6.546A pdb=" N ILE B 210 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N HIS B 252 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE B 212 " --> pdb=" O HIS B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 38 through 39 removed outlier: 6.689A pdb=" N THR C 44 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL C 55 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU C 46 " --> pdb=" O ALA C 53 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 38 through 39 removed outlier: 14.167A pdb=" N THR C 24 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 14.166A pdb=" N SER C 72 " --> pdb=" O THR C 24 " (cutoff:3.500A) removed outlier: 12.616A pdb=" N VAL C 26 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 10.859A pdb=" N HIS C 74 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N CYS C 28 " --> pdb=" O HIS C 74 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N CYS C 76 " --> pdb=" O CYS C 28 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG C 30 " --> pdb=" O CYS C 76 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N PHE C 32 " --> pdb=" O PRO C 78 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE C 418 " --> pdb=" O ALA C 401 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL C 419 " --> pdb=" O TYR C 426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.318A pdb=" N TRP C 80 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ARG C 127 " --> pdb=" O TRP C 80 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP C 82 " --> pdb=" O ARG C 127 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 210 through 213 removed outlier: 6.547A pdb=" N ILE C 210 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N HIS C 252 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE C 212 " --> pdb=" O HIS C 252 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 38 through 39 removed outlier: 6.689A pdb=" N THR D 44 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL D 55 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU D 46 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 38 through 39 removed outlier: 14.166A pdb=" N THR D 24 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 14.165A pdb=" N SER D 72 " --> pdb=" O THR D 24 " (cutoff:3.500A) removed outlier: 12.617A pdb=" N VAL D 26 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 10.859A pdb=" N HIS D 74 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N CYS D 28 " --> pdb=" O HIS D 74 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N CYS D 76 " --> pdb=" O CYS D 28 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG D 30 " --> pdb=" O CYS D 76 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N PHE D 32 " --> pdb=" O PRO D 78 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE D 418 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL D 419 " --> pdb=" O TYR D 426 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 80 through 85 removed outlier: 6.318A pdb=" N TRP D 80 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ARG D 127 " --> pdb=" O TRP D 80 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP D 82 " --> pdb=" O ARG D 127 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 210 through 213 removed outlier: 6.547A pdb=" N ILE D 210 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N HIS D 252 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE D 212 " --> pdb=" O HIS D 252 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 38 through 39 removed outlier: 6.690A pdb=" N THR E 44 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL E 55 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU E 46 " --> pdb=" O ALA E 53 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 38 through 39 removed outlier: 14.166A pdb=" N THR E 24 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 14.166A pdb=" N SER E 72 " --> pdb=" O THR E 24 " (cutoff:3.500A) removed outlier: 12.615A pdb=" N VAL E 26 " --> pdb=" O SER E 72 " (cutoff:3.500A) removed outlier: 10.859A pdb=" N HIS E 74 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N CYS E 28 " --> pdb=" O HIS E 74 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N CYS E 76 " --> pdb=" O CYS E 28 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG E 30 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N PHE E 32 " --> pdb=" O PRO E 78 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE E 418 " --> pdb=" O ALA E 401 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL E 419 " --> pdb=" O TYR E 426 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 80 through 85 removed outlier: 6.318A pdb=" N TRP E 80 " --> pdb=" O SER E 125 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ARG E 127 " --> pdb=" O TRP E 80 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ASP E 82 " --> pdb=" O ARG E 127 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 210 through 213 removed outlier: 6.547A pdb=" N ILE E 210 " --> pdb=" O ALA E 250 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N HIS E 252 " --> pdb=" O ILE E 210 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE E 212 " --> pdb=" O HIS E 252 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 38 through 39 removed outlier: 6.689A pdb=" N THR F 44 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL F 55 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU F 46 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 38 through 39 removed outlier: 14.167A pdb=" N THR F 24 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 14.166A pdb=" N SER F 72 " --> pdb=" O THR F 24 " (cutoff:3.500A) removed outlier: 12.616A pdb=" N VAL F 26 " --> pdb=" O SER F 72 " (cutoff:3.500A) removed outlier: 10.859A pdb=" N HIS F 74 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N CYS F 28 " --> pdb=" O HIS F 74 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N CYS F 76 " --> pdb=" O CYS F 28 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG F 30 " --> pdb=" O CYS F 76 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N PHE F 32 " --> pdb=" O PRO F 78 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE F 418 " --> pdb=" O ALA F 401 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL F 419 " --> pdb=" O TYR F 426 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 80 through 85 removed outlier: 6.318A pdb=" N TRP F 80 " --> pdb=" O SER F 125 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ARG F 127 " --> pdb=" O TRP F 80 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP F 82 " --> pdb=" O ARG F 127 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 210 through 213 removed outlier: 6.547A pdb=" N ILE F 210 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N HIS F 252 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE F 212 " --> pdb=" O HIS F 252 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 38 through 39 removed outlier: 6.691A pdb=" N THR G 44 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL G 55 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU G 46 " --> pdb=" O ALA G 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 38 through 39 removed outlier: 14.166A pdb=" N THR G 24 " --> pdb=" O ASP G 70 " (cutoff:3.500A) removed outlier: 14.165A pdb=" N SER G 72 " --> pdb=" O THR G 24 " (cutoff:3.500A) removed outlier: 12.615A pdb=" N VAL G 26 " --> pdb=" O SER G 72 " (cutoff:3.500A) removed outlier: 10.860A pdb=" N HIS G 74 " --> pdb=" O VAL G 26 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N CYS G 28 " --> pdb=" O HIS G 74 