Starting phenix.real_space_refine on Fri Jun 13 22:14:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j38_61109/06_2025/9j38_61109_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j38_61109/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9j38_61109/06_2025/9j38_61109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j38_61109/06_2025/9j38_61109.map" model { file = "/net/cci-nas-00/data/ceres_data/9j38_61109/06_2025/9j38_61109_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j38_61109/06_2025/9j38_61109_neut.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: G, F, H, C, B, D Time building chain proxies: 7.05, per 1000 atoms: 0.45 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: 4.54 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.50 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: 4.78 Time building geometry restraints manager: 5.29 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: 0.12 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 0.930 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.170 Process input model: 34.400 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.240 ------------------------------------------------------------------------------- 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 : 9.05 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.040 0.002 TRP C 191 HIS 0.002 0.001 HIS B 262 PHE 0.019 0.001 PHE G 13 TYR 0.008 0.001 TYR A 553 ARG 0.003 0.000 ARG A 563 Details of bonding type rmsd hydrogen bonds : bond 0.11563 ( 1193) hydrogen bonds : angle 5.71593 ( 3555) covalent geometry : bond 0.00238 (15916) covalent geometry : angle 0.53428 (21488) *********************** 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 : 1.745 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: 0.9140 time to fit residues: 300.0780 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 : 1.607 ------------------------------------------------------------------------------- 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 162 optimal weight: 7.9990 chunk 145 optimal weight: 50.0000 chunk 80 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 150 optimal weight: 50.0000 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 174 optimal weight: 0.0070 overall best weight: 1.5402 ------------------------------------------------------------------------------- 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 = 0.4639 r_free = 0.4639 target = 0.221025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.117011 restraints weight = 19955.273| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.89 r_work: 0.3057 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15916 Z= 0.143 Angle : 0.503 6.478 21488 Z= 0.269 Chirality : 0.037 0.189 2416 Planarity : 0.004 0.039 2704 Dihedral : 4.888 58.966 2161 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 5.30 % Allowed : 15.30 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.19), residues: 1928 helix: 2.03 (0.13), residues: 1540 sheet: None (None), residues: 0 loop : 0.60 (0.34), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 191 HIS 0.003 0.000 HIS D 130 PHE 0.007 0.001 PHE B 236 TYR 0.012 0.001 TYR A 108 ARG 0.002 0.000 ARG C 526 Details of bonding type rmsd hydrogen bonds : bond 0.05079 ( 1193) hydrogen bonds : angle 4.57062 ( 3555) covalent geometry : bond 0.00302 (15916) covalent geometry : angle 0.50267 (21488) *********************** 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 321 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 234 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 ARG cc_start: 0.7654 (mtt180) cc_final: 0.7412 (tpt-90) REVERT: A 552 GLN cc_start: 0.7123 (mp10) cc_final: 0.6492 (pt0) REVERT: A 553 TYR cc_start: 0.7206 (t80) cc_final: 0.6919 (t80) REVERT: B 191 TRP cc_start: 0.6240 (p-90) cc_final: 0.5889 (p-90) REVERT: B 542 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.6105 (tmm160) REVERT: B 552 GLN cc_start: 0.7199 (mp10) cc_final: 0.6571 (pt0) REVERT: C 232 ARG cc_start: 0.7662 (mtt180) cc_final: 0.7408 (tpt-90) REVERT: C 547 LYS cc_start: 0.8336 (ttpt) cc_final: 0.8119 (ttpp) REVERT: C 552 GLN cc_start: 0.7641 (mp10) cc_final: 0.6670 (pt0) REVERT: D 288 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8799 (mm-30) REVERT: D 362 HIS cc_start: 0.7688 (OUTLIER) cc_final: 0.7429 (m-70) REVERT: D 552 GLN cc_start: 0.7137 (mp10) cc_final: 0.6579 (pt0) REVERT: E 52 MET cc_start: 0.4990 (tmm) cc_final: 0.4706 (tmm) REVERT: F 52 MET cc_start: 0.4882 (tmm) cc_final: 0.4587 (tmm) REVERT: G 52 MET cc_start: 0.4934 (tmm) cc_final: 0.4628 (tmm) REVERT: H 72 MET cc_start: -0.0680 (mtp) cc_final: -0.0902 (mtt) REVERT: H 79 ASP cc_start: 0.1490 (p0) cc_final: 0.1264 (p0) REVERT: H 111 THR cc_start: 0.6959 (m) cc_final: 0.6467 (p) outliers start: 87 outliers final: 36 residues processed: 285 average time/residue: 1.1626 time to fit residues: 369.7470 Evaluate side-chains 252 