Starting phenix.real_space_refine on Thu Sep 18 08:47:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j38_61109/09_2025/9j38_61109_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j38_61109/09_2025/9j38_61109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j38_61109/09_2025/9j38_61109_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j38_61109/09_2025/9j38_61109_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j38_61109/09_2025/9j38_61109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j38_61109/09_2025/9j38_61109.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 10056 2.51 5 N 2684 2.21 5 O 2768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15596 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2791 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 9, 'TRANS': 334} Chain breaks: 1 Chain: "E" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Restraints were copied for chains: B, C, D, F, G, H Time building chain proxies: 3.19, per 1000 atoms: 0.20 Number of scatterers: 15596 At special positions: 0 Unit cell: (127.41, 127.41, 118.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 2768 8.00 N 2684 7.00 C 10056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 729.4 milliseconds Enol-peptide restraints added in 1.4 microseconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3640 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 4 sheets defined 84.7% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 103 through 121 Processing helix chain 'A' and resid 125 through 148 removed outlier: 4.108A pdb=" N TYR A 129 " --> pdb=" O TRP A 125 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 182 Processing helix chain 'A' and resid 183 through 188 removed outlier: 4.753A pdb=" N CYS A 186 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG A 187 " --> pdb=" O CYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 199 Processing helix chain 'A' and resid 200 through 223 Processing helix chain 'A' and resid 224 through 235 Processing helix chain 'A' and resid 238 through 245 removed outlier: 4.002A pdb=" N MET A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 262 Processing helix chain 'A' and resid 262 through 289 Processing helix chain 'A' and resid 292 through 296 removed outlier: 3.891A pdb=" N SER A 296 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 321 through 340 Processing helix chain 'A' and resid 340 through 363 removed outlier: 3.512A pdb=" N GLY A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 384 removed outlier: 3.802A pdb=" N ASP A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 540 Processing helix chain 'A' and resid 545 through 576 Processing helix chain 'B' and resid 104 through 121 Processing helix chain 'B' and resid 125 through 148 removed outlier: 4.109A pdb=" N TYR B 129 " --> pdb=" O TRP B 125 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 182 Processing helix chain 'B' and resid 183 through 188 removed outlier: 4.753A pdb=" N CYS B 186 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG B 187 " --> pdb=" O CYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 199 Processing helix chain 'B' and resid 200 through 223 Processing helix chain 'B' and resid 224 through 235 Processing helix chain 'B' and resid 238 through 245 removed outlier: 4.002A pdb=" N MET B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET B 245 " --> pdb=" O ARG B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 262 Processing helix chain 'B' and resid 262 through 289 Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.891A pdb=" N SER B 296 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 321 through 340 Processing helix chain 'B' and resid 340 through 363 removed outlier: 3.512A pdb=" N GLY B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 384 removed outlier: 3.801A pdb=" N ASP B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 540 Processing helix chain 'B' and resid 545 through 576 Processing helix chain 'C' and resid 104 through 121 Processing helix chain 'C' and resid 125 through 148 removed outlier: 4.108A pdb=" N TYR C 129 " --> pdb=" O TRP C 125 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 182 Processing helix chain 'C' and resid 183 through 188 removed outlier: 4.754A pdb=" N CYS C 186 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG C 187 " --> pdb=" O CYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 199 Processing helix chain 'C' and resid 200 through 223 Processing helix chain 'C' and resid 224 through 235 Processing helix chain 'C' and resid 238 through 245 removed outlier: 4.001A pdb=" N MET C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET C 245 " --> pdb=" O ARG C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 262 Processing helix chain 'C' and resid 262 through 289 Processing helix chain 'C' and resid 292 through 296 removed outlier: 3.891A pdb=" N SER C 296 " --> pdb=" O LYS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 310 Processing helix chain 'C' and resid 321 through 340 Processing helix chain 'C' and resid 340 through 363 removed outlier: 3.513A pdb=" N GLY C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE C 363 " --> pdb=" O ARG C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 384 removed outlier: 3.801A pdb=" N ASP C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 540 Processing helix chain 'C' and resid 545 through 576 Processing helix chain 'D' and resid 104 through 121 Processing helix chain 'D' and resid 125 through 148 removed outlier: 4.109A pdb=" N TYR D 129 " --> pdb=" O TRP D 125 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 182 Processing helix chain 'D' and resid 183 through 188 removed outlier: 4.754A pdb=" N CYS D 186 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG D 187 " --> pdb=" O CYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 199 Processing helix chain 'D' and resid 200 through 223 Processing helix chain 'D' and resid 224 through 235 Processing helix chain 'D' and resid 238 through 245 removed outlier: 4.002A pdb=" N MET D 242 " --> pdb=" O GLN D 238 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 262 Processing helix chain 'D' and resid 262 through 289 Processing helix chain 'D' and resid 292 through 296 removed outlier: 3.891A pdb=" N SER D 296 " --> pdb=" O LYS D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 310 Processing helix chain 'D' and resid 321 through 340 Processing helix chain 'D' and resid 340 through 363 removed outlier: 3.512A pdb=" N GLY D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE D 363 " --> pdb=" O ARG D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 384 removed