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N CYS G 76 " --> pdb=" O CYS G 28 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG G 30 " --> pdb=" O CYS G 76 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N PHE G 32 " --> pdb=" O PRO G 78 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE G 418 " --> pdb=" O ALA G 401 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL G 419 " --> pdb=" O TYR G 426 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 80 through 85 removed outlier: 6.318A pdb=" N TRP G 80 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ARG G 127 " --> pdb=" O TRP G 80 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP G 82 " --> pdb=" O ARG G 127 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 210 through 213 removed outlier: 6.546A pdb=" N ILE G 210 " --> pdb=" O ALA G 250 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N HIS G 252 " --> pdb=" O ILE G 210 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE G 212 " --> pdb=" O HIS G 252 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 38 through 39 removed outlier: 6.689A pdb=" N THR H 44 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL H 55 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 6.776A 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: 14.166A pdb=" N THR H 24 " --> pdb=" O ASP H 70 " (cutoff:3.500A) removed outlier: 14.166A pdb=" N SER H 72 " --> pdb=" O THR H 24 " (cutoff:3.500A) removed outlier: 12.616A pdb=" N VAL H 26 " --> pdb=" O SER H 72 " (cutoff:3.500A) removed outlier: 10.859A pdb=" N HIS H 74 " --> pdb=" O VAL H 26 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N CYS H 28 " --> pdb=" O HIS H 74 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N CYS H 76 " --> pdb=" O CYS H 28 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG H 30 " --> pdb=" O CYS H 76 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N PHE H 32 " --> pdb=" O PRO H 78 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE H 418 " --> pdb=" O ALA H 401 " (cutoff:3.500A) removed outlier: 6.416A 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: 6.318A pdb=" N TRP H 80 " --> pdb=" O SER H 125 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ARG H 127 " --> pdb=" O TRP H 80 " (cutoff:3.500A) removed outlier: 7.118A 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: 6.547A pdb=" N ILE H 210 " --> pdb=" O ALA H 250 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N HIS H 252 " --> pdb=" O ILE H 210 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE H 212 " --> pdb=" O HIS H 252 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 2832 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: 4.58 Time building geometry restraints manager: 2.67 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: 4872 1.33 - 1.45: 5632 1.45 - 1.57: 13464 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 24112 Sorted by residual: bond pdb=" NZ KCX C 211 " pdb=" CX KCX C 211 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" NZ KCX E 211 " pdb=" CX KCX E 211 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" NZ KCX B 211 " pdb=" CX KCX B 211 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" NZ KCX D 211 " pdb=" CX KCX D 211 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" NZ KCX G 211 " pdb=" CX KCX G 211 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.73e+01 ... (remaining 24107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 32428 2.40 - 4.79: 299 4.79 - 7.19: 25 7.19 - 9.59: 8 9.59 - 11.98: 8 Bond angle restraints: 32768 Sorted by residual: angle pdb=" N GLY F 347 " pdb=" CA GLY F 347 " pdb=" C GLY F 347 " ideal model delta sigma weight residual 114.48 102.50 11.98 1.19e+00 7.06e-01 1.01e+02 angle pdb=" N GLY C 347 " pdb=" CA GLY C 347 " pdb=" C GLY C 347 " ideal model delta sigma weight residual 114.48 102.50 11.98 1.19e+00 7.06e-01 1.01e+02 angle pdb=" N GLY D 347 " pdb=" CA GLY D 347 " pdb=" C GLY D 347 " ideal model delta sigma weight residual 114.37 102.50 11.87 1.26e+00 6.30e-01 8.88e+01 angle pdb=" N GLY H 347 " pdb=" CA GLY H 347 " pdb=" C GLY H 347 " ideal model delta sigma weight residual 114.37 102.50 11.87 1.26e+00 6.30e-01 8.87e+01 angle pdb=" N GLY G 347 " pdb=" CA GLY G 347 " pdb=" C GLY G 347 " ideal model delta sigma weight residual 114.37 102.50 11.87 1.26e+00 6.30e-01 8.87e+01 ... (remaining 32763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 12260 16.86 - 33.73: 1396 33.73 - 50.59: 400 50.59 - 67.45: 160 67.45 - 84.32: 40 Dihedral angle restraints: 14256 sinusoidal: 5376 harmonic: 8880 Sorted by residual: dihedral pdb=" CA ASP E 49 " pdb=" CB ASP E 49 " pdb=" CG ASP E 49 " pdb=" OD1 ASP E 49 " ideal model delta sinusoidal sigma weight residual -30.00 -89.58 59.58 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP D 49 " pdb=" CB ASP D 49 " pdb=" CG ASP D 49 " pdb=" OD1 ASP D 49 " ideal model delta sinusoidal sigma weight residual -30.00 -89.57 59.57 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP C 49 " pdb=" CB ASP C 49 " pdb=" CG ASP C 49 " pdb=" OD1 ASP C 49 " ideal model delta sinusoidal sigma weight residual -30.00 -89.57 59.57 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 14253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3167 0.065 - 0.130: 457 0.130 - 0.194: 24 0.194 - 0.259: 0 0.259 - 0.324: 8 Chirality restraints: 3656 Sorted by residual: chirality pdb=" CA VAL C 348 " pdb=" N VAL C 348 " pdb=" C VAL C 348 " pdb=" CB VAL C 348 " both_signs ideal model delta sigma weight residual False 2.44 2.77 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CA VAL F 348 " pdb=" N VAL F 348 " pdb=" C VAL F 348 " pdb=" CB VAL F 348 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA VAL G 348 " pdb=" N VAL G 348 " pdb=" C VAL G 348 " pdb=" CB VAL G 348 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 3653 not shown) Planarity restraints: 4344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 344 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C THR D 344 " 0.055 2.00e-02 2.50e+03 pdb=" O THR D 344 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP D 345 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 344 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C THR C 344 " -0.055 2.00e-02 2.50e+03 pdb=" O THR C 344 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP C 345 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR H 344 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C THR H 344 " -0.055 2.00e-02 2.50e+03 pdb=" O THR H 344 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP H 345 " 0.019 2.00e-02 2.50e+03 ... (remaining 4341 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5740 2.80 - 3.32: 20651 3.32 - 3.85: 39260 3.85 - 4.37: 48297 4.37 - 4.90: 83894 Nonbonded interactions: 197842 Sorted by model distance: nonbonded pdb=" OE2 GLU F 256 " pdb=" OG SER F 277 " model vdw 2.273 3.040 nonbonded pdb=" OE2 GLU D 256 " pdb=" OG SER D 277 " model vdw 2.274 3.040 nonbonded pdb=" OE2 GLU H 256 " pdb=" OG SER H 277 " model vdw 2.274 3.040 nonbonded pdb=" OE2 GLU C 256 " pdb=" OG SER C 277 " model vdw 2.274 3.040 nonbonded pdb=" OE2 GLU A 256 " pdb=" OG SER A 277 " model vdw 2.274 3.040 ... (remaining 197837 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' 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: 3.940 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.190 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.212 24152 Z= 0.252 Angle : 0.572 11.982 32784 Z= 0.355 Chirality : 0.047 0.324 3656 Planarity : 0.004 0.040 4344 Dihedral : 17.022 84.318 8616 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.63 % Allowed : 23.06 % Favored : 76.31 % 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: 0.11 (0.15), residues: 3104 helix: 0.88 (0.15), residues: 1296 sheet: 0.53 (0.26), residues: 384 loop : -0.77 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 48 TYR 0.008 0.001 TYR E 334 PHE 0.005 0.001 PHE E 123 TRP 0.004 0.001 TRP E 152 HIS 0.007 0.001 HIS F 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.22 (24112) covalent geometry : angle 0.57249 / 0.36 (32768) SS BOND : bond 0.00208 / 0.13 ( 8) SS BOND : angle 0.37194 / 0.23 ( 16) hydrogen bonds : bond 0.16439 / 11.36 ( 1040) hydrogen bonds : angle 5.02593 / 3.57 ( 2832) metal coordination : bond 0.10568 / 7.01 ( 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 525 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 510 time to evaluate : 0.740 Fit side-chains REVERT: A 43 HIS cc_start: 0.7560 (m90) cc_final: 0.7314 (m90) REVERT: A 142 ASN cc_start: 0.8441 (m-40) cc_final: 0.8179 (m-40) REVERT: A 224 SER cc_start: 0.7571 (t) cc_final: 0.7349 (m) REVERT: B 128 ASP cc_start: 0.7556 (t0) cc_final: 0.7313 (t70) REVERT: B 156 LYS cc_start: 0.7449 (mttt) cc_final: 0.6579 (tptp) REVERT: C 43 HIS cc_start: 0.7566 (m90) cc_final: 0.7295 (m90) REVERT: C 142 ASN cc_start: 0.8435 (m-40) cc_final: 0.8184 (m-40) REVERT: C 224 SER cc_start: 0.7547 (t) cc_final: 0.7307 (m) REVERT: D 128 ASP cc_start: 0.7594 (t0) cc_final: 0.7382 (t70) REVERT: D 156 LYS cc_start: 0.7502 (mttt) cc_final: 0.6631 (tptp) REVERT: E 128 ASP cc_start: 0.7565 (t0) cc_final: 0.7351 (t70) REVERT: E 156 LYS cc_start: 0.7501 (mttt) cc_final: 0.6622 (tptp) REVERT: F 156 LYS cc_start: 0.7498 (mttt) cc_final: 0.6629 (tptp) REVERT: G 43 HIS cc_start: 0.7613 (m90) cc_final: 0.7347 (m90) REVERT: G 142 ASN cc_start: 0.8451 (m-40) cc_final: 0.8212 (m-40) REVERT: G 224 SER cc_start: 0.7575 (t) cc_final: 0.7350 (m) REVERT: H 43 HIS cc_start: 0.7571 (m90) cc_final: 0.7294 (m90) REVERT: H 142 ASN cc_start: 0.8441 (m-40) cc_final: 0.8204 (m-40) REVERT: H 224 SER cc_start: 0.7550 (t) cc_final: 0.7344 (m) outliers start: 15 outliers final: 4 residues processed: 521 average time/residue: 0.6473 time to fit residues: 383.5623 Evaluate side-chains 281 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 277 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain G 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: 8.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.3980 overall best weight: 2.6788 ------------------------------------------------------------------------------- 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 136 HIS A 177 HIS A 373 GLN B 27 HIS B 272 HIS B 351 HIS C 90 GLN C 177 HIS C 373 GLN ** D 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 HIS E 27 HIS E 272 HIS E 351 HIS F 272 HIS F 351 HIS G 90 GLN G 177 HIS G 373 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 HIS H 177 HIS H 373 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.138640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.115527 restraints weight = 25492.559| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.81 r_work: 0.3174 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.7492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.784 24152 Z= 0.378 Angle : 0.637 5.905 32784 Z= 0.345 Chirality : 0.049 0.159 3656 Planarity : 0.005 0.034 4344 Dihedral : 5.785 58.006 3520 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 6.08 % Allowed : 20.73 % Favored : 73.18 % 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: -0.10 (0.15), residues: 3104 helix: 0.70 (0.15), residues: 1280 sheet: 0.60 (0.28), residues: 384 loop : -0.92 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 335 TYR 0.017 0.002 TYR D 245 PHE 0.028 0.003 PHE E 418 TRP 0.016 0.002 TRP B 290 HIS 0.008 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.24 (24112) covalent geometry : angle 0.63745 / 0.34 (32768) SS BOND : bond 0.00065 / 0.04 ( 8) SS BOND : angle 0.70658 / 0.46 ( 16) hydrogen bonds : bond 0.05788 / 3.99 ( 1040) hydrogen bonds : angle 4.22129 / 3.01 ( 2832) metal coordination : bond 0.23918 / 13.04 ( 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 522 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 378 time to evaluate : 0.625 Fit side-chains REVERT: A 27 HIS cc_start: 0.7916 (m170) cc_final: 0.7412 (m-70) REVERT: A 156 LYS cc_start: 0.8565 (mttt) cc_final: 0.7252 (tptm) REVERT: A 257 GLU cc_start: 0.7691 (tp30) cc_final: 0.7450 (tp30) REVERT: A 326 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.7083 (mm) REVERT: A 327 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7912 (mt0) REVERT: B 30 ARG cc_start: 0.7087 (mtm180) cc_final: 0.6053 (mtp85) REVERT: B 35 ARG cc_start: 0.8255 (ttm170) cc_final: 0.8017 (ttm170) REVERT: B 36 SER cc_start: 0.8048 (m) cc_final: 0.7769 (m) REVERT: B 52 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8202 (mt) REVERT: B 285 LYS cc_start: 0.8522 (tttt) cc_final: 0.8229 (ttmt) REVERT: C 27 HIS cc_start: 0.7897 (m170) cc_final: 0.7390 (m-70) REVERT: C 70 ASP cc_start: 0.7867 (t70) cc_final: 0.7640 (OUTLIER) REVERT: C 156 LYS cc_start: 0.8567 (mttt) cc_final: 0.7243 (tptm) REVERT: C 257 GLU cc_start: 0.7708 (tp30) cc_final: 0.7447 (tp30) REVERT: C 326 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.7070 (mm) REVERT: C 327 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7889 (mt0) REVERT: D 30 ARG cc_start: 0.7096 (mtm180) cc_final: 0.6077 (mtp85) REVERT: D 36 SER cc_start: 0.8037 (m) cc_final: 0.7773 (m) REVERT: D 55 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8202 (m) REVERT: D 285 LYS cc_start: 0.8522 (tttt) cc_final: 0.8229 (ttmt) REVERT: E 30 ARG cc_start: 0.7176 (mtm180) cc_final: 0.6143 (mtp85) REVERT: E 35 ARG cc_start: 0.8288 (ttm170) cc_final: 0.8054 (ttm170) REVERT: E 36 SER cc_start: 0.8068 (m) cc_final: 0.7801 (m) REVERT: E 55 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8197 (m) REVERT: E 285 LYS cc_start: 0.8511 (tttt) cc_final: 0.8222 (ttmt) REVERT: F 30 ARG cc_start: 0.7076 (mtm180) cc_final: 0.6058 (mtp85) REVERT: F 36 SER cc_start: 0.8028 (m) cc_final: 0.7787 (m) REVERT: F 55 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8204 (m) REVERT: F 285 LYS cc_start: 0.8525 (tttt) cc_final: 0.8235 (ttmt) REVERT: G 27 HIS cc_start: 0.7895 (m170) cc_final: 0.7388 (m-70) REVERT: G 70 ASP cc_start: 0.7878 (t70) cc_final: 0.7664 (OUTLIER) REVERT: G 156 LYS cc_start: 0.8562 (mttt) cc_final: 0.7247 (tptm) REVERT: G 257 GLU cc_start: 0.7694 (tp30) cc_final: 0.7446 (tp30) REVERT: G 326 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7110 (mm) REVERT: G 327 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7919 (mt0) REVERT: H 27 HIS cc_start: 0.7891 (m170) cc_final: 0.7383 (m-70) REVERT: H 156 LYS cc_start: 0.8573 (mttt) cc_final: 0.7244 (tptm) REVERT: H 257 GLU cc_start: 0.7682 (tp30) cc_final: 0.7418 (tp30) REVERT: H 326 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.7088 (mm) REVERT: H 327 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7918 (mt0) outliers start: 144 outliers final: 48 residues processed: 483 average time/residue: 0.6858 time to fit residues: 373.4728 Evaluate side-chains 327 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 269 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 327 GLN Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 327 GLN Chi-restraints excluded: chain H residue 357 GLU Chi-restraints excluded: chain H residue 407 