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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 546 VAL 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 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 288 GLU Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 546 VAL 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 15 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 184 optimal weight: 10.0000 chunk 183 optimal weight: 0.0970 chunk 71 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 D 358 HIS D 368 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.223445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.120218 restraints weight = 20097.767| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.91 r_work: 0.3118 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15916 Z= 0.112 Angle : 0.455 6.373 21488 Z= 0.243 Chirality : 0.036 0.195 2416 Planarity : 0.003 0.040 2704 Dihedral : 4.028 37.825 2157 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 4.15 % Allowed : 16.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.20), residues: 1928 helix: 2.26 (0.13), residues: 1540 sheet: None (None), residues: 0 loop : 0.61 (0.35), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 191 HIS 0.001 0.000 HIS D 130 PHE 0.006 0.001 PHE C 350 TYR 0.008 0.001 TYR A 108 ARG 0.002 0.000 ARG A 526 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 1193) hydrogen bonds : angle 4.31150 ( 3555) covalent geometry : bond 0.00213 (15916) covalent geometry : angle 0.45539 (21488) *********************** 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 319 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 251 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 CYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7039 (p) REVERT: A 232 ARG cc_start: 0.7554 (mtt180) cc_final: 0.7303 (tpt-90) REVERT: A 549 VAL cc_start: 0.7452 (p) cc_final: 0.7158 (p) REVERT: A 552 GLN cc_start: 0.7153 (mp10) cc_final: 0.6652 (pt0) REVERT: A 553 TYR cc_start: 0.7198 (t80) cc_final: 0.6635 (t80) REVERT: B 184 CYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7130 (p) REVERT: B 191 TRP cc_start: 0.6195 (p-90) cc_final: 0.5852 (p-90) REVERT: B 232 ARG cc_start: 0.6175 (tpt170) cc_final: 0.4496 (tpt-90) REVERT: B 235 ARG cc_start: 0.5642 (ppt170) cc_final: 0.5342 (ppt170) REVERT: B 552 GLN cc_start: 0.7187 (mp10) cc_final: 0.6690 (pt0) REVERT: B 553 TYR cc_start: 0.7209 (t80) cc_final: 0.6627 (t80) REVERT: C 184 CYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7066 (p) REVERT: C 232 ARG cc_start: 0.7560 (mtt180) cc_final: 0.7348 (tpt-90) REVERT: C 542 ARG cc_start: 0.6707 (OUTLIER) cc_final: 0.5901 (tmm160) REVERT: C 547 LYS cc_start: 0.8202 (ttpt) cc_final: 0.7461 (tmmm) REVERT: C 549 VAL cc_start: 0.7250 (p) cc_final: 0.6976 (p) REVERT: C 552 GLN cc_start: 0.7603 (mp10) cc_final: 0.6661 (pt0) REVERT: C 553 TYR cc_start: 0.7163 (t80) cc_final: 0.6709 (t80) REVERT: D 184 CYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7068 (p) REVERT: D 232 ARG cc_start: 0.6111 (tpt170) cc_final: 0.4299 (tpt-90) REVERT: D 362 HIS cc_start: 0.7628 (OUTLIER) cc_final: 0.7097 (t-90) REVERT: D 552 GLN cc_start: 0.7108 (mp10) cc_final: 0.6628 (pt0) REVERT: D 558 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8085 (tm) REVERT: D 565 LYS cc_start: 0.8400 (mmtm) cc_final: 0.8146 (mmmm) REVERT: E 52 MET cc_start: 0.4812 (tmm) cc_final: 0.4596 (tmm) REVERT: E 111 THR cc_start: 0.6807 (m) cc_final: 0.6417 (p) REVERT: F 52 MET cc_start: 0.4784 (tmm) cc_final: 0.4521 (tmm) REVERT: F 72 MET cc_start: -0.1116 (ttp) cc_final: -0.1344 (ttp) REVERT: F 111 THR cc_start: 0.6928 (m) cc_final: 0.6505 (p) REVERT: G 52 MET cc_start: 0.5035 (tmm) cc_final: 0.4811 (tmm) REVERT: H 111 THR cc_start: 0.6832 (m) cc_final: 0.6386 (p) outliers start: 68 outliers final: 26 residues processed: 291 average time/residue: 1.1593 time to fit residues: 379.1820 Evaluate side-chains 271 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 362 HIS 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 133 VAL Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 362 HIS 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 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 362 HIS 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 362 HIS 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 3 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 368 ASN C 531 HIS D 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.219894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.118548 restraints weight = 19813.434| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.92 r_work: 0.2956 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15916 Z= 0.190 Angle : 0.530 6.788 21488 Z= 0.284 Chirality : 0.039 0.207 2416 Planarity : 0.004 0.040 2704 Dihedral : 3.618 29.258 2144 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 4.02 % Allowed : 17.44 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.19), residues: 