outlier: 3.802A pdb=" N ASP D 384 " --> pdb=" O SER D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 540 Processing helix chain 'D' and resid 545 through 576 Processing helix chain 'E' and resid 7 through 22 removed outlier: 3.773A pdb=" N LEU E 19 " --> pdb=" O GLU E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 40 removed outlier: 3.924A pdb=" N VAL E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 65 through 75 removed outlier: 3.863A pdb=" N ARG E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 93 removed outlier: 3.985A pdb=" N GLU E 83 " --> pdb=" O ASP E 79 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU E 84 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 113 removed outlier: 3.570A pdb=" N THR E 111 " --> pdb=" O ARG E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 129 Processing helix chain 'E' and resid 139 through 148 removed outlier: 3.702A pdb=" N ALA E 148 " --> pdb=" O GLN E 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 22 removed outlier: 3.774A pdb=" N LEU F 19 " --> pdb=" O GLU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 40 removed outlier: 3.924A pdb=" N VAL F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 55 Processing helix chain 'F' and resid 65 through 75 removed outlier: 3.863A pdb=" N ARG F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 removed outlier: 3.985A pdb=" N GLU F 83 " --> pdb=" O ASP F 79 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU F 84 " --> pdb=" O THR F 80 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 113 removed outlier: 3.571A pdb=" N THR F 111 " --> pdb=" O ARG F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 129 Processing helix chain 'F' and resid 139 through 148 removed outlier: 3.701A pdb=" N ALA F 148 " --> pdb=" O GLN F 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 22 removed outlier: 3.773A pdb=" N LEU G 19 " --> pdb=" O GLU G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 40 removed outlier: 3.925A pdb=" N VAL G 36 " --> pdb=" O GLU G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 55 Processing helix chain 'G' and resid 65 through 75 removed outlier: 3.863A pdb=" N ARG G 75 " --> pdb=" O THR G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 93 removed outlier: 3.985A pdb=" N GLU G 83 " --> pdb=" O ASP G 79 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU G 84 " --> pdb=" O THR G 80 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE G 93 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 113 removed outlier: 3.569A pdb=" N THR G 111 " --> pdb=" O ARG G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 129 Processing helix chain 'G' and resid 139 through 148 removed outlier: 3.702A pdb=" N ALA G 148 " --> pdb=" O GLN G 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 22 removed outlier: 3.773A pdb=" N LEU H 19 " --> pdb=" O GLU H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 40 removed outlier: 3.924A pdb=" N VAL H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 55 Processing helix chain 'H' and resid 65 through 75 removed outlier: 3.863A pdb=" N ARG H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 removed outlier: 3.985A pdb=" N GLU H 83 " --> pdb=" O ASP H 79 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU H 84 " --> pdb=" O THR H 80 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 113 removed outlier: 3.570A pdb=" N THR H 111 " --> pdb=" O ARG H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 129 Processing helix chain 'H' and resid 139 through 148 removed outlier: 3.701A pdb=" N ALA H 148 " --> pdb=" O GLN H 144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 100 through 102 removed outlier: 3.535A pdb=" N VAL E 137 " --> pdb=" O ILE E 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 100 through 102 removed outlier: 3.534A pdb=" N VAL F 137 " --> pdb=" O ILE F 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 100 through 102 removed outlier: 3.535A pdb=" N VAL G 137 " --> pdb=" O ILE G 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 102 removed outlier: 3.534A pdb=" N VAL H 137 " --> pdb=" O ILE H 101 " (cutoff:3.500A) 1193 hydrogen bonds defined for protein. 3555 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: 2.89 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5014 1.34 - 1.46: 2393 1.46 - 1.58: 8365 1.58 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 15916 Sorted by residual: bond pdb=" CA ARG A 241 " pdb=" C ARG A 241 " ideal model delta sigma weight residual 1.524 1.505 0.018 1.26e-02 6.30e+03 2.14e+00 bond pdb=" CA ARG D 241 " pdb=" C ARG D 241 " ideal model delta sigma weight residual 1.524 1.506 0.018 1.26e-02 6.30e+03 2.08e+00 bond pdb=" CA ARG B 241 " pdb=" C ARG B 241 " ideal model delta sigma weight residual 1.524 1.506 0.018 1.26e-02 6.30e+03 1.97e+00 bond pdb=" CA ARG C 241 " pdb=" C ARG C 241 " ideal model delta sigma weight residual 1.524 1.506 0.018 1.26e-02 6.30e+03 1.97e+00 bond pdb=" CA LYS B 361 " pdb=" C LYS B 361 " ideal model delta sigma weight residual 1.523 1.505 0.018 1.30e-02 5.92e+03 1.94e+00 ... (remaining 15911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 21328 2.35 - 4.71: 133 4.71 - 7.06: 23 7.06 - 9.42: 0 9.42 - 11.77: 4 Bond angle restraints: 21488 Sorted by residual: angle pdb=" CB MET F 73 " pdb=" CG MET F 73 " pdb=" SD MET F 73 " ideal model delta sigma weight residual 112.70 124.47 -11.77 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CB MET E 73 " pdb=" CG MET E 73 " pdb=" SD MET E 73 " ideal model delta sigma weight residual 112.70 124.46 -11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CB MET H 73 " pdb=" CG MET H 73 " pdb=" SD MET H 73 " ideal model delta sigma weight residual 112.70 124.45 -11.75 3.00e+00 1.11e-01 1.53e+01 angle pdb=" CB MET G 73 " pdb=" CG MET G 73 " pdb=" SD MET G 73 " ideal model delta sigma weight residual 112.70 124.41 -11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" N ARG D 241 " pdb=" CA ARG D 241 " pdb=" C ARG D 241 " ideal model delta sigma weight residual 111.14 107.28 3.86 1.08e+00 8.57e-01 1.28e+01 ... (remaining 21483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 8145 14.97 - 29.94: 899 29.94 - 44.91: 304 44.91 - 59.88: 84 59.88 - 74.84: 12 Dihedral angle restraints: 9444 sinusoidal: 3804 harmonic: 5640 Sorted by residual: dihedral pdb=" N MET H 146 " pdb=" CA MET H 146 " pdb=" CB MET H 146 " pdb=" CG MET H 146 " ideal model delta sinusoidal sigma weight residual -180.00 -121.37 -58.63 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N MET G 146 " pdb=" CA MET G 146 " pdb=" CB MET G 146 " pdb=" CG MET G 146 " ideal model delta sinusoidal sigma weight residual -180.00 -121.38 -58.62 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N MET E 146 " pdb=" CA MET E 146 " pdb=" CB MET E 146 " pdb=" CG MET E 146 " ideal model delta sinusoidal sigma weight residual -180.00 -121.39 -58.61 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 9441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2019 0.050 - 0.101: 366 0.101 - 0.151: 27 0.151 - 0.201: 0 0.201 - 0.252: 4 Chirality restraints: 2416 Sorted by residual: chirality pdb=" CB ILE A 208 " pdb=" CA ILE A 208 " pdb=" CG1 ILE A 208 " pdb=" CG2 ILE A 208 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE B 208 " pdb=" CA ILE B 208 " pdb=" CG1 ILE B 208 " pdb=" CG2 ILE B 208 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB ILE D 208 " pdb=" CA ILE D 208 " pdb=" CG1 ILE D 208 " pdb=" CG2 ILE D 208 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 2413 not shown) Planarity restraints: 2704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 191 " -0.015 2.00e-02 2.50e+03 1.47e-02 5.43e+00 pdb=" CG TRP C 191 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP C 191 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP C 191 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 191 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 191 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 191 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 191 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 191 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 191 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 191 " -0.015 2.00e-02 2.50e+03 1.47e-02 5.41e+00 pdb=" CG TRP B 191 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 191 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 191 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 191 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 191 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 191 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 191 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 191 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 191 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 191 " -0.015 2.00e-02 2.50e+03 1.47e-02 5.37e+00 pdb=" CG TRP D 191 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP D 191 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP D 191 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 191 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 191 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 191 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 191 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 191 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 191 " -0.000 2.00e-02 2.50e+03 ... (remaining 2701 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 3708 2.78 - 3.31: 15962 3.31 - 3.84: 27003 3.84 - 4.37: 29175 4.37 - 4.90: 50193 Nonbonded interactions: 126041 Sorted by model distance: nonbonded pdb=" OD2 ASP H 94 " pdb=" OH TYR H 139 " model vdw 2.256 3.040 nonbonded pdb=" OD2 ASP G 94 " pdb=" OH TYR G 139 " model vdw 2.256 3.040 nonbonded pdb=" OD2 ASP F 94 " pdb=" OH TYR F 139 " model vdw 2.256 3.040 nonbonded pdb=" OD2 ASP E 94 " pdb=" OH TYR E 139 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR C 129 " pdb=" OE1 GLU C 174 " model vdw 2.271 3.040 ... (remaining 126036 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.410 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:9.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 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 : 0.002 0.028 15916 Z= 0.140 Angle : 0.534 11.775 21488 Z= 0.301 Chirality : 0.037 0.252 2416 Planarity : 0.004 0.039 2704 Dihedral : 14.764 74.844 5804 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.71 % Allowed : 14.15 % Favored : 84.15 % 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 aren not related in a simple way. whole: 2.17 (0.19), residues: 1928 helix: 1.75 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : 0.40 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 563 TYR 0.008 0.001 TYR A 553 PHE 0.019 0.001 PHE G 13 TRP 0.040 0.002 TRP C 191 HIS 0.002 0.001 HIS B 262 Details of bonding type rmsd covalent geometry : bond 0.00238 (15916) covalent geometry : angle 0.53428 (21488) hydrogen bonds : bond 0.11563 ( 1193) hydrogen bonds : angle 5.71593 ( 3555) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 264 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 PHE cc_start: 0.7952 (p90) cc_final: 0.6886 (t80) REVERT: A 552 GLN cc_start: 0.7315 (mp10) cc_final: 0.6610 (pt0) REVERT: B 236 PHE cc_start: 0.8038 (p90) cc_final: 0.6772 (t80) REVERT: B 552 GLN cc_start: 0.7300 (mp10) cc_final: 0.6601 (pt0) REVERT: C 192 GLN cc_start: 0.7111 (tp40) cc_final: 0.6878 (tp40) REVERT: C 236 PHE cc_start: 0.7965 (p90) cc_final: 0.6875 (t80) REVERT: C 552 GLN cc_start: 0.7346 (mp10) cc_final: 0.6812 (pt0) REVERT: D 552 GLN cc_start: 0.7178 (mp10) cc_final: 0.6563 (pt0) REVERT: E 48 GLU cc_start: 0.5782 (pt0) cc_final: 0.5552 (pp20) REVERT: E 111 THR cc_start: 0.7248 (m) cc_final: 0.6818 (p) REVERT: F 111 THR cc_start: 0.7195 (m) cc_final: 0.6716 (p) REVERT: H 111 THR cc_start: 0.7154 (m) cc_final: 0.6724 (p) outliers start: 28 outliers final: 17 residues processed: 288 average time/residue: 0.4610 time to fit residues: 150.4456 Evaluate side-chains 242 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 225 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 549 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN B 531 HIS ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN D 531 HIS ** D 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.221419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.127884 restraints weight = 20082.223| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 5.23 r_work: 0.2976 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15916 Z= 0.136 Angle : 0.496 6.681 21488 Z= 0.265 Chirality : 0.037 0.186 2416 Planarity : 0.004 0.039 2704 Dihedral : 4.811 57.312 2161 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 4.88 % Allowed : 15.79 % Favored : 79.33 % 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 aren not related in a simple way. whole: 2.62 (0.19), residues: 1928 helix: 2.08 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : 0.49 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 526 TYR 0.011 0.001 TYR A 108 PHE 0.007 0.001 PHE H 13 TRP 0.026 0.002 TRP B 191 HIS 0.002 0.000 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00281 (15916) covalent geometry : angle 0.49591 (21488) hydrogen bonds : bond 0.04961 ( 1193) hydrogen bonds : angle 4.54948 ( 3555) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 