VAL Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 425 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 155 optimal weight: 0.7980 chunk 279 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 295 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 289 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 197 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 136 HIS C 90 GLN C 351 HIS D 136 HIS D 272 HIS E 136 HIS F 136 HIS G 90 GLN G 351 HIS H 90 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.140052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.116467 restraints weight = 25020.998| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.91 r_work: 0.3130 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.7614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.798 24152 Z= 0.209 Angle : 0.476 6.902 32784 Z= 0.250 Chirality : 0.044 0.135 3656 Planarity : 0.004 0.035 4344 Dihedral : 4.957 41.870 3512 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 4.48 % Allowed : 22.72 % Favored : 72.80 % 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: 0.30 (0.15), residues: 3104 helix: 1.14 (0.15), residues: 1296 sheet: 0.72 (0.28), residues: 384 loop : -0.80 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.010 0.001 TYR C 245 PHE 0.015 0.001 PHE F 418 TRP 0.004 0.001 TRP G 152 HIS 0.006 0.001 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (24112) covalent geometry : angle 0.47628 / 0.25 (32768) SS BOND : bond 0.00069 / 0.04 ( 8) SS BOND : angle 0.30341 / 0.20 ( 16) hydrogen bonds : bond 0.04004 / 2.75 ( 1040) hydrogen bonds : angle 3.68057 / 2.62 ( 2832) metal coordination : bond 0.14117 / 11.76 ( 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 370 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 264 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.7824 (m170) cc_final: 0.7396 (m-70) REVERT: A 52 ILE cc_start: 0.8445 (mt) cc_final: 0.8242 (mm) REVERT: A 326 ILE cc_start: 0.7262 (OUTLIER) cc_final: 0.6923 (mm) REVERT: B 30 ARG cc_start: 0.7111 (mtm180) cc_final: 0.6081 (mtp85) REVERT: B 55 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.8064 (m) REVERT: B 285 LYS cc_start: 0.8399 (tttt) cc_final: 0.8113 (ttmt) REVERT: B 316 ARG cc_start: 0.7095 (ttt180) cc_final: 0.6728 (mtp-110) REVERT: C 27 HIS cc_start: 0.7812 (m170) cc_final: 0.7174 (m-70) REVERT: C 52 ILE cc_start: 0.8437 (mt) cc_final: 0.8229 (mm) REVERT: C 70 ASP cc_start: 0.7932 (t70) cc_final: 0.7710 (OUTLIER) REVERT: C 326 ILE cc_start: 0.7253 (OUTLIER) cc_final: 0.6913 (mm) REVERT: D 30 ARG cc_start: 0.7056 (mtm180) cc_final: 0.6081 (mtp85) REVERT: D 55 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8106 (m) REVERT: D 281 MET cc_start: 0.8317 (mtm) cc_final: 0.7983 (mtt) REVERT: D 285 LYS cc_start: 0.8385 (tttt) cc_final: 0.8090 (ttmt) REVERT: D 316 ARG cc_start: 0.7124 (ttt180) cc_final: 0.6699 (mtp-110) REVERT: E 30 ARG cc_start: 0.7052 (mtm180) cc_final: 0.6077 (mtp85) REVERT: E 48 ARG cc_start: 0.7434 (mtp-110) cc_final: 0.6870 (ttm110) REVERT: E 55 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8103 (m) REVERT: E 285 LYS cc_start: 0.8403 (tttt) cc_final: 0.8121 (ttmt) REVERT: E 316 ARG cc_start: 0.7108 (ttt180) cc_final: 0.6693 (mtp-110) REVERT: F 30 ARG cc_start: 0.7098 (mtm180) cc_final: 0.6091 (mtp85) REVERT: F 55 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.8120 (m) REVERT: F 285 LYS cc_start: 0.8403 (tttt) cc_final: 0.8115 (ttmt) REVERT: F 316 ARG cc_start: 0.7107 (ttt180) cc_final: 0.6686 (mtp-110) REVERT: G 27 HIS cc_start: 0.7826 (m170) cc_final: 0.7365 (m-70) REVERT: G 33 ASP cc_start: 0.7053 (t0) cc_final: 0.6852 (t0) REVERT: G 52 ILE cc_start: 0.8439 (mt) cc_final: 0.8235 (mm) REVERT: G 70 ASP cc_start: 0.7962 (t70) cc_final: 0.7738 (OUTLIER) REVERT: G 326 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.6947 (mm) REVERT: H 27 HIS cc_start: 0.7821 (m170) cc_final: 0.7370 (m-70) REVERT: H 52 ILE cc_start: 0.8439 (mt) cc_final: 0.8235 (mm) REVERT: H 326 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6931 (mm) outliers start: 106 outliers final: 49 residues processed: 349 average time/residue: 0.6509 time to fit residues: 258.2245 Evaluate side-chains 295 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 240 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 252 HIS Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 363 GLU Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 363 GLU Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 425 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 224 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 chunk 216 optimal weight: 5.9990 chunk 168 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 203 optimal weight: 6.9990 chunk 306 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.135740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.113740 restraints weight = 25135.868| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.61 r_work: 0.3215 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.7902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 24152 Z= 0.229 Angle : 0.576 5.273 32784 Z= 0.306 Chirality : 0.048 0.149 3656 Planarity : 0.005 0.037 4344 Dihedral : 5.515 44.258 3512 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.94 % Allowed : 22.38 % Favored : 72.68 % 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: -0.02 (0.15), residues: 3104 helix: 0.80 (0.15), residues: 1296 sheet: 0.65 (0.28), residues: 384 loop : -0.94 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 35 TYR 0.015 0.002 TYR A 245 PHE 0.014 0.002 PHE B 418 TRP 0.008 0.002 TRP E 290 HIS 0.006 0.001 HIS D 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.23 (24112) covalent geometry : angle 0.57613 / 0.31 (32768) SS BOND : bond 0.00125 / 0.07 ( 8) SS BOND : angle 0.41991 / 0.28 ( 16) hydrogen bonds : bond 0.05837 / 4.02 ( 1040) hydrogen bonds : angle 3.96046 / 2.82 ( 2832) metal coordination : bond 0.00667 / 0.50 ( 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 366 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 249 time to evaluate : 0.911 Fit side-chains REVERT: A 27 HIS cc_start: 0.7975 (m170) cc_final: 0.7582 (m-70) REVERT: A 33 ASP cc_start: 0.7309 (t0) cc_final: 0.7069 (t0) REVERT: A 326 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7126 (mm) REVERT: A 327 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: B 30 ARG cc_start: 0.7533 (mtm180) cc_final: 0.6451 (mtp85) REVERT: B 55 VAL cc_start: 0.8448 (OUTLIER) cc_final: 0.8228 (m) REVERT: B 285 LYS cc_start: 0.8543 (tttt) cc_final: 0.8263 (ttmt) REVERT: B 316 ARG cc_start: 0.7395 (ttt180) cc_final: 0.7120 (mtp-110) REVERT: C 27 HIS cc_start: 0.8035 (m170) cc_final: 0.7615 (m-70) REVERT: C 33 ASP cc_start: 0.7354 (t0) cc_final: 0.7123 (t0) REVERT: C 70 ASP cc_start: 0.8315 (t70) cc_final: 0.8014 (t70) REVERT: C 326 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7140 (mm) REVERT: C 327 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8048 (mt0) REVERT: D 30 ARG cc_start: 0.7551 (mtm180) cc_final: 0.6444 (mtp85) REVERT: D 285 LYS cc_start: 0.8581 (tttt) cc_final: 0.8305 (ttmt) REVERT: D 316 ARG cc_start: 0.7458 (ttt180) cc_final: 0.7144 (mtp-110) REVERT: E 30 ARG cc_start: 0.7536 (mtm180) cc_final: 0.6443 (mtp85) REVERT: E 48 ARG cc_start: 0.7633 (mtp-110) cc_final: 0.7125 (ttm110) REVERT: E 55 VAL cc_start: 0.8464 (OUTLIER) cc_final: 0.8256 (m) REVERT: E 285 LYS cc_start: 0.8515 (tttt) cc_final: 0.8252 (ttmt) REVERT: E 316 ARG cc_start: 0.7396 (ttt180) cc_final: 0.7133 (mtp-110) REVERT: F 30 