1928 helix: 1.96 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : 0.83 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 191 HIS 0.003 0.001 HIS D 358 PHE 0.013 0.001 PHE D 338 TYR 0.013 0.002 TYR A 108 ARG 0.005 0.000 ARG C 241 Details of bonding type rmsd hydrogen bonds : bond 0.05545 ( 1193) hydrogen bonds : angle 4.46991 ( 3555) covalent geometry : bond 0.00431 (15916) covalent geometry : angle 0.53000 (21488) *********************** 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 304 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 238 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 CYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7042 (p) REVERT: A 232 ARG cc_start: 0.7653 (mtt180) cc_final: 0.7374 (tpt-90) REVERT: A 549 VAL cc_start: 0.7336 (p) cc_final: 0.6996 (p) REVERT: A 552 GLN cc_start: 0.7578 (mp10) cc_final: 0.6588 (pt0) REVERT: A 553 TYR cc_start: 0.7202 (t80) cc_final: 0.6650 (t80) REVERT: A 561 LEU cc_start: 0.7641 (tp) cc_final: 0.7395 (tp) REVERT: B 184 CYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7125 (p) REVERT: B 191 TRP cc_start: 0.6131 (p-90) cc_final: 0.5787 (p-90) REVERT: B 232 ARG cc_start: 0.6143 (tpt170) cc_final: 0.4433 (tpt-90) REVERT: B 542 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6037 (ttp80) REVERT: B 552 GLN cc_start: 0.7542 (mp10) cc_final: 0.6536 (pt0) REVERT: B 553 TYR cc_start: 0.7185 (t80) cc_final: 0.6724 (t80) REVERT: B 561 LEU cc_start: 0.7627 (tp) cc_final: 0.7372 (tp) REVERT: B 565 LYS cc_start: 0.8513 (mmmm) cc_final: 0.8309 (mmmm) REVERT: C 184 CYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7071 (p) REVERT: C 232 ARG cc_start: 0.7678 (mtt180) cc_final: 0.7397 (tpt-90) REVERT: C 542 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.6017 (tmm160) REVERT: C 549 VAL cc_start: 0.7254 (p) cc_final: 0.6970 (p) REVERT: C 552 GLN cc_start: 0.7576 (mp10) cc_final: 0.6628 (pt0) REVERT: C 561 LEU cc_start: 0.7724 (tp) cc_final: 0.7475 (tp) REVERT: C 565 LYS cc_start: 0.8494 (mmmm) cc_final: 0.8280 (mmmm) REVERT: D 184 CYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7049 (p) REVERT: D 542 ARG cc_start: 0.6707 (OUTLIER) cc_final: 0.6043 (ttp80) REVERT: D 552 GLN cc_start: 0.7043 (mp10) cc_final: 0.6606 (pt0) REVERT: E 52 MET cc_start: 0.4873 (tmm) cc_final: 0.4644 (tmm) REVERT: E 111 THR cc_start: 0.6841 (m) cc_final: 0.6445 (p) REVERT: F 52 MET cc_start: 0.4866 (tmm) cc_final: 0.4566 (tmm) REVERT: F 72 MET cc_start: -0.0851 (ttp) cc_final: -0.1103 (ttp) REVERT: F 111 THR cc_start: 0.6985 (m) cc_final: 0.6559 (p) REVERT: G 52 MET cc_start: 0.4858 (tmm) cc_final: 0.4620 (tmm) REVERT: G 111 THR cc_start: 0.6997 (m) cc_final: 0.6589 (p) REVERT: H 52 MET cc_start: 0.4741 (tmm) cc_final: 0.4434 (tmm) REVERT: H 77 MET cc_start: -0.0640 (pp-130) cc_final: -0.0946 (pp-130) REVERT: H 111 THR cc_start: 0.6871 (m) cc_final: 0.6446 (p) outliers start: 66 outliers final: 37 residues processed: 282 average time/residue: 1.0869 time to fit residues: 342.1201 Evaluate side-chains 270 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 169 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 546 VAL 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 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 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 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 542 ARG Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 571 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 50.0000 chunk 32 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 183 optimal weight: 0.0270 chunk 70 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 150 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 GLN 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 = 0.4628 r_free = 0.4628 target = 0.220099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.114890 restraints weight = 20193.370| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.97 r_work: 0.3027 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15916 Z= 0.165 Angle : 0.513 7.665 21488 Z= 0.275 Chirality : 0.038 0.213 2416 Planarity : 0.004 0.040 2704 Dihedral : 3.529 29.286 2141 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 4.09 % Allowed : 17.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.19), residues: 1928 helix: 1.96 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : 0.79 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 191 HIS 0.002 0.001 HIS D 358 PHE 0.011 0.001 PHE D 338 TYR 0.013 0.002 TYR A 108 ARG 0.008 0.000 ARG C 241 Details of bonding type rmsd hydrogen bonds : bond 0.05212 ( 1193) hydrogen bonds : angle 4.41572 ( 3555) covalent geometry : bond 0.00366 (15916) covalent geometry : angle 0.51302 (21488) *********************** 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: 67 poor density : 235 time to evaluate : 2.