236 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 ARG cc_start: 0.7691 (mtt180) cc_final: 0.7375 (tpt-90) REVERT: A 547 LYS cc_start: 0.8347 (ttpt) cc_final: 0.8057 (ttpp) REVERT: A 552 GLN cc_start: 0.7163 (mp10) cc_final: 0.6670 (pt0) REVERT: A 553 TYR cc_start: 0.7226 (t80) cc_final: 0.6760 (t80) REVERT: B 191 TRP cc_start: 0.6239 (p-90) cc_final: 0.5887 (p-90) REVERT: B 542 ARG cc_start: 0.6616 (OUTLIER) cc_final: 0.5945 (tmm160) REVERT: B 547 LYS cc_start: 0.8389 (ttpt) cc_final: 0.8037 (ttpp) REVERT: B 552 GLN cc_start: 0.7216 (mp10) cc_final: 0.6717 (pt0) REVERT: B 553 TYR cc_start: 0.7164 (t80) cc_final: 0.6799 (t80) REVERT: C 232 ARG cc_start: 0.7749 (mtt180) cc_final: 0.7437 (tpt-90) REVERT: C 542 ARG cc_start: 0.6511 (OUTLIER) cc_final: 0.6042 (tmm160) REVERT: C 547 LYS cc_start: 0.8273 (ttpt) cc_final: 0.7947 (tmmm) REVERT: C 552 GLN cc_start: 0.7658 (mp10) cc_final: 0.6690 (pt0) REVERT: D 362 HIS cc_start: 0.7740 (OUTLIER) cc_final: 0.7458 (m-70) REVERT: D 552 GLN cc_start: 0.7171 (mp10) cc_final: 0.6587 (pt0) REVERT: E 52 MET cc_start: 0.4965 (tmm) cc_final: 0.4683 (tmm) REVERT: F 52 MET cc_start: 0.4874 (tmm) cc_final: 0.4582 (tmm) REVERT: G 52 MET cc_start: 0.4931 (tmm) cc_final: 0.4651 (tmm) REVERT: H 72 MET cc_start: -0.0673 (mtp) cc_final: -0.0889 (mtt) REVERT: H 79 ASP cc_start: 0.1545 (p0) cc_final: 0.1309 (p0) REVERT: H 111 THR cc_start: 0.6955 (m) cc_final: 0.6461 (p) outliers start: 80 outliers final: 34 residues processed: 280 average time/residue: 0.5395 time to fit residues: 167.4902 Evaluate side-chains 251 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 542 ARG Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 571 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 129 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 178 optimal weight: 40.0000 chunk 187 optimal weight: 0.0970 chunk 115 optimal weight: 0.0980 chunk 134 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS B 358 HIS B 368 ASN C 358 HIS C 368 ASN C 531 HIS D 358 HIS D 368 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.222031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.122310 restraints weight = 20152.129| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 4.27 r_work: 0.2996 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15916 Z= 0.127 Angle : 0.476 6.445 21488 Z= 0.255 Chirality : 0.036 0.196 2416 Planarity : 0.004 0.040 2704 Dihedral : 4.113 38.169 2157 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 4.02 % Allowed : 16.89 % Favored : 79.09 % 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 aren not related in a simple way. whole: 2.80 (0.19), residues: 1928 helix: 2.16 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : 0.72 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 542 TYR 0.010 0.001 TYR A 108 PHE 0.007 0.001 PHE C 338 TRP 0.024 0.002 TRP A 191 HIS 0.002 0.000 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00259 (15916) covalent geometry : angle 0.47590 (21488) hydrogen bonds : bond 0.04719 ( 1193) hydrogen bonds : angle 4.37848 ( 3555) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 236 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 CYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7055 (p) REVERT: A 232 ARG cc_start: 0.7564 (mtt180) cc_final: 0.7335 (tpt-90) REVERT: A 542 ARG cc_start: 0.6638 (OUTLIER) cc_final: 0.5815 (tmm160) REVERT: A 547 LYS cc_start: 0.8311 (ttpt) cc_final: 0.7968 (tmmm) REVERT: A 552 GLN cc_start: 0.7588 (mp10) cc_final: 0.6639 (pt0) REVERT: A 553 TYR cc_start: 0.7178 (t80) cc_final: 0.6625 (t80) REVERT: B 184 CYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7153 (p) REVERT: B 191 TRP cc_start: 0.6134 (p-90) cc_final: 0.5740 (p-90) REVERT: B 542 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.6040 (tmm160) REVERT: B 547 LYS cc_start: 0.8307 (ttpt) cc_final: 0.7971 (tmmm) REVERT: B 552 GLN cc_start: 0.7575 (mp10) cc_final: 0.6636 (pt0) REVERT: B 553 TYR cc_start: 0.7194 (t80) cc_final: 0.6591 (t80) REVERT: C 184 CYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7075 (p) REVERT: C 232 ARG cc_start: 0.7602 (mtt180) cc_final: 0.7354 (tpt-90) REVERT: C 542 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.5876 (tmm160) REVERT: C 547 LYS cc_start: 0.8185 (ttpt) cc_final: 0.7968 (tmmm) REVERT: C 549 VAL cc_start: 0.7185 (p) cc_final: 0.6902 (p) REVERT: C 552 GLN cc_start: 0.7605 (mp10) cc_final: 0.6668 (pt0) REVERT: C 553 TYR cc_start: 0.7158 (t80) cc_final: 0.6733 (t80) REVERT: D 184 CYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7066 (p) REVERT: D 552 GLN cc_start: 0.7113 (mp10) cc_final: 0.6636 (pt0) REVERT: D 565 LYS cc_start: 0.8381 (mmtm) cc_final: 0.8089 (mmmm) REVERT: E 52 MET cc_start: 0.4788 (tmm) cc_final: 0.4526 (tmm) REVERT: E 111 THR cc_start: 0.6813 (m) cc_final: 0.6424 (p) REVERT: F 52 MET cc_start: 0.4751 (tmm) cc_final: 0.4514 (tmm) REVERT: F 72 MET cc_start: -0.1159 (ttp) cc_final: -0.1386 (ttp) REVERT: F 111 THR cc_start: 0.6911 (m) cc_final: 0.6472 (p) REVERT: G 52 MET cc_start: 0.5083 (tmm) cc_final: 0.4857 (tmm) REVERT: H 111 THR cc_start: 0.6817 (m) cc_final: 0.6392 (p) outliers start: 66 outliers final: 25 residues processed: 281 average time/residue: 0.5100 time to fit residues: 159.8734 Evaluate side-chains 258 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 542 ARG Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 571 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 161 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 145 optimal weight: 40.0000 chunk 140 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN B 368 ASN C 238 GLN C 368 ASN D 238 GLN D 368 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.219016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.126876 restraints weight = 20124.692| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 5.31 r_work: 0.2903 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15916 Z= 0.212 Angle : 0.543 6.958 21488 Z= 0.292 Chirality : 0.040 0.213 2416 Planarity : 0.004 0.039 2704 Dihedral : 3.740 29.415 2145 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.88 % Allowed : 16.22 % Favored : 78.90 % 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 aren not related in a simple way. whole: 2.43 (0.19), residues: 1928 helix: 1.86 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : 0.78 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 241 TYR 0.014 0.002 TYR A 108 PHE 0.015 0.001 PHE A 338 TRP 0.023 0.002 TRP A 191 HIS 0.003 0.001 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00486 (15916) covalent geometry : angle 0.54297 (21488) hydrogen bonds : bond 0.05762 ( 