ARG cc_start: 0.7551 (mtm180) cc_final: 0.6452 (mtp85) REVERT: F 285 LYS cc_start: 0.8573 (tttt) cc_final: 0.8314 (ttmt) REVERT: F 316 ARG cc_start: 0.7461 (ttt180) cc_final: 0.7149 (mtp-110) REVERT: G 27 HIS cc_start: 0.7979 (m170) cc_final: 0.7569 (m-70) REVERT: G 70 ASP cc_start: 0.8261 (t70) cc_final: 0.7989 (t70) REVERT: G 326 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7109 (mm) REVERT: G 327 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.8020 (mt0) REVERT: H 27 HIS cc_start: 0.8053 (m170) cc_final: 0.7629 (m-70) REVERT: H 33 ASP cc_start: 0.7354 (t0) cc_final: 0.7123 (t0) REVERT: H 326 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7161 (mm) REVERT: H 327 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8046 (mt0) outliers start: 117 outliers final: 70 residues processed: 347 average time/residue: 0.6574 time to fit residues: 259.2137 Evaluate side-chains 308 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 228 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 327 GLN Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain G residue 363 GLU Chi-restraints excluded: chain G residue 385 ILE Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain H residue 252 HIS Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 327 GLN Chi-restraints excluded: chain H residue 357 GLU Chi-restraints excluded: chain H residue 363 GLU Chi-restraints excluded: chain H residue 385 ILE Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 425 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 311 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 305 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 280 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.113768 restraints weight = 25076.949| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.68 r_work: 0.3242 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.7957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24152 Z= 0.148 Angle : 0.506 5.304 32784 Z= 0.267 Chirality : 0.045 0.136 3656 Planarity : 0.004 0.038 4344 Dihedral : 5.215 45.809 3512 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 4.39 % Allowed : 23.14 % Favored : 72.47 % 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: 0.14 (0.15), residues: 3104 helix: 0.98 (0.15), residues: 1296 sheet: 0.74 (0.28), residues: 384 loop : -0.90 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 35 TYR 0.011 0.001 TYR A 245 PHE 0.011 0.002 PHE E 418 TRP 0.005 0.001 TRP E 290 HIS 0.006 0.001 HIS G 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (24112) covalent geometry : angle 0.50656 / 0.27 (32768) SS BOND : bond 0.00074 / 0.04 ( 8) SS BOND : angle 0.31219 / 0.21 ( 16) hydrogen bonds : bond 0.04479 / 3.08 ( 1040) hydrogen bonds : angle 3.75884 / 2.67 ( 2832) metal coordination : bond 0.00491 / 0.34 ( 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 332 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 228 time to evaluate : 0.925 Fit side-chains REVERT: A 27 HIS cc_start: 0.7962 (m170) cc_final: 0.7568 (m-70) REVERT: A 38 LYS cc_start: 0.6984 (mtmt) cc_final: 0.6469 (mtpp) REVERT: A 326 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.7094 (mm) REVERT: A 327 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7975 (mt0) REVERT: B 38 LYS cc_start: 0.7762 (mtpt) cc_final: 0.7106 (mmtm) REVERT: B 285 LYS cc_start: 0.8540 (tttt) cc_final: 0.8297 (ttmt) REVERT: B 316 ARG cc_start: 0.7438 (ttt180) cc_final: 0.7177 (mtp-110) REVERT: C 27 HIS cc_start: 0.7970 (m170) cc_final: 0.7559 (m-70) REVERT: C 38 LYS cc_start: 0.6976 (mtmt) cc_final: 0.6457 (mtpp) REVERT: C 70 ASP cc_start: 0.8365 (t70) cc_final: 0.8010 (t70) REVERT: C 326 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7066 (mm) REVERT: C 327 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7960 (mt0) REVERT: D 38 LYS cc_start: 0.7765 (mtpt) cc_final: 0.7100 (mmtm) REVERT: D 48 ARG cc_start: 0.7627 (mtp-110) cc_final: 0.7209 (ttm110) REVERT: D 285 LYS cc_start: 0.8536 (tttt) cc_final: 0.8298 (ttmt) REVERT: D 316 ARG cc_start: 0.7452 (ttt180) cc_final: 0.7218 (mtp-110) REVERT: E 38 LYS cc_start: 0.7780 (mtpt) cc_final: 0.7122 (mmtm) REVERT: E 48 ARG cc_start: 0.7624 (mtp-110) cc_final: 0.7182 (ttm110) REVERT: E 285 LYS cc_start: 0.8501 (tttt) cc_final: 0.8243 (ttmt) REVERT: E 316 ARG cc_start: 0.7403 (ttt180) cc_final: 0.7179 (mtp-110) REVERT: F 38 LYS cc_start: 0.7776 (mtpt) cc_final: 0.7116 (mmtm) REVERT: F 48 ARG cc_start: 0.7627 (mtp-110) cc_final: 0.7199 (ttm110) REVERT: F 285 LYS cc_start: 0.8486 (tttt) cc_final: 0.8235 (ttmt) REVERT: F 316 ARG cc_start: 0.7451 (ttt180) cc_final: 0.7209 (mtp-110) REVERT: G 27 HIS cc_start: 0.7955 (m170) cc_final: 0.7546 (m-70) REVERT: G 38 LYS cc_start: 0.6960 (mtmt) cc_final: 0.6467 (mtpp) REVERT: G 70 ASP cc_start: 0.8366 (t70) cc_final: 0.8004 (t70) REVERT: G 326 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7091 (mm) REVERT: G 327 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7965 (mt0) REVERT: H 27 HIS cc_start: 0.7999 (m170) cc_final: 0.7610 (m-70) REVERT: H 38 LYS cc_start: 0.6985 (mtmt) cc_final: 0.6466 (mtpp) REVERT: H 326 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.7073 (mm) REVERT: H 327 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7950 (mt0) outliers start: 104 outliers final: 73 residues processed: 322 average time/residue: 0.6539 time to fit residues: 239.4875 Evaluate side-chains 308 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 227 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain G residue 252 HIS Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 327 GLN Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain G residue 363 GLU Chi-restraints excluded: chain G residue 385 ILE Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain H residue 252 HIS Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 327 GLN Chi-restraints excluded: chain H residue 357 GLU Chi-restraints excluded: chain H residue 363 GLU Chi-restraints excluded: chain H residue 385 ILE Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 425 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 119 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 274 optimal weight: 2.9990 chunk 123 optimal weight: 0.0670 chunk 56 optimal weight: 5.9990 chunk 261 optimal weight: 0.0870 chunk 64 optimal weight: 4.9990 chunk 250 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 overall best weight: 2.