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 CYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7048 (p) REVERT: A 232 ARG cc_start: 0.7624 (mtt180) cc_final: 0.7363 (tpt-90) REVERT: A 379 ARG cc_start: 0.4449 (OUTLIER) cc_final: 0.4169 (mmm-85) REVERT: A 542 ARG cc_start: 0.6753 (OUTLIER) cc_final: 0.6180 (tmm160) REVERT: A 549 VAL cc_start: 0.7312 (p) cc_final: 0.7051 (p) REVERT: A 552 GLN cc_start: 0.7576 (mp10) cc_final: 0.6618 (pt0) REVERT: A 553 TYR cc_start: 0.7201 (t80) cc_final: 0.6644 (t80) REVERT: B 184 CYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7032 (p) REVERT: B 191 TRP cc_start: 0.6183 (p-90) cc_final: 0.5819 (p-90) REVERT: B 379 ARG cc_start: 0.4440 (OUTLIER) cc_final: 0.4141 (mmm-85) REVERT: B 542 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6177 (tmm160) REVERT: B 549 VAL cc_start: 0.7352 (p) cc_final: 0.6991 (p) REVERT: B 552 GLN cc_start: 0.7523 (mp10) cc_final: 0.6543 (pt0) REVERT: B 553 TYR cc_start: 0.7177 (t80) cc_final: 0.6685 (t80) REVERT: B 561 LEU cc_start: 0.7680 (tp) cc_final: 0.7409 (tp) REVERT: C 184 CYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7021 (p) REVERT: C 379 ARG cc_start: 0.4399 (OUTLIER) cc_final: 0.4175 (mmm-85) REVERT: C 542 ARG cc_start: 0.6731 (OUTLIER) cc_final: 0.6174 (tmm160) REVERT: C 549 VAL cc_start: 0.7295 (p) cc_final: 0.6947 (p) REVERT: C 552 GLN cc_start: 0.7581 (mp10) cc_final: 0.6600 (pt0) REVERT: C 561 LEU cc_start: 0.7764 (tp) cc_final: 0.7507 (tp) REVERT: D 184 CYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7022 (p) REVERT: D 379 ARG cc_start: 0.4441 (OUTLIER) cc_final: 0.4121 (mmm-85) REVERT: D 542 ARG cc_start: 0.6702 (OUTLIER) cc_final: 0.6008 (ttp80) REVERT: D 552 GLN cc_start: 0.7123 (mp10) cc_final: 0.6623 (pt0) REVERT: E 52 MET cc_start: 0.4774 (tmm) cc_final: 0.4542 (tmm) REVERT: E 77 MET cc_start: -0.0659 (pp-130) cc_final: -0.0891 (pp-130) REVERT: E 88 GLU cc_start: 0.7040 (pt0) cc_final: 0.6616 (mm-30) REVERT: E 111 THR cc_start: 0.6838 (m) cc_final: 0.6451 (p) REVERT: F 52 MET cc_start: 0.4644 (tmm) cc_final: 0.4380 (tmm) REVERT: F 72 MET cc_start: -0.0830 (ttp) cc_final: -0.1094 (ttp) REVERT: F 111 THR cc_start: 0.6950 (m) cc_final: 0.6542 (p) REVERT: G 52 MET cc_start: 0.4988 (tmm) cc_final: 0.4740 (tmm) REVERT: H 52 MET cc_start: 0.4888 (tmm) cc_final: 0.4626 (tmm) REVERT: H 111 THR cc_start: 0.6977 (m) cc_final: 0.6560 (p) outliers start: 67 outliers final: 36 residues processed: 283 average time/residue: 1.3418 time to fit residues: 425.3436 Evaluate side-chains 276 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 228 time to evaluate : 1.894 ------------------------------------------------------------------------------- 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 165 PHE 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 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 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 211 ILE 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 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 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 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 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 211 ILE 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 94 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 152 optimal weight: 40.0000 chunk 34 optimal weight: 10.0000 chunk 143 optimal weight: 30.0000 chunk 78 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 chunk 33 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.4621 r_free = 0.4621 target = 0.219471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122489 restraints weight = 19948.461| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 5.06 r_work: 0.2919 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2241 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= 0.181 Angle : 0.535 8.404 21488 Z= 0.285 Chirality : 0.039 0.218 2416 Planarity : 0.004 0.040 2704 Dihedral : 3.574 29.580 2141 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.84 % Allowed : 18.48 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.19), residues: 1928 helix: 1.89 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : 0.80 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 191 HIS 0.002 0.001 HIS B 130 PHE 0.013 0.001 PHE C 338 TYR 0.013 0.002 TYR A 108 ARG 0.009 0.000 ARG B 241 Details of bonding type rmsd hydrogen bonds : bond 0.05410 ( 1193) hydrogen bonds : angle 4.45143 ( 3555) covalent geometry : bond 0.00409 (15916) covalent geometry : angle 0.53511 (21488) *********************** 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 297 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 234 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 CYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7044 (p) REVERT: A 542 ARG cc_start: 0.6759 (OUTLIER) cc_final: 0.6268 (tmm160) REVERT: A 549 VAL cc_start: 0.7257 (p) cc_final: 0.6996 (p) REVERT: A 552 GLN cc_start: 0.7543 (mp10) cc_final: 0.6591 (pt0) REVERT: A 553 TYR cc_start: 0.7183 (t80) cc_final: 0.6680 (t80) REVERT: B 184 CYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7054 (p) REVERT: B 191 TRP cc_start: 0.6194 (p-90) cc_final: 0.5808 (p-90) REVERT: B 542 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6172 (tmm160) REVERT: B 549 VAL cc_start: 0.7332 (p) cc_final: 0.6964 (p) REVERT: B 552 GLN cc_start: 0.7511 (mp10) cc_final: 0.6560 (pt0) REVERT: B 553 TYR cc_start: 0.7168 (t80) cc_final: 0.6725 (t80) REVERT: C 184 CYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7051 (p) REVERT: C 542 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.6125 (tmm160) REVERT: C 549 VAL cc_start: 0.7260 (p) cc_final: 0.6855 (p) REVERT: C 552 GLN cc_start: 0.7547 (mp10) cc_final: 0.6625 (pt0) REVERT: D 184 CYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7032 (p) REVERT: D 552 GLN cc_start: 0.7091 (mp10) cc_final: 0.6624 (pt0) REVERT: E 52 MET cc_start: 0.4742 (tmm) cc_final: 0.4529 (tmm) REVERT: E 88 GLU cc_start: 0.6990 (pt0) cc_final: 0.6634 (mm-30) REVERT: E 111 THR cc_start: 0.6855 (m) cc_final: 0.6469 (p) REVERT: F 52 MET cc_start: 0.4772 (tmm) cc_final: 0.4536 (tmm) REVERT: F 72 MET cc_start: -0.0916 (ttp) cc_final: -0.1186 (ttp) REVERT: F 111 THR cc_start: 0.6996 (m) cc_final: 0.6584 (p) REVERT: G 52 MET cc_start: 0.4887 (tmm) cc_final: 0.4630 (tmm) REVERT: H 52 MET cc_start: 0.4629 (tmm) cc_final: 0.4341 (tmm) REVERT: H 111 THR cc_start: 0.6958 (m) cc_final: 0.6553 (p) outliers start: 63 outliers final: 41 residues processed: 274 average time/residue: 1.0458 time to fit residues: 322.1821 Evaluate side-chains 276 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 228 time to evaluate : 1.732 ------------------------------------------------------------------------------- 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 165 PHE 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 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 151 GLU 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 211 ILE 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 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 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 184 CYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 211 ILE 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 546 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 54 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 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 = 0.4632 r_free = 0.4632 target = 0.220740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.115545 restraints weight = 20023.744| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.93 r_work: 0.3044 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15916 Z= 0.141 Angle : 0.515 9.146 21488 Z= 0.272 Chirality : 0.038 0.234 2416 Planarity : 0.004 0.039 2704 Dihedral : 3.519 29.379 2141 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 3.17 % Allowed : 19.21 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.19), residues: 1928 helix: 2.02 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : 0.81 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 191 HIS 0.002 0.001 HIS B 557 PHE 0.010 0.001 PHE D 537 TYR 0.012 0.001 TYR A 108 ARG 0.008 0.000 ARG B 241 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 1193) hydrogen bonds : angle 4.35592 ( 3555) covalent geometry : bond 0.00302 (15916) covalent geometry : angle 0.51528 (21488) *********************** 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 292 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 240 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 CYS cc_start: 0.7815 (OUTLIER) cc_final: 0.6986 (p) REVERT: A 542 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6361 (tmm160) REVERT: A 549 VAL cc_start: 0.7287 (p) cc_final: 0.7029 (p) REVERT: A 552 GLN cc_start: 0.7574 (mp10) cc_final: 0.6626 (pt0) REVERT: A 553 TYR cc_start: 0.7200 (t80) cc_final: 0.6597 (t80) REVERT: A 561 LEU cc_start: 0.7707 (tp) cc_final: 0.7436 (tp) REVERT: B 184 CYS cc_start: 0.7810 (OUTLIER) cc_final: 0.6979 (p) REVERT: B 191 TRP cc_start: 0.6134 (p-90) cc_final: 0.5755 (p-90) REVERT: B 542 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.6228 (tmm160) REVERT: B 549 VAL cc_start: 0.7347 (p) cc_final: 0.6962 (p) REVERT: B 552 GLN cc_start: 0.7517 (mp10) cc_final: 0.6558 (pt0) REVERT: B 553 TYR cc_start: 0.7123 (t80) cc_final: 0.6651 (t80) REVERT: C 184 CYS cc_start: 0.7808 (OUTLIER) cc_final: 0.6982 (p) REVERT: C 542 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.6243 (tmm160) REVERT: C 549 VAL cc_start: 0.7264 (p) cc_final: 0.6899 (p) REVERT: C 552 GLN cc_start: 0.7550 (mp10) cc_final: 0.6642 (pt0) REVERT: D 184 CYS cc_start: 0.7772 (OUTLIER) cc_final: 0.6991 (p) REVERT: D 379 ARG cc_start: 0.4728 (OUTLIER) cc_final: 0.4499 (mmm-85) REVERT: D 542 ARG cc_start: 0.6753 (OUTLIER) cc_final: 0.6040 (ttp80) REVERT: D 552 GLN cc_start: 0.7115 (mp10) cc_final: 0.6594 (pt0) REVERT: E 52 MET cc_start: 0.4923 (tmm) cc_final: 0.4685 (tmm) REVERT: E 88 GLU