1193) hydrogen bonds : angle 4.53526 ( 3555) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 238 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 CYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7047 (p) REVERT: A 232 ARG cc_start: 0.7674 (mtt180) cc_final: 0.7383 (tpt-90) REVERT: A 542 ARG cc_start: 0.6708 (OUTLIER) cc_final: 0.5977 (tmm160) REVERT: A 547 LYS cc_start: 0.8237 (ttpt) cc_final: 0.7958 (tmmm) REVERT: A 552 GLN cc_start: 0.7550 (mp10) cc_final: 0.6627 (pt0) REVERT: A 553 TYR cc_start: 0.7220 (t80) cc_final: 0.6952 (t80) REVERT: A 561 LEU cc_start: 0.7582 (tp) cc_final: 0.7373 (tp) REVERT: B 184 CYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7011 (p) REVERT: B 191 TRP cc_start: 0.6147 (p-90) cc_final: 0.5784 (p-90) REVERT: B 542 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.5938 (tmm160) REVERT: B 547 LYS cc_start: 0.8216 (ttpt) cc_final: 0.7930 (tmmm) REVERT: B 552 GLN cc_start: 0.7503 (mp10) cc_final: 0.6568 (pt0) REVERT: B 553 TYR cc_start: 0.7193 (t80) cc_final: 0.6923 (t80) REVERT: B 561 LEU cc_start: 0.7611 (tp) cc_final: 0.7363 (tp) REVERT: C 184 CYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7085 (p) REVERT: C 542 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.5950 (tmm160) REVERT: C 547 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7955 (tmmm) REVERT: C 552 GLN cc_start: 0.7564 (mp10) cc_final: 0.6586 (pt0) REVERT: C 553 TYR cc_start: 0.7199 (t80) cc_final: 0.6987 (t80) REVERT: C 561 LEU cc_start: 0.7678 (tp) cc_final: 0.7434 (tp) REVERT: D 184 CYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7066 (p) REVERT: D 379 ARG cc_start: 0.4398 (OUTLIER) cc_final: 0.4171 (mmm-85) REVERT: D 552 GLN cc_start: 0.7051 (mp10) cc_final: 0.6576 (pt0) REVERT: D 565 LYS cc_start: 0.8406 (mmtm) cc_final: 0.8160 (mmmm) REVERT: E 52 MET cc_start: 0.4658 (tmm) cc_final: 0.4404 (tmm) REVERT: E 111 THR cc_start: 0.6889 (m) cc_final: 0.6487 (p) REVERT: F 52 MET cc_start: 0.4775 (tmm) cc_final: 0.4498 (tmm) REVERT: F 72 MET cc_start: -0.0769 (ttp) cc_final: -0.1012 (ttp) REVERT: F 111 THR cc_start: 0.7062 (m) cc_final: 0.6636 (p) REVERT: G 52 MET cc_start: 0.4974 (tmm) cc_final: 0.4679 (tmm) REVERT: G 111 THR cc_start: 0.7067 (m) cc_final: 0.6661 (p) REVERT: H 77 MET cc_start: -0.0665 (pp-130) cc_final: -0.0942 (pp-130) REVERT: H 111 THR cc_start: 0.6932 (m) cc_final: 0.6481 (p) outliers start: 80 outliers final: 42 residues processed: 289 average time/residue: 0.4967 time to fit residues: 160.2603 Evaluate side-chains 278 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 228 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 542 ARG Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain H residue 52 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 88 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 168 optimal weight: 50.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN C 238 GLN C 368 ASN D 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.221663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.117405 restraints weight = 20149.958| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.93 r_work: 0.3064 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15916 Z= 0.125 Angle : 0.491 7.787 21488 Z= 0.262 Chirality : 0.037 0.213 2416 Planarity : 0.004 0.040 2704 Dihedral : 3.502 30.026 2141 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 3.41 % Allowed : 17.62 % Favored : 78.96 % 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 aren not related in a simple way. whole: 2.76 (0.19), residues: 1928 helix: 2.11 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : 0.81 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 241 TYR 0.011 0.001 TYR A 108 PHE 0.011 0.001 PHE G 142 TRP 0.025 0.002 TRP A 191 HIS 0.002 0.001 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00256 (15916) covalent geometry : angle 0.49062 (21488) hydrogen bonds : bond 0.04602 ( 1193) hydrogen bonds : angle 4.33509 ( 3555) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 246 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 CYS cc_start: 0.7814 (OUTLIER) cc_final: 0.6985 (p) REVERT: A 232 ARG cc_start: 0.7637 (mtt180) cc_final: 0.7347 (tpt-90) REVERT: A 379 ARG cc_start: 0.4517 (OUTLIER) cc_final: 0.4240 (mmm-85) REVERT: A 542 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.6113 (tmm160) REVERT: A 547 LYS cc_start: 0.8266 (ttpt) cc_final: 0.8010 (tmmm) REVERT: A 549 VAL cc_start: 0.7236 (p) cc_final: 0.6946 (p) REVERT: A 552 GLN cc_start: 0.7557 (mp10) cc_final: 0.6615 (pt0) REVERT: A 553 TYR cc_start: 0.7187 (t80) cc_final: 0.6610 (t80) REVERT: B 184 CYS cc_start: 0.7786 (OUTLIER) cc_final: 0.6963 (p) REVERT: B 191 TRP cc_start: 0.6174 (p-90) cc_final: 0.5833 (p-90) REVERT: B 379 ARG cc_start: 0.4585 (OUTLIER) cc_final: 0.4288 (mmm-85) REVERT: B 542 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6116 (tmm160) REVERT: B 547 LYS cc_start: 0.8287 (ttpt) cc_final: 0.8011 (tmmm) REVERT: B 549 VAL cc_start: 0.7220 (p) cc_final: 0.6896 (p) REVERT: B 552 GLN cc_start: 0.7509 (mp10) cc_final: 0.6567 (pt0) REVERT: B 553 TYR cc_start: 0.7171 (t80) cc_final: 0.6590 (t80) REVERT: B 561 LEU cc_start: 0.7683 (tp) cc_final: 0.7458 (tp) REVERT: C 184 CYS cc_start: 0.7800 (OUTLIER) cc_final: 0.6972 (p) REVERT: C 379 ARG cc_start: 0.4397 (OUTLIER) cc_final: 0.4161 (mmm-85) REVERT: C 542 ARG cc_start: 0.6787 (OUTLIER) cc_final: 0.6025 (tmm160) REVERT: C 547 LYS cc_start: 0.8294 (ttpt) cc_final: 0.8037 (tmmm) REVERT: C 549 VAL cc_start: 0.7253 (p) cc_final: 0.6868 (p) REVERT: C 552 GLN cc_start: 0.7567 (mp10) cc_final: 0.6606 (pt0) REVERT: C 553 TYR cc_start: 0.7192 (t80) cc_final: 0.6737 (t80) REVERT: D 184 CYS cc_start: 0.7742 (OUTLIER) cc_final: 0.6962 (p) REVERT: D 379 ARG cc_start: 0.4656 (OUTLIER) cc_final: 0.4304 (mmm-85) REVERT: D 552 GLN cc_start: 0.7106 (mp10) cc_final: 0.6547 (pt0) REVERT: E 52 MET cc_start: 0.4749 (tmm) cc_final: 0.4497 (tmm) REVERT: E 77 MET cc_start: -0.0614 (pp-130) cc_final: -0.0844 (pp-130) REVERT: E 111 THR cc_start: 0.6810 (m) cc_final: 0.6415 (p) REVERT: F 52 MET cc_start: 0.4810 (tmm) cc_final: 0.4539 (tmm) REVERT: F 72 MET cc_start: -0.1184 (ttp) cc_final: -0.1442 (ttp) REVERT: F 111 THR cc_start: 0.6867 (m) cc_final: 0.6446 (p) REVERT: G 52 MET cc_start: 0.4937 (tmm) cc_final: 0.4640 (tmm) REVERT: G 111 THR cc_start: 0.6895 (m) cc_final: 0.6500 (p) REVERT: H 111 THR cc_start: 0.6935 (m) cc_final: 0.6513 (p) outliers start: 56 outliers final: 27 residues processed: 291 average time/residue: 0.5156 time to fit residues: 166.2867 Evaluate side-chains 272 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 234 