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.134708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.112933 restraints weight = 25151.471| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.66 r_work: 0.3231 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.8024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24152 Z= 0.168 Angle : 0.523 5.228 32784 Z= 0.278 Chirality : 0.046 0.140 3656 Planarity : 0.005 0.039 4344 Dihedral : 5.282 45.648 3512 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.19 % Allowed : 22.30 % Favored : 72.51 % 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: 0.11 (0.15), residues: 3104 helix: 0.92 (0.15), residues: 1296 sheet: 0.79 (0.28), residues: 384 loop : -0.91 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 35 TYR 0.012 0.001 TYR C 245 PHE 0.010 0.002 PHE H 123 TRP 0.005 0.001 TRP F 290 HIS 0.006 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (24112) covalent geometry : angle 0.52330 / 0.28 (32768) SS BOND : bond 0.00078 / 0.04 ( 8) SS BOND : angle 0.31490 / 0.21 ( 16) hydrogen bonds : bond 0.04828 / 3.31 ( 1040) hydrogen bonds : angle 3.80064 / 2.70 ( 2832) metal coordination : bond 0.00579 / 0.40 ( 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 363 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 240 time to evaluate : 0.857 Fit side-chains REVERT: A 27 HIS cc_start: 0.7943 (m170) cc_final: 0.7548 (m-70) REVERT: A 38 LYS cc_start: 0.6995 (mtmt) cc_final: 0.6424 (mtpp) REVERT: A 326 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7090 (mm) REVERT: A 327 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7981 (mt0) REVERT: B 38 LYS cc_start: 0.7779 (mtpt) cc_final: 0.7111 (mmtm) REVERT: B 48 ARG cc_start: 0.7678 (mtp-110) cc_final: 0.7225 (ttm110) REVERT: B 285 LYS cc_start: 0.8525 (tttt) cc_final: 0.8284 (ttmt) REVERT: B 316 ARG cc_start: 0.7478 (ttt180) cc_final: 0.7256 (mtp-110) REVERT: C 27 HIS cc_start: 0.7933 (m170) cc_final: 0.7543 (m-70) REVERT: C 38 LYS cc_start: 0.6982 (mtmt) cc_final: 0.6406 (mtpp) REVERT: C 70 ASP cc_start: 0.8362 (t70) cc_final: 0.7998 (t70) REVERT: C 326 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7077 (mm) REVERT: C 327 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7969 (mt0) REVERT: D 48 ARG cc_start: 0.7609 (mtp-110) cc_final: 0.7182 (ttm110) REVERT: D 285 LYS cc_start: 0.8504 (tttt) cc_final: 0.8251 (ttmt) REVERT: D 316 ARG cc_start: 0.7412 (ttt180) cc_final: 0.7209 (mtp-110) REVERT: E 48 ARG cc_start: 0.7591 (mtp-110) cc_final: 0.7196 (ttm110) REVERT: E 285 LYS cc_start: 0.8510 (tttt) cc_final: 0.8248 (ttmt) REVERT: F 48 ARG cc_start: 0.7619 (mtp-110) cc_final: 0.7197 (ttm110) REVERT: F 285 LYS cc_start: 0.8506 (tttt) cc_final: 0.8244 (ttmt) REVERT: F 316 ARG cc_start: 0.7422 (ttt180) cc_final: 0.7212 (mtp-110) REVERT: G 27 HIS cc_start: 0.7933 (m170) cc_final: 0.7517 (m-70) REVERT: G 38 LYS cc_start: 0.7035 (mtmt) cc_final: 0.6465 (mtpp) REVERT: G 326 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.7076 (mm) REVERT: G 327 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7975 (mt0) REVERT: H 27 HIS cc_start: 0.7959 (m170) cc_final: 0.7570 (m-70) REVERT: H 38 LYS cc_start: 0.6975 (mtmt) cc_final: 0.6398 (mtpp) REVERT: H 326 ILE cc_start: 0.7468 (OUTLIER) cc_final: 0.7078 (mm) REVERT: H 327 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7967 (mt0) outliers start: 123 outliers final: 84 residues processed: 343 average time/residue: 0.6250 time to fit residues: 245.5909 Evaluate side-chains 330 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 238 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 363 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 C residue 425 VAL Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain G residue 252 HIS Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 327 GLN Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain G residue 363 GLU Chi-restraints excluded: chain G residue 385 ILE Chi-restraints excluded: chain G residue 400 VAL Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain H residue 252 HIS Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 327 GLN Chi-restraints excluded: chain H residue 357 GLU Chi-restraints excluded: chain H residue 363 GLU Chi-restraints excluded: chain H residue 385 ILE Chi-restraints excluded: chain H residue 400 VAL Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 425 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 298 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 219 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.116676 restraints weight = 25038.470| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.61 r_work: 0.3281 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.8049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24152 Z= 0.105 Angle : 0.463 5.623 32784 Z= 0.243 Chirality : 0.043 0.132 3656 Planarity : 0.004 0.054 4344 Dihedral : 4.941 48.236 3512 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.31 % Allowed : 23.23 % Favored : 72.47 % 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: 0.38 (0.15), residues: 3104 helix: 1.23 (0.15), residues: 1296 sheet: 0.92 (0.28), residues: 384 loop : -0.86 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 316 TYR 0.008 0.001 TYR G 245 PHE 0.008 0.001 PHE B 418 TRP 0.003 0.001 TRP B 152 HIS 0.006 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (24112) covalent geometry : angle 0.46315 / 0.24 (32768) SS BOND : bond 0.00025 / 0.01 ( 8) SS BOND : angle 0.26228 / 0.17 ( 16) hydrogen bonds : bond 0.03554 / 2.43 ( 1040) hydrogen bonds : angle 3.58512 / 2.55 ( 2832) metal coordination : bond 0.00290 / 0.20 ( 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 365 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 263 time to evaluate : 0.890 Fit side-chains REVERT: A 27 HIS cc_start: 0.7911 (m170) cc_final: 0.7499 (m-70) REVERT: A 38 LYS cc_start: 0.6826 (mtmt) cc_final: 0.6305 (mtpp) REVERT: A 326 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.7084 (mm) REVERT: A 327 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7963 (mt0) REVERT: B 36 SER cc_start: 0.8228 (m) cc_final: 0.8016 (t) REVERT: B 38 LYS cc_start: 0.7731 (mtpt) cc_final: 0.7057 (mmtm) REVERT: B 48 ARG cc_start: 0.7655 (mtp-110) cc_final: 0.7188 (ttm110) REVERT: B 285 LYS cc_start: 0.8510 (tttt) cc_final: 0.8278 (ttmt) REVERT: C 27 HIS cc_start: 0.7910 (m170) cc_final: 0.7500 (m-70) REVERT: C 38 LYS cc_start: 0.6812 (mtmt) cc_final: 0.6289 (mtpp) REVERT: C 326 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7079 (mm) REVERT: C 327 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7943 (mt0) REVERT: D 48 ARG cc_start: 0.7611 (mtp-110) cc_final: 0.7192 (ttm110) REVERT: D 285 LYS cc_start: 0.8498 (tttt) cc_final: 0.8240 (ttmt) REVERT: E 48 ARG cc_start: 0.7574 (mtp-110) cc_final: 0.7168 (ttm110) REVERT: E 285 LYS cc_start: 0.8478 (tttt) cc_final: 0.8233 (ttmt) REVERT: F 48 ARG cc_start: 0.7609 (mtp-110) cc_final: 0.7204 (ttm110) REVERT: F 285 LYS cc_start: 0.8472 (tttt) cc_final: 0.8230 (ttmt) REVERT: F 316 ARG cc_start: 0.7367 (ttt180) cc_final: 0.7163 (mtp-110) REVERT: G 27 HIS cc_start: 0.7941 (m170) cc_final: 0.7528 (m-70) REVERT: G 38 LYS cc_start: 0.6911 (mtmt) cc_final: 0.6419 (mtpp) REVERT: G 70 ASP cc_start: 0.8328 (t70) cc_final: 0.7942 (t70) REVERT: G 326 ILE cc_start: 0.7446 (OUTLIER) cc_final: 0.7095 (mm) REVERT: G 327 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7953 (mt0) REVERT: H 27 HIS cc_start: 0.7918 (m170) cc_final: 0.7514 (m-70) REVERT: H 38 LYS cc_start: 0.6802 (mtmt) cc_final: 0.6281 (mtpp) REVERT: H 326 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7100 (mm) REVERT: H 327 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7948 (mt0) outliers start: 102 outliers final: 73 residues processed: 342 average time/residue: 0.6066 time to fit residues: 237.6346 Evaluate side-chains 329 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 248 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain G residue 252 HIS Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 327 GLN Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain G residue 363 GLU Chi-restraints excluded: chain G residue 385 ILE Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain H residue 252 HIS Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 327 GLN Chi-restraints excluded: chain H residue 357 GLU Chi-restraints excluded: chain H residue 363 GLU Chi-restraints excluded: chain H residue 385 ILE Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 425 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 308 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 105 optimal weight: 0.0030 chunk 244 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 267 optimal weight: 0.7980 chunk 298 optimal weight: 4.