cc_start: 0.7050 (pt0) cc_final: 0.6597 (mm-30) REVERT: E 111 THR cc_start: 0.6846 (m) cc_final: 0.6447 (p) REVERT: F 52 MET cc_start: 0.4860 (tmm) cc_final: 0.4634 (tmm) REVERT: F 72 MET cc_start: -0.1113 (ttp) cc_final: -0.1401 (ttp) REVERT: F 111 THR cc_start: 0.6892 (m) cc_final: 0.6476 (p) REVERT: G 52 MET cc_start: 0.5011 (tmm) cc_final: 0.4777 (tmm) REVERT: H 52 MET cc_start: 0.4690 (tmm) cc_final: 0.4372 (tmm) REVERT: H 88 GLU cc_start: 0.6895 (pt0) cc_final: 0.6422 (mm-30) REVERT: H 111 THR cc_start: 0.6939 (m) cc_final: 0.6521 (p) outliers start: 52 outliers final: 34 residues processed: 278 average time/residue: 1.1581 time to fit residues: 363.1522 Evaluate side-chains 276 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 233 time to evaluate : 1.715 ------------------------------------------------------------------------------- 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 165 PHE 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 362 HIS 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 151 GLU 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 156 optimal weight: 9.9990 chunk 180 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 0.0770 chunk 136 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 overall best weight: 3.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN A 368 ASN B 368 ASN 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 = 0.4614 r_free = 0.4614 target = 0.218446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.113358 restraints weight = 19741.639| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.93 r_work: 0.3003 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15916 Z= 0.214 Angle : 0.580 10.422 21488 Z= 0.307 Chirality : 0.040 0.230 2416 Planarity : 0.004 0.044 2704 Dihedral : 3.672 29.369 2141 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.35 % Allowed : 19.51 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.19), residues: 1928 helix: 1.77 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : 0.78 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 191 HIS 0.003 0.001 HIS D 130 PHE 0.016 0.001 PHE D 537 TYR 0.014 0.002 TYR A 108 ARG 0.009 0.000 ARG D 241 Details of bonding type rmsd hydrogen bonds : bond 0.05727 ( 1193) hydrogen bonds : angle 4.51077 ( 3555) covalent geometry : bond 0.00496 (15916) covalent geometry : angle 0.58020 (21488) *********************** 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 290 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 235 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 CYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7036 (p) REVERT: A 542 ARG cc_start: 0.6773 (tmm160) cc_final: 0.6398 (tmm160) REVERT: A 549 VAL cc_start: 0.7330 (p) cc_final: 0.6994 (p) REVERT: A 552 GLN cc_start: 0.7563 (mp10) cc_final: 0.6570 (pt0) REVERT: A 553 TYR cc_start: 0.7266 (t80) cc_final: 0.6790 (t80) REVERT: B 184 CYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7022 (p) REVERT: B 191 TRP cc_start: 0.6188 (p-90) cc_final: 0.5832 (p-90) REVERT: B 542 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6253 (tmm160) REVERT: B 549 VAL cc_start: 0.7387 (p) cc_final: 0.7033 (p) REVERT: B 552 GLN cc_start: 0.7550 (mp10) cc_final: 0.6583 (pt0) REVERT: B 553 TYR cc_start: 0.7206 (t80) cc_final: 0.6998 (t80) REVERT: C 184 CYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7013 (p) REVERT: C 542 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.6415 (tmm160) REVERT: C 549 VAL cc_start: 0.7324 (p) cc_final: 0.6934 (p) REVERT: C 552 GLN cc_start: 0.7556 (mp10) cc_final: 0.6642 (pt0) REVERT: D 184 CYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7055 (p) REVERT: D 379 ARG cc_start: 0.4587 (OUTLIER) cc_final: 0.4357 (mmm-85) REVERT: D 552 GLN cc_start: 0.7104 (mp10) cc_final: 0.6610 (pt0) REVERT: E 52 MET cc_start: 0.4839 (tmm) cc_final: 0.4605 (tmm) REVERT: E 88 GLU cc_start: 0.7028 (pt0) cc_final: 0.6612 (mm-30) REVERT: E 111 THR cc_start: 0.6944 (m) cc_final: 0.6518 (p) REVERT: F 52 MET cc_start: 0.4858 (tmm) cc_final: 0.4627 (tmm) REVERT: F 72 MET cc_start: -0.0748 (ttp) cc_final: -0.1016 (ttp) REVERT: F 111 THR cc_start: 0.7022 (m) cc_final: 0.6590 (p) REVERT: G 52 MET cc_start: 0.4927 (tmm) cc_final: 0.4656 (tmm) REVERT: G 77 MET cc_start: 0.0532 (pp-130) cc_final: 0.0104 (pp-130) REVERT: H 52 MET cc_start: 0.4628 (tmm) cc_final: 0.4303 (tmm) REVERT: H 88 GLU cc_start: 0.6966 (pt0) cc_final: 0.6581 (mm-30) REVERT: H 111 THR cc_start: 0.7009 (m) cc_final: 0.6581 (p) outliers start: 55 outliers final: 37 residues processed: 268 average time/residue: 1.1054 time to fit residues: 335.7264 Evaluate side-chains 277 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 233 time to evaluate : 1.690 ------------------------------------------------------------------------------- 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 165 PHE 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 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 