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain A residue 542 ARG Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 571 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 160 optimal weight: 30.0000 chunk 15 optimal weight: 0.9990 chunk 191 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 153 optimal weight: 0.0470 chunk 13 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 154 optimal weight: 20.0000 chunk 111 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN B 368 ASN C 238 GLN C 368 ASN D 368 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.222532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.128131 restraints weight = 20051.436| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 5.04 r_work: 0.3005 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15916 Z= 0.117 Angle : 0.495 8.635 21488 Z= 0.260 Chirality : 0.037 0.219 2416 Planarity : 0.004 0.041 2704 Dihedral : 3.358 12.804 2140 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.80 % Allowed : 19.27 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.86 (0.19), residues: 1928 helix: 2.18 (0.13), residues: 1548 sheet: None (None), residues: 0 loop : 0.84 (0.35), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 241 TYR 0.010 0.001 TYR A 108 PHE 0.007 0.001 PHE G 142 TRP 0.029 0.002 TRP D 191 HIS 0.001 0.000 HIS B 557 Details of bonding type rmsd covalent geometry : bond 0.00230 (15916) covalent geometry : angle 0.49469 (21488) hydrogen bonds : bond 0.04358 ( 1193) hydrogen bonds : angle 4.25276 ( 3555) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 241 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 CYS cc_start: 0.7750 (OUTLIER) cc_final: 0.6949 (p) REVERT: A 232 ARG cc_start: 0.7670 (mtt180) cc_final: 0.7347 (tpt-90) REVERT: A 542 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.6028 (tmm160) REVERT: A 547 LYS cc_start: 0.8174 (ttpt) cc_final: 0.7964 (tmmm) REVERT: A 549 VAL cc_start: 0.7159 (p) cc_final: 0.6859 (p) REVERT: A 552 GLN cc_start: 0.7530 (mp10) cc_final: 0.6633 (pt0) REVERT: A 553 TYR cc_start: 0.7148 (t80) cc_final: 0.6609 (t80) REVERT: B 184 CYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7038 (p) REVERT: B 191 TRP cc_start: 0.6192 (p-90) cc_final: 0.5825 (p-90) REVERT: B 542 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6086 (tmm160) REVERT: B 547 LYS cc_start: 0.8180 (ttpt) cc_final: 0.7965 (tmmm) REVERT: B 549 VAL cc_start: 0.7230 (p) cc_final: 0.6906 (p) REVERT: B 552 GLN cc_start: 0.7537 (mp10) cc_final: 0.6638 (pt0) REVERT: B 553 TYR cc_start: 0.7163 (t80) cc_final: 0.6585 (t80) REVERT: C 184 CYS cc_start: 0.7757 (OUTLIER) cc_final: 0.6959 (p) REVERT: C 542 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.6078 (tmm160) REVERT: C 547 LYS cc_start: 0.8144 (ttpt) cc_final: 0.7930 (tmmm) REVERT: C 549 VAL cc_start: 0.7235 (p) cc_final: 0.6934 (p) REVERT: C 552 GLN cc_start: 0.7547 (mp10) cc_final: 0.6643 (pt0) REVERT: C 553 TYR cc_start: 0.7152 (t80) cc_final: 0.6755 (t80) REVERT: D 184 CYS cc_start: 0.7686 (OUTLIER) cc_final: 0.6938 (p) REVERT: D 549 VAL cc_start: 0.7336 (p) cc_final: 0.6926 (p) REVERT: D 552 GLN cc_start: 0.7081 (mp10) cc_final: 0.6577 (pt0) REVERT: E 52 MET cc_start: 0.4677 (tmm) cc_final: 0.4401 (tmm) REVERT: E 88 GLU cc_start: 0.6970 (pt0) cc_final: 0.6538 (mm-30) REVERT: E 111 THR cc_start: 0.6666 (m) cc_final: 0.6296 (p) REVERT: F 52 MET cc_start: 0.4855 (tmm) cc_final: 0.4629 (tmm) REVERT: F 72 MET cc_start: -0.1195 (ttp) cc_final: -0.1434 (ttp) REVERT: F 111 THR cc_start: 0.6788 (m) cc_final: 0.6400 (p) REVERT: G 52 MET cc_start: 0.4903 (tmm) cc_final: 0.4657 (tmm) REVERT: H 52 MET cc_start: 0.4904 (tmm) cc_final: 0.4606 (OUTLIER) REVERT: H 111 THR cc_start: 0.6746 (m) cc_final: 0.6348 (p) outliers start: 46 outliers final: 28 residues processed: 276 average time/residue: 0.5029 time to fit residues: 154.8895 Evaluate side-chains 267 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 542 ARG Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 560 MET Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 558 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 43 optimal weight: 6.9990 chunk 191 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN C 238 GLN C 368 ASN D 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.221780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.117024 restraints weight = 19881.680| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.95 r_work: 0.3058 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15916 Z= 0.132 Angle : 0.509 9.548 21488 Z= 0.267 Chirality : 0.037 0.225 2416 Planarity : 0.004 0.040 2704 Dihedral : 3.359 12.609 2140 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.74 % Allowed : 19.33 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.85 (0.19), residues: 1928 helix: 2.14 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : 0.98 (0.35), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 241 TYR 0.011 0.001 TYR A 108 PHE 0.009 0.001 PHE A 537 TRP 0.033 0.002 TRP D 191 HIS 0.002 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00275 (15916) covalent geometry : angle 0.50893 (21488) hydrogen bonds : bond 0.04709 ( 1193) hydrogen bonds : angle 4.26377 ( 3555) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 235 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 CYS cc_start: 0.7740 (OUTLIER) cc_final: 0.6904 (p) REVERT: A 232 ARG cc_start: 0.7597 (mtt180) cc_final: 0.7333 (tpt-90) REVERT: A 542 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.6049 (tmm160) REVERT: A 547 LYS cc_start: 0.8173 (ttpt) cc_final: 0.7963 (tmmm) REVERT: A 549 VAL cc_start: 0.7190 (p) cc_final: 0.6872 (p) REVERT: A 552 GLN cc_start: 0.7531 (mp10) cc_final: 0.6628 (pt0) REVERT: A 553 TYR cc_start: 0.7115 (t80) cc_final: 0.6594 (t80) REVERT: B 184 CYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7013 (p) REVERT: B 191 TRP cc_start: 0.6187 (p-90) cc_final: 0.5837 (p-90) REVERT: B 542 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.6232 (tmm160) REVERT: B 549 VAL cc_start: 0.7213 (p) cc_final: 0.6891 (p) REVERT: B 552 GLN cc_start: 0.7492 (mp10) cc_final: 0.6603 (pt0) REVERT: B 553 TYR cc_start: 0.7163 (t80) cc_final: 0.6559 (t80) REVERT: C 184 CYS cc_start: 0.7726 (OUTLIER) cc_final: 0.6938 (p) REVERT: C 542 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.6046 (tmm160) REVERT: C 549 VAL cc_start: 0.7227 (p) cc_final: 0.6926 (p) REVERT: C 552 GLN cc_start: 0.7523 (mp10) cc_final: 0.6624 (pt0) REVERT: C 553 TYR cc_start: 0.7119 (t80) cc_final: 0.6719 (t80) REVERT: D 184 CYS cc_start: 0.7681 (OUTLIER) cc_final: 0.6903 (p) REVERT: D 542 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6273 (ttp80) REVERT: D 549 VAL cc_start: 0.7341 (p) cc_final: 0.6956 (p) REVERT: D 552 GLN cc_start: 0.7053 (mp10) cc_final: 0.6598 (pt0) REVERT: E 52 MET cc_start: 0.4725 (tmm) cc_final: 0.4440 (tmm) REVERT: E 88 GLU cc_start: 0.7082 (pt0) cc_final: 0.6657 (mm-30) REVERT: E 111 THR cc_start: 0.6642 (m) cc_final: 0.6303 (p) REVERT: F 52 MET cc_start: 0.4800 (tmm) cc_final: 0.4574 (tmm) REVERT: F 72 MET cc_start: -0.1177 (ttp) cc_final: -0.1424 (ttp) REVERT: F 111 THR cc_start: 0.6790 (m) cc_final: 0.6411 (p) REVERT: G 52 MET cc_start: 0.4891 (tmm) cc_final: 0.4586 (tmm) REVERT: G 77 MET cc_start: 0.0358 (pp-130) cc_final: 0.0070 (pp-130) REVERT: H 52 MET cc_start: 0.4856 (tmm) cc_final: 0.4526 (tmm) REVERT: H 111 THR cc_start: 0.6742 (m) cc_final: 0.6354 (p) outliers start: 45 outliers final: 29 residues processed: 269 average time/residue: 0.4341 time to fit residues: 130.7320 Evaluate side-chains 268 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 542 ARG Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 558 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 20 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 151 optimal weight: 20.0000 chunk 134 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 178 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 188 optimal weight: 20.0000 chunk 13 optimal weight: 0.6980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 368 ASN D 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.220204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.114878 restraints weight = 19901.992| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.91 r_work: 0.3026 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15916 Z= 0.162 Angle : 0.543 10.595 21488 Z= 0.285 Chirality : 0.038 0.223 2416 Planarity : 0.004 0.043 2704 Dihedral : 3.452 12.438 2140 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.74 % Allowed : 19.82 % Favored : 77.44 % 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 aren not related in a simple way. whole: 2.69 (0.19), residues: 1928 helix: 2.05 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : 0.85 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 241 TYR 0.012 0.001 TYR D 108 PHE 0.012 0.001 PHE A 537 TRP 0.037 0.002 TRP D 191 HIS 0.002 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00359 (15916) covalent geometry : angle 0.54336 (21488) hydrogen bonds : bond 0.05185 ( 1193) hydrogen bonds : angle 4.34635 ( 3555) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 CYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7000 (p) REVERT: A 542 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6125 (tmm160) REVERT: A 549 VAL cc_start: 0.7229 (p) cc_final: 0.6925 (p) REVERT: A 552 GLN cc_start: 0.7538 (mp10) cc_final: 0.6640 (pt0) REVERT: A 553 TYR cc_start: 0.7152 (t80) cc_final: 0.6634 (t80) REVERT: B 184 CYS cc_start: 0.7743 (OUTLIER) cc_final: 0.6948 (p) REVERT: B 191 TRP cc_start: 0.6165 (p-90) cc_final: 0.5805 (p-90) REVERT: B 542 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.6313 (tmm160) REVERT: B 549 VAL cc_start: 0.7279 (p) cc_final: 0.6974 (p) REVERT: B 552 GLN cc_start: 0.7509 (mp10) cc_final: 0.6591 (pt0) REVERT: B 553 TYR cc_start: 0.7147 (t80) cc_final: 0.6683 (t80) REVERT: C 184 CYS cc_start: 0.7737 (OUTLIER) cc_final: 0.6963 (p) REVERT: C 542 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.6210 (tmm160) REVERT: C 549 VAL cc_start: 0.7254 (p) cc_final: 0.6956 (p) REVERT: C 552 GLN cc_start: 0.7564 (mp10) cc_final: 0.6635 (pt0) REVERT: D 184 CYS cc_start: 0.7746 (OUTLIER) cc_final: 0.6991 (p) REVERT: D 549 VAL cc_start: 0.7356 (p) cc_final: 0.6969 (p) REVERT: D 552 GLN cc_start: 0.7061 (mp10) cc_final: 0.6610 (pt0) REVERT: E 52 MET cc_start: 0.4662 (tmm) cc_final: 0.4372 (tmm) REVERT: E 88 GLU cc_start: 0.7089 (pt0) cc_final: 0.6641 (mm-30) REVERT: E 111 THR cc_start: 0.6733 (m) cc_final: 0.6365 (p) REVERT: F 52 MET cc_start: 0.4820 (tmm) cc_final: 0.4596 (tmm) REVERT: F 72 MET cc_start: -0.1260 (ttp) cc_final: -0.1540 (ttp) REVERT: F 111 THR cc_start: 0.6833 (m) cc_final: 0.6439 (p) REVERT: G 52 MET cc_start: 0.4838 (tmm) cc_final: 0.4575 (tmm) REVERT: H 52 MET cc_start: 0.4711 (tmm) cc_final: 0.4368 (tmm) REVERT: H 111 THR cc_start: 0.6808 (m) cc_final: 0.6416 (p) outliers start: 45 outliers final: 32 residues processed: 265 average time/residue: 0.4207 time to fit residues: 125.1030 Evaluate side-chains 270 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 542 ARG Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 571 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 145 optimal weight: 40.0000 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 115 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN C 368 ASN D 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.222062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117631 restraints weight = 20000.854| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.93 r_work: 0.3081 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15916 Z= 0.121 Angle : 0.519 12.202 21488 Z= 0.270 Chirality : 0.037 0.242 2416 Planarity : 0.004 0.044 2704 Dihedral : 3.341 12.154 2140 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.38 % Allowed : 20.18 % Favored : 77.44 % 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 aren not related in a simple way. whole: 2.85 (0.19), residues: 1928 helix: 2.18 (0.13), residues: 1548 sheet: None (None), residues: 0 loop : 0.83 (0.35), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 241 TYR 0.010 0.001 TYR A 108 PHE 0.008 0.001 PHE F 142 TRP 0.040 0.002 TRP D 191 HIS 0.002 0.000 HIS B 557 Details of bonding type rmsd covalent geometry : bond 0.00242 (15916) covalent geometry : angle 0.51887 (21488) hydrogen bonds : bond 0.04439 ( 1193) hydrogen bonds : angle 4.22711 ( 3555) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 244 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 CYS cc_start: 0.7735 (OUTLIER) cc_final: 0.6896 (p) REVERT: A 232 ARG cc_start: 0.7562 (mtt180) cc_final: 0.7291 (tpt-90) REVERT: A 542 ARG cc_start: 0.6731 (OUTLIER) cc_final: 0.6215 (tmm160) REVERT: A 549 VAL cc_start: 0.7203 (p) cc_final: 0.6914 (p) REVERT: A 552 GLN cc_start: 0.7523 (mp10) cc_final: 0.6634 (pt0) REVERT: A 553 TYR cc_start: 0.7132 (t80) cc_final: 0.6578 (t80) REVERT: B 184 CYS cc_start: 0.7719 (OUTLIER) cc_final: 0.6893 (p) REVERT: B 191 TRP cc_start: 0.6159 (p-90) cc_final: 0.5806 (p-90) REVERT: B 542 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6311 (tmm160) REVERT: B 549 VAL cc_start: 0.7233 (p) cc_final: 0.6914 (p) REVERT: B 552 GLN cc_start: 0.7503 (mp10) cc_final: 0.6612 (pt0) REVERT: B 553 TYR cc_start: 0.7108 (t80) cc_final: 0.6677 (t80) REVERT: C 184 CYS cc_start: 0.7702 (OUTLIER) cc_final: 0.6911 (p) REVERT: C 542 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6310 (tmm160) REVERT: C 549 VAL cc_start: 0.7185 (p) cc_final: 0.6913 (p) REVERT: C 552 GLN cc_start: 0.7525 (mp10) cc_final: 0.6629 (pt0) REVERT: D 184 CYS cc_start: 0.7694 (OUTLIER) cc_final: 0.6925 (p) REVERT: D 542 ARG cc_start: 0.6973 (OUTLIER) cc_final: 0.6327 (tmm160) REVERT: D 549 VAL cc_start: 0.7335 (p) cc_final: 0.6914 (p) REVERT: D 552 GLN cc_start: 0.7071 (mp10) cc_final: 0.6612 (pt0) REVERT: D 553 TYR cc_start: 0.7186 (t80) cc_final: 0.6570 (t80) REVERT: E 52 MET cc_start: 0.4692 (tmm) cc_final: 0.4385 (tmm) REVERT: E 88 GLU cc_start: 0.7161 (pt0) cc_final: 0.6701 (mm-30) REVERT: E 111 THR cc_start: 0.6635 (m) cc_final: 0.6281 (p) REVERT: F 52 MET cc_start: 0.4814 (tmm) cc_final: 0.4580 (tmm) REVERT: F 72 MET cc_start: -0.1279 (ttp) cc_final: -0.1541 (ttp) REVERT: F 111 THR cc_start: 0.6769 (m) cc_final: 0.6385 (p) REVERT: G 52 MET cc_start: 0.4870 (tmm) cc_final: 0.4617 (tmm) REVERT: G 141 GLU cc_start: 0.6681 (tm-30) cc_final: 0.6104 (pm20) REVERT: H 52 MET cc_start: 0.4589 (tmm) cc_final: 0.4224 (tmm) REVERT: H 111 THR cc_start: 0.6712 (m) cc_final: 0.6317 (p) outliers start: 39 outliers final: 26 residues processed: 272 average time/residue: 0.4549 time to fit residues: 137.7193 Evaluate side-chains 269 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 542 ARG Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 560 MET Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 558 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 37 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 161 optimal weight: 0.0370 chunk 165 optimal weight: 30.0000 chunk 146 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN C 368 ASN D 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.221662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.117916 restraints weight = 19907.707| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.91 r_work: 0.3069 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15916 Z= 0.131 Angle : 0.550 12.329 21488 Z= 0.286 Chirality : 0.037 0.241 2416 Planarity : 0.004 0.046 2704 Dihedral : 3.379 13.980 2140 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.20 % Allowed : 21.04 % Favored : 76.77 % 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 aren not related in a simple way. whole: 2.80 (0.19), residues: 1928 helix: 2.07 (0.13), residues: 1560 sheet: None (None), residues: 0 loop : 1.13 (0.36), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 241 TYR 0.011 0.001 TYR A 108 PHE 0.009 0.001 PHE A 537 TRP 0.046 0.002 TRP C 191 HIS 0.002 0.001 HIS B 557 Details of bonding type rmsd covalent geometry : bond 0.00270 (15916) covalent geometry : angle 0.55013 (21488) hydrogen bonds : bond 0.04635 ( 1193) hydrogen bonds : angle 4.24307 ( 3555) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 CYS cc_start: 0.7724 (OUTLIER) cc_final: 0.6931 (p) REVERT: A 232 ARG cc_start: 0.7560 (mtt180) cc_final: 0.7279 (tpt-90) REVERT: A 542 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6370 (tmm160) REVERT: A 549 VAL cc_start: 0.7298 (p) cc_final: 0.6974 (p) REVERT: A 552 GLN cc_start: 0.7515 (mp10) cc_final: 0.6622 (pt0) REVERT: A 553 TYR cc_start: 0.7174 (t80) cc_final: 0.6617 (t80) REVERT: B 184 CYS cc_start: 0.7727 (OUTLIER) cc_final: 0.6926 (p) REVERT: B 191 TRP cc_start: 0.6158 (p-90) cc_final: 0.5815 (p-90) REVERT: B 542 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.6277 (tmm160) REVERT: B 549 VAL cc_start: 0.7236 (p) cc_final: 0.6916 (p) REVERT: B 552 GLN cc_start: 0.7499 (mp10) cc_final: 0.6604 (pt0) REVERT: B 553 TYR cc_start: 0.7144 (t80) cc_final: 0.6528 (t80) REVERT: C 542 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6335 (tmm160) REVERT: C 549 VAL cc_start: 0.7255 (p) cc_final: 0.6950 (p) REVERT: C 552 GLN cc_start: 0.7526 (mp10) cc_final: 0.6640 (pt0) REVERT: C 553 TYR cc_start: 0.7350 (t80) cc_final: 0.6761 (t80) REVERT: D 184 CYS cc_start: 0.7675 (OUTLIER) cc_final: 0.6927 (p) REVERT: D 542 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6362 (tmm160) REVERT: D 549 VAL cc_start: 0.7351 (p) cc_final: 0.6972 (p) REVERT: D 552 GLN cc_start: 0.7065 (mp10) cc_final: 0.6606 (pt0) REVERT: D 553 TYR cc_start: 0.7211 (t80) cc_final: 0.6520 (t80) REVERT: E 52 MET cc_start: 0.4666 (tmm) cc_final: 0.4364 (tmm) REVERT: E 88 GLU cc_start: 0.7142 (pt0) cc_final: 0.6721 (mm-30) REVERT: E 111 THR cc_start: 0.6646 (m) cc_final: 0.6286 (p) REVERT: F 52 MET cc_start: 0.4788 (tmm) cc_final: 0.4558 (tmm) REVERT: F 72 MET cc_start: -0.1309 (ttp) cc_final: -0.1572 (ttp) REVERT: F 79 ASP cc_start: 0.0637 (p0) cc_final: -0.0004 (p0) REVERT: F 81 ASP cc_start: 0.5308 (p0) cc_final: 0.4509 (m-30) REVERT: F 111 THR cc_start: 0.6762 (m) cc_final: 0.6377 (p) REVERT: G 52 MET cc_start: 0.4790 (tmm) cc_final: 0.4537 (tmm) REVERT: G 141 GLU cc_start: 0.6683 (tm-30) cc_final: 0.6133 (pm20) REVERT: H 52 MET cc_start: 0.4566 (tmm) cc_final: 0.4202 (tmm) REVERT: H 111 THR cc_start: 0.6707 (m) cc_final: 0.6308 (p) outliers start: 36 outliers final: 24 residues processed: 266 average time/residue: 0.4658 time to fit residues: 138.4946 Evaluate side-chains 269 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 542 ARG Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 558 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 101 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN C 368 ASN D 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.217507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113275 restraints weight = 19938.327| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 4.14 r_work: 0.2921 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 15916 Z= 0.294 Angle : 0.653 10.799 21488 Z= 0.345 Chirality : 0.043 0.217 2416 Planarity : 0.005 0.049 2704 Dihedral : 3.734 13.800 2140 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.95 % Allowed : 21.16 % Favored : 76.89 % 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 aren not related in a simple way. whole: 2.16 (0.19), residues: 1928 helix: 1.66 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : 0.77 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 241 TYR 0.016 0.002 TYR A 108 PHE 0.021 0.002 PHE A 338 TRP 0.046 0.003 TRP C 191 HIS 0.004 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00691 (15916) covalent geometry : angle 0.65340 (21488) hydrogen bonds : bond 0.06299 ( 1193) hydrogen bonds : angle 4.61164 ( 3555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11899.58 seconds wall clock time: 201 minutes 42.73 seconds (12102.73 seconds total)