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.115581 restraints weight = 24836.181| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.59 r_work: 0.3269 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.8102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24152 Z= 0.125 Angle : 0.484 5.177 32784 Z= 0.254 Chirality : 0.044 0.132 3656 Planarity : 0.004 0.052 4344 Dihedral : 4.985 46.290 3512 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.18 % Allowed : 23.56 % Favored : 72.26 % 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: 0.53 (0.15), residues: 3104 helix: 1.55 (0.15), residues: 1240 sheet: 1.01 (0.30), residues: 344 loop : -0.83 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 316 TYR 0.010 0.001 TYR A 245 PHE 0.008 0.001 PHE B 418 TRP 0.003 0.001 TRP D 290 HIS 0.006 0.001 HIS G 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 (24112) covalent geometry : angle 0.48396 / 0.25 (32768) SS BOND : bond 0.00061 / 0.04 ( 8) SS BOND : angle 0.27013 / 0.18 ( 16) hydrogen bonds : bond 0.03981 / 2.73 ( 1040) hydrogen bonds : angle 3.62967 / 2.58 ( 2832) metal coordination : bond 0.00380 / 0.26 ( 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 345 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 246 time to evaluate : 0.824 Fit side-chains REVERT: A 27 HIS cc_start: 0.7915 (m170) cc_final: 0.7507 (m-70) REVERT: A 38 LYS cc_start: 0.6831 (mtmt) cc_final: 0.6322 (mtpp) REVERT: A 326 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.7109 (mm) REVERT: A 327 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7966 (mt0) REVERT: B 36 SER cc_start: 0.8237 (m) cc_final: 0.8018 (t) REVERT: B 38 LYS cc_start: 0.7752 (mtpt) cc_final: 0.7091 (mmtm) REVERT: B 48 ARG cc_start: 0.7628 (mtp-110) cc_final: 0.7182 (ttm110) REVERT: B 285 LYS cc_start: 0.8532 (tttt) cc_final: 0.8290 (ttmt) REVERT: C 27 HIS cc_start: 0.7902 (m170) cc_final: 0.7493 (m-70) REVERT: C 38 LYS cc_start: 0.6822 (mtmt) cc_final: 0.6309 (mtpp) REVERT: C 326 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7107 (mm) REVERT: C 327 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7947 (mt0) REVERT: D 48 ARG cc_start: 0.7598 (mtp-110) cc_final: 0.7204 (ttm110) REVERT: D 285 LYS cc_start: 0.8473 (tttt) cc_final: 0.8230 (ttmt) REVERT: E 48 ARG cc_start: 0.7566 (mtp-110) cc_final: 0.7178 (ttm110) REVERT: E 281 MET cc_start: 0.8502 (mtp) cc_final: 0.8267 (mtt) REVERT: E 285 LYS cc_start: 0.8484 (tttt) cc_final: 0.8237 (ttmt) REVERT: F 48 ARG cc_start: 0.7575 (mtp-110) cc_final: 0.7215 (ttm110) REVERT: F 281 MET cc_start: 0.8519 (mtp) cc_final: 0.8280 (mtt) REVERT: F 285 LYS cc_start: 0.8477 (tttt) cc_final: 0.8235 (ttmt) REVERT: F 316 ARG cc_start: 0.7408 (ttt180) cc_final: 0.7200 (mtp-110) REVERT: G 27 HIS cc_start: 0.7951 (m170) cc_final: 0.7542 (m-70) REVERT: G 38 LYS cc_start: 0.6977 (mtmt) cc_final: 0.6449 (mtpp) REVERT: G 70 ASP cc_start: 0.8322 (t70) cc_final: 0.7945 (t70) REVERT: G 308 ASP cc_start: 0.7580 (m-30) cc_final: 0.7168 (t70) REVERT: G 326 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7107 (mm) REVERT: G 327 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7945 (mt0) REVERT: H 27 HIS cc_start: 0.7909 (m170) cc_final: 0.7506 (m-70) REVERT: H 38 LYS cc_start: 0.6821 (mtmt) cc_final: 0.6302 (mtpp) REVERT: H 308 ASP cc_start: 0.7576 (m-30) cc_final: 0.7163 (t70) REVERT: H 326 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7100 (mm) REVERT: H 327 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7946 (mt0) outliers start: 99 outliers final: 82 residues processed: 330 average time/residue: 0.6204 time to fit residues: 233.8790 Evaluate side-chains 330 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 240 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 327 GLN Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain G residue 363 GLU Chi-restraints excluded: chain G residue 385 ILE Chi-restraints excluded: chain G residue 400 VAL Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain H residue 252 HIS Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 327 GLN Chi-restraints excluded: chain H residue 357 GLU Chi-restraints excluded: chain H residue 363 GLU Chi-restraints excluded: chain H residue 385 ILE Chi-restraints excluded: chain H residue 400 VAL Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 425 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 42 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 240 optimal weight: 0.5980 chunk 161 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.135719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.114047 restraints weight = 25055.787| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.67 r_work: 0.3245 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.8124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24152 Z= 0.145 Angle : 0.502 5.228 32784 Z= 0.264 Chirality : 0.045 0.135 3656 Planarity : 0.004 0.040 4344 Dihedral : 5.092 45.510 3512 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.39 % Allowed : 22.97 % Favored : 72.64 % 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: 0.45 (0.15), residues: 3104 helix: 1.51 (0.15), residues: 1232 sheet: 0.97 (0.30), residues: 344 loop : -0.89 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 316 TYR 0.011 0.001 TYR C 245 PHE 0.009 0.002 PHE G 123 TRP 0.005 0.001 TRP F 290 HIS 0.006 0.001 HIS G 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (24112) covalent geometry : angle 0.50255 / 0.26 (32768) SS BOND : bond 0.00074 / 0.04 ( 8) SS BOND : angle 0.28645 / 0.19 ( 16) hydrogen bonds : bond 0.04354 / 2.98 ( 1040) hydrogen bonds : angle 3.69235 / 2.62 ( 2832) metal coordination : bond 0.00477 / 0.33 ( 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 352 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 248 time to evaluate : 0.668 Fit side-chains REVERT: A 27 HIS cc_start: 0.7926 (m170) cc_final: 0.7541 (m-70) REVERT: A 38 LYS cc_start: 0.6918 (mtmt) cc_final: 0.6334 (mtpp) REVERT: A 321 ARG cc_start: 0.7549 (ttp-170) cc_final: 0.7308 (ttp80) REVERT: A 326 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7145 (mm) REVERT: A 327 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7969 (mt0) REVERT: B 48 ARG cc_start: 0.7625 (mtp-110) cc_final: 0.7168 (ttm110) REVERT: B 54 GLN cc_start: 0.8603 (pt0) cc_final: 0.8384 (pt0) REVERT: B 285 LYS cc_start: 0.8554 (tttt) cc_final: 0.8308 (ttmt) REVERT: C 27 HIS cc_start: 0.7921 (m170) cc_final: 0.7536 (m-70) REVERT: C 38 LYS cc_start: 0.6866 (mtmt) cc_final: 0.6335 (mtpp) REVERT: C 321 ARG cc_start: 0.7546 (ttp-170) cc_final: 0.7304 (ttp80) REVERT: C 326 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7142 (mm) REVERT: C 327 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7949 (mt0) REVERT: D 48 ARG cc_start: 0.7576 (mtp-110) cc_final: 0.7204 (ttm110) REVERT: D 285 LYS cc_start: 0.8495 (tttt) cc_final: 0.8245 (ttmt) REVERT: E 48 ARG cc_start: 0.7560 (mtp-110) cc_final: 0.7179 (ttm110) REVERT: E 285 LYS cc_start: 0.8518 (tttt) cc_final: 0.8268 (ttmt) REVERT: F 48 ARG cc_start: 0.7583 (mtp-110) cc_final: 0.7218 (ttm110) REVERT: F 285 LYS cc_start: 0.8509 (tttt) cc_final: 0.8262 (ttmt) REVERT: G 27 HIS cc_start: 0.7956 (m170) cc_final: 0.7541 (m-70) REVERT: G 38 LYS cc_start: 0.6990 (mtmt) cc_final: 0.6450 (mtpp) REVERT: G 308 ASP cc_start: 0.7595 (m-30) cc_final: 0.7178 (t70) REVERT: G 321 ARG