211 ILE 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 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 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 379 ARG Chi-restraints excluded: chain D residue 546 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 171 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN A 368 ASN B 368 ASN 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 = 0.4635 r_free = 0.4635 target = 0.221134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.117250 restraints weight = 19896.996| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.91 r_work: 0.3062 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15916 Z= 0.128 Angle : 0.536 12.134 21488 Z= 0.280 Chirality : 0.037 0.254 2416 Planarity : 0.004 0.042 2704 Dihedral : 3.495 28.408 2141 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.62 % Allowed : 19.70 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.19), residues: 1928 helix: 2.08 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : 0.71 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 191 HIS 0.002 0.001 HIS A 557 PHE 0.012 0.001 PHE E 142 TYR 0.011 0.001 TYR A 108 ARG 0.010 0.000 ARG C 241 Details of bonding type rmsd hydrogen bonds : bond 0.04621 ( 1193) hydrogen bonds : angle 4.30764 ( 3555) covalent geometry : bond 0.00264 (15916) covalent geometry : angle 0.53638 (21488) *********************** 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 286 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 243 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 CYS cc_start: 0.7809 (OUTLIER) cc_final: 0.6959 (p) REVERT: A 542 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6298 (tmm160) REVERT: A 549 VAL cc_start: 0.7237 (p) cc_final: 0.6975 (p) REVERT: A 552 GLN cc_start: 0.7543 (mp10) cc_final: 0.6635 (pt0) REVERT: A 553 TYR cc_start: 0.7117 (t80) cc_final: 0.6537 (t80) REVERT: B 184 CYS cc_start: 0.7785 (OUTLIER) cc_final: 0.6944 (p) REVERT: B 191 TRP cc_start: 0.6137 (p-90) cc_final: 0.5780 (p-90) REVERT: B 542 ARG cc_start: 0.6732 (OUTLIER) cc_final: 0.6117 (tmm160) REVERT: B 549 VAL cc_start: 0.7311 (p) cc_final: 0.7039 (p) REVERT: B 552 GLN cc_start: 0.7558 (mp10) cc_final: 0.6629 (pt0) REVERT: B 553 TYR cc_start: 0.7130 (t80) cc_final: 0.6665 (t80) REVERT: C 184 CYS cc_start: 0.7780 (OUTLIER) cc_final: 0.6934 (p) REVERT: C 542 ARG cc_start: 0.6800 (OUTLIER) cc_final: 0.6430 (tmm160) REVERT: C 549 VAL cc_start: 0.7237 (p) cc_final: 0.6974 (p) REVERT: C 552 GLN cc_start: 0.7535 (mp10) cc_final: 0.6628 (pt0) REVERT: D 184 CYS cc_start: 0.7765 (OUTLIER) cc_final: 0.6970 (p) REVERT: D 549 VAL cc_start: 0.7356 (p) cc_final: 0.6965 (p) REVERT: D 552 GLN cc_start: 0.7126 (mp10) cc_final: 0.6568 (pt0) REVERT: E 52 MET cc_start: 0.4836 (tmm) cc_final: 0.4604 (tmm) REVERT: E 88 GLU cc_start: 0.7123 (pt0) cc_final: 0.6670 (mm-30) REVERT: E 111 THR cc_start: 0.6814 (m) cc_final: 0.6419 (p) REVERT: F 52 MET cc_start: 0.4778 (tmm) cc_final: 0.4515 (tmm) REVERT: F 72 MET cc_start: -0.1284 (ttp) cc_final: -0.1570 (ttp) REVERT: F 79 ASP cc_start: 0.0965 (p0) cc_final: 0.0330 (p0) REVERT: F 81 ASP cc_start: 0.5287 (p0) cc_final: 0.4545 (m-30) REVERT: F 111 THR cc_start: 0.6855 (m) cc_final: 0.6447 (p) REVERT: G 52 MET cc_start: 0.5009 (tmm) cc_final: 0.4762 (tmm) REVERT: G 77 MET cc_start: 0.0489 (pp-130) cc_final: 0.0056 (pp-130) REVERT: G 141 GLU cc_start: 0.6666 (tm-30) cc_final: 0.6047 (pm20) REVERT: H 52 MET cc_start: 0.4731 (tmm) cc_final: 0.4435 (tmm) REVERT: H 88 GLU cc_start: 0.7017 (pt0) cc_final: 0.6653 (mm-30) REVERT: H 111 THR cc_start: 0.6806 (m) cc_final: 0.6379 (p) outliers start: 43 outliers final: 28 residues processed: 270 average time/residue: 1.5538 time to fit residues: 470.8018 Evaluate side-chains 270 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 3.424 ------------------------------------------------------------------------------- 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 165 PHE 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 151 GLU 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 542 ARG 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 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 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 558 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 144 optimal weight: 0.2980 chunk 102 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 165 optimal weight: 40.0000 chunk 95 optimal weight: 30.0000 chunk 190 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 188 optimal weight: 20.0000 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN B 238 GLN B 368 ASN 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 = 0.4610 r_free = 0.4610 target = 0.217479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.116926 restraints weight = 19885.703| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 4.51 r_work: 0.2900 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 15916 Z= 0.307 Angle : 0.661 11.451 21488 Z= 0.350 Chirality : 0.044 0.218 2416 Planarity : 0.005 0.056 2704 Dihedral : 3.840 29.870 2141 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.56 % Allowed : 20.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.19), residues: 1928 helix: 1.52 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : 0.72 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP A 191 HIS 0.003 0.001 HIS C 130 PHE 0.021 0.002 PHE D 537 TYR 0.016 0.002 TYR A 108 ARG 0.010 0.001 ARG C 241 Details of bonding type rmsd hydrogen bonds : bond 0.06384 ( 1193) hydrogen bonds : angle 4.65306 ( 3555) covalent geometry : bond 0.00727 (15916) covalent geometry : angle 0.66147 (21488) ********************** 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 272 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 CYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7122 (p) REVERT: A 542 ARG cc_start: 0.6673 (tmm160) cc_final: 0.6259 (tmm160) REVERT: A 549 VAL cc_start: 0.7272 (p) cc_final: 0.6960 (p) REVERT: A 552 GLN cc_start: 0.7552 (mp10) cc_final: 0.6607 (pt0) REVERT: A 553 TYR cc_start: 0.7171 (t80) cc_final: 0.6848 (t80) REVERT: B 184 CYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7036 (p) REVERT: B 191 TRP cc_start: 0.6237 (p-90) cc_final: 0.5865 (p-90) REVERT: B 542 ARG cc_start: 0.6700 (tmm160) cc_final: 0.6239 (tmm160) REVERT: B 549 VAL cc_start: 0.7323 (p) cc_final: 0.6938 (p) REVERT: B 552 GLN cc_start: 0.7562 (mp10) cc_final: 0.6590 (pt0) REVERT: B 553 TYR cc_start: 0.7171 (t80) cc_final: 0.6855 (t80) REVERT: C 184 CYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7064 (p) REVERT: C 542 ARG cc_start: 0.6729 (tmm160) cc_final: 0.6374 (tmm160) REVERT: C 549 VAL cc_start: 0.7304 (p) cc_final: 0.6909 (p) REVERT: C 552 GLN cc_start: 0.7558 (mp10) cc_final: 0.6584 (pt0) REVERT: D 184 CYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7096 (p) REVERT: D 379 ARG cc_start: 0.4352 (OUTLIER) cc_final: 0.4106 (mmm-85) REVERT: D 552 GLN cc_start: 0.7115 (mp10) cc_final: 0.6624 (pt0) REVERT: E 52 MET cc_start: 0.4595 (tmm) cc_final: 0.4370 (tmm) REVERT: E 77 MET cc_start: 0.0495 (pp-130) cc_final: 0.0111 (pp-130) REVERT: E 88 GLU cc_start: 0.7126 (pt0) cc_final: 0.6735 (mm-30) REVERT: F 52 MET cc_start: 0.4717 (tmm) cc_final: 0.4447 (tmm) REVERT: F 72 MET cc_start: -0.0912 (ttp) cc_final: -0.1125 (ttp) REVERT: F 79 ASP cc_start: 0.1172 (p0) cc_final: 0.0513 (p0) REVERT: F 81 ASP cc_start: 0.5425 (p0) cc_final: 0.4675 (m-30) REVERT: F 111 THR cc_start: 0.7047 (m) cc_final: 0.6583 (p) REVERT: G 52 MET cc_start: 0.4804 (tmm) cc_final: 0.4449 (ttt) REVERT: G 77 MET cc_start: 0.0312 (pp-130) cc_final: -0.0090 (pp-130) REVERT: H 52 MET cc_start: 0.4553 (tmm) cc_final: 0.4242 (tmm) REVERT: H 88 GLU cc_start: 0.6968 (pt0) cc_final: 0.6625 (mm-30) outliers start: 42 outliers final: 28 residues processed: 255 average time/residue: 1.1317 time to fit residues: 322.9200 Evaluate side-chains 256 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 223 time to evaluate : 1.793 ------------------------------------------------------------------------------- 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 165 PHE 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 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 377 VAL 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 184 CYS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 217 VAL 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 379 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 136 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 183 optimal weight: 0.1980 chunk 147 optimal weight: 6.9990 chunk 152 optimal weight: 30.0000 chunk 70 optimal weight: 4.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN B 238 GLN B 368 ASN 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 = 0.4619 r_free = 0.4619 target = 0.218737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.118900 restraints weight = 19813.172| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 4.65 r_work: 0.2928 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15916 Z= 0.217 Angle : 0.611 12.701 21488 Z= 0.322 Chirality : 0.041 0.249 2416 Planarity : 0.004 0.050 2704 Dihedral : 3.748 29.159 2141 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.44 % Allowed : 20.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.19), residues: 1928 helix: 1.61 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : 0.80 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP C 191 HIS 0.003 0.001 HIS C 557 PHE 0.016 0.002 PHE D 171 TYR 0.015 0.002 TYR A 108 ARG 0.010 0.000 ARG C 241 Details of bonding type rmsd hydrogen bonds : bond 0.05749 ( 1193) hydrogen bonds : angle 4.52439 ( 3555) covalent geometry : bond 0.00501 (15916) covalent geometry : angle 0.61118 (21488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25800.62 seconds wall clock time: 448 minutes 0.06 seconds (26880.06 seconds total)