cc_start: 0.7545 (ttp-170) cc_final: 0.7309 (ttp80) REVERT: G 326 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7136 (mm) REVERT: G 327 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7942 (mt0) REVERT: H 27 HIS cc_start: 0.7931 (m170) cc_final: 0.7526 (m-70) REVERT: H 38 LYS cc_start: 0.6852 (mtmt) cc_final: 0.6328 (mtpp) REVERT: H 308 ASP cc_start: 0.7589 (m-30) cc_final: 0.7169 (t70) REVERT: H 321 ARG cc_start: 0.7554 (ttp-170) cc_final: 0.7312 (ttp80) REVERT: H 326 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7129 (mm) REVERT: H 327 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7943 (mt0) outliers start: 104 outliers final: 90 residues processed: 330 average time/residue: 0.6460 time to fit residues: 242.0546 Evaluate side-chains 343 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 245 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 327 GLN Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain G residue 363 GLU Chi-restraints excluded: chain G residue 385 ILE Chi-restraints excluded: chain G residue 400 VAL Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain H residue 252 HIS Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 327 GLN Chi-restraints excluded: chain H residue 357 GLU Chi-restraints excluded: chain H residue 363 GLU Chi-restraints excluded: chain H residue 385 ILE Chi-restraints excluded: chain H residue 400 VAL Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 425 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 177 optimal weight: 3.9990 chunk 293 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 307 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 215 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 GLN E 54 GLN E 428 GLN F 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.138024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.116869 restraints weight = 25012.256| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.61 r_work: 0.3287 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.8140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24152 Z= 0.105 Angle : 0.466 6.281 32784 Z= 0.244 Chirality : 0.043 0.133 3656 Planarity : 0.004 0.059 4344 Dihedral : 4.868 46.754 3512 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.97 % Allowed : 23.35 % Favored : 72.68 % 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: 0.61 (0.15), residues: 3104 helix: 1.69 (0.15), residues: 1232 sheet: 1.04 (0.30), residues: 344 loop : -0.84 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 316 TYR 0.008 0.001 TYR D 334 PHE 0.007 0.001 PHE E 418 TRP 0.003 0.001 TRP E 152 HIS 0.006 0.001 HIS G 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.10 (24112) covalent geometry : angle 0.46613 / 0.24 (32768) SS BOND : bond 0.00056 / 0.03 ( 8) SS BOND : angle 0.24856 / 0.16 ( 16) hydrogen bonds : bond 0.03481 / 2.38 ( 1040) hydrogen bonds : angle 3.56805 / 2.53 ( 2832) metal coordination : bond 0.00279 / 0.19 ( 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 344 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 250 time to evaluate : 0.919 Fit side-chains REVERT: A 27 HIS cc_start: 0.7890 (m170) cc_final: 0.7483 (m-70) REVERT: A 38 LYS cc_start: 0.6830 (mtmt) cc_final: 0.6287 (mtpp) REVERT: A 308 ASP cc_start: 0.7538 (m-30) cc_final: 0.7101 (t70) REVERT: A 326 ILE cc_start: 0.7415 (OUTLIER) cc_final: 0.7066 (mm) REVERT: A 327 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7959 (mt0) REVERT: B 36 SER cc_start: 0.8208 (m) cc_final: 0.8008 (t) REVERT: B 48 ARG cc_start: 0.7587 (mtp-110) cc_final: 0.7173 (ttm110) REVERT: B 285 LYS cc_start: 0.8546 (tttt) cc_final: 0.8300 (ttmt) REVERT: C 27 HIS cc_start: 0.7873 (m170) cc_final: 0.7465 (m-70) REVERT: C 38 LYS cc_start: 0.6803 (mtmt) cc_final: 0.6290 (mtpp) REVERT: C 308 ASP cc_start: 0.7562 (m-30) cc_final: 0.7136 (t70) REVERT: C 326 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.7049 (mm) REVERT: C 327 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7935 (mt0) REVERT: D 48 ARG cc_start: 0.7559 (mtp-110) cc_final: 0.7184 (ttm110) REVERT: D 285 LYS cc_start: 0.8468 (tttt) cc_final: 0.8226 (ttmt) REVERT: E 48 ARG cc_start: 0.7550 (mtp-110) cc_final: 0.7161 (ttm110) REVERT: E 285 LYS cc_start: 0.8495 (tttt) cc_final: 0.8261 (ttmt) REVERT: F 48 ARG cc_start: 0.7568 (mtp-110) cc_final: 0.7219 (ttm110) REVERT: F 285 LYS cc_start: 0.8483 (tttt) cc_final: 0.8251 (ttmt) REVERT: G 27 HIS cc_start: 0.7929 (m170) cc_final: 0.7520 (m-70) REVERT: G 38 LYS cc_start: 0.6939 (mtmt) cc_final: 0.6442 (mtpp) REVERT: G 308 ASP cc_start: 0.7551 (m-30) cc_final: 0.7111 (t70) REVERT: G 326 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7061 (mm) REVERT: G 327 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7929 (mt0) REVERT: H 27 HIS cc_start: 0.7911 (m170) cc_final: 0.7515 (m-70) REVERT: H 38 LYS cc_start: 0.6772 (mtmt) cc_final: 0.6259 (mtpp) REVERT: H 308 ASP cc_start: 0.7543 (m-30) cc_final: 0.7104 (t70) REVERT: H 326 ILE cc_start: 0.7406 (OUTLIER) cc_final: 0.7053 (mm) REVERT: H 327 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7951 (mt0) outliers start: 94 outliers final: 76 residues processed: 327 average time/residue: 0.6598 time to fit residues: 245.0052 Evaluate side-chains 325 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 241 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain G residue 276 MET Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 327 GLN Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain G residue 363 GLU Chi-restraints excluded: chain G residue 400 VAL Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain H residue 252 HIS Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 326 ILE Chi-restraints excluded: chain H residue 327 GLN Chi-restraints excluded: chain H residue 357 GLU Chi-restraints excluded: chain H residue 363 GLU Chi-restraints excluded: chain H residue 400 VAL Chi-restraints excluded: chain H residue 425 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 194 optimal weight: 3.9990 chunk 72 optimal weight: 0.0040 chunk 75 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 chunk 216 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 272 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN D 54 GLN E 54 GLN F 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117328 restraints weight = 24979.859| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.60 r_work: 0.3291 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.8137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24152 Z= 0.101 Angle : 0.458 5.953 32784 Z= 0.240 Chirality : 0.043 0.132 3656 Planarity : 0.004 0.053 4344 Dihedral : 4.789 47.229 3512 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.29 % Allowed : 24.20 % Favored : 72.51 % 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: 0.67 (0.15), residues: 3104 helix: 1.71 (0.15), residues: 1240 sheet: 1.09 (0.30), residues: 344 loop : -0.80 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 316 TYR 0.009 0.001 TYR A 245 PHE 0.007 0.001 PHE D 418 TRP 0.003 0.000 TRP B 152 HIS 0.006 0.001 HIS G 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (24112) covalent geometry : angle 0.45857 / 0.24 (32768) SS BOND : bond 0.00047 / 0.03 ( 8) SS BOND : angle 0.25372 / 0.17 ( 16) hydrogen bonds : bond 0.03436 / 2.35 ( 1040) hydrogen bonds : angle 3.56069 / 2.53 ( 2832) metal coordination : bond 0.00264 / 0.18 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7302.68 seconds wall clock time: 125 minutes 1.38 seconds (7501.38 seconds total)