Starting phenix.real_space_refine on Fri Jul 3 12:36:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rk5_19260/07_2026/8rk5_19260.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rk5_19260/07_2026/8rk5_19260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rk5_19260/07_2026/8rk5_19260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rk5_19260/07_2026/8rk5_19260.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rk5_19260/07_2026/8rk5_19260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rk5_19260/07_2026/8rk5_19260.map" } resolution = 4.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 48 5.16 5 C 9177 2.51 5 N 2496 2.21 5 O 2703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14424 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2470 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 295} Chain: "B" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2338 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 285} Restraints were copied for chains: C, D, E, F Time building chain proxies: 3.18, per 1000 atoms: 0.22 Number of scatterers: 14424 At special positions: 0 Unit cell: (118.371, 114.203, 145.046, 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 48 16.00 O 2703 8.00 N 2496 7.00 C 9177 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS F 142 " - pdb=" SG CYS F 174 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 696.0 milliseconds 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3336 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 21 sheets defined 11.1% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.534A pdb=" N ILE A 98 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 223 removed outlier: 3.618A pdb=" N TYR A 222 " --> pdb=" O GLU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'B' and resid 10 through 25 removed outlier: 3.533A pdb=" N LEU B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 217 through 223 removed outlier: 3.560A pdb=" N ILE B 221 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 25 Processing helix chain 'C' and resid 25 through 31 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.533A pdb=" N ILE C 98 " --> pdb=" O PRO C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 223 removed outlier: 3.618A pdb=" N TYR C 222 " --> pdb=" O GLU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 308 through 310 No H-bonds generated for 'chain 'C' and resid 308 through 310' Processing helix chain 'E' and resid 10 through 25 removed outlier: 3.533A pdb=" N LEU E 14 " --> pdb=" O ASN E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 184 Processing helix chain 'E' and resid 217 through 223 removed outlier: 3.560A pdb=" N ILE E 221 " --> pdb=" O ASP E 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 25 Processing helix chain 'D' and resid 25 through 31 Processing helix chain 'D' and resid 94 through 98 removed outlier: 3.534A pdb=" N ILE D 98 " --> pdb=" O PRO D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 223 removed outlier: 3.618A pdb=" N TYR D 222 " --> pdb=" O GLU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 308 through 310 No H-bonds generated for 'chain 'D' and resid 308 through 310' Processing helix chain 'F' and resid 10 through 25 removed outlier: 3.533A pdb=" N LEU F 14 " --> pdb=" O ASN F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 184 Processing helix chain 'F' and resid 217 through 223 removed outlier: 3.561A pdb=" N ILE F 221 " --> pdb=" O ASP F 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 8 removed outlier: 4.882A pdb=" N LEU A 166 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 41 removed outlier: 6.466A pdb=" N THR A 56 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP A 40 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLN A 54 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 116 " --> pdb=" O TYR A 172 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR A 172 " --> pdb=" O GLN A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 225 through 227 removed outlier: 9.889A pdb=" N LYS A 256 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N GLY A 276 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU A 258 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY A 272 " --> pdb=" O PHE A 260 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR A 262 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TYR A 270 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY A 276 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 247 removed outlier: 4.585A pdb=" N TYR B 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TYR B 250 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA B 241 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY B 252 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 8 removed outlier: 5.719A pdb=" N ALA B 8 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR B 98 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N PHE B 97 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA B 116 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N HIS B 110 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE B 125 " --> pdb=" O HIS B 110 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N HIS B 112 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL B 123 " --> pdb=" O HIS B 112 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLU B 114 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ARG B 121 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLN B 139 " --> pdb=" O ARG B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 28 through 32 removed outlier: 5.031A pdb=" N THR B 29 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N HIS B 40 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR B 45 " --> pdb=" O ASN B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 257 through 261 removed outlier: 4.310A pdb=" N THR B 277 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 8 removed outlier: 4.882A pdb=" N LEU C 166 " --> pdb=" O ARG C 201 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 36 through 41 removed outlier: 6.465A pdb=" N THR C 56 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP C 40 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLN C 54 " --> pdb=" O ASP C 40 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN C 116 " --> pdb=" O TYR C 172 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR C 172 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 225 through 227 removed outlier: 9.889A pdb=" N LYS C 256 " --> pdb=" O GLY C 276 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N GLY C 276 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU C 258 " --> pdb=" O PHE C 274 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY C 272 " --> pdb=" O PHE C 260 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR C 262 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TYR C 270 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY C 276 " --> pdb=" O ARG C 316 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 246 through 247 removed outlier: 4.584A pdb=" N TYR E 250 " --> pdb=" O ARG C 247 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TYR E 250 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA E 241 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY E 252 " --> pdb=" O ILE E 239 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 8 removed outlier: 5.719A pdb=" N ALA E 8 " --> pdb=" O THR E 98 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR E 98 " --> pdb=" O ALA E 8 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N PHE E 97 " --> pdb=" O ALA E 116 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA E 116 " --> pdb=" O PHE E 97 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N HIS E 110 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE E 125 " --> pdb=" O HIS E 110 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N HIS E 112 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL E 123 " --> pdb=" O HIS E 112 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU E 114 " --> pdb=" O ARG E 121 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ARG E 121 " --> pdb=" O GLU E 114 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN E 139 " --> pdb=" O ARG E 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 28 through 32 removed outlier: 5.031A pdb=" N THR E 29 " --> pdb=" O HIS E 40 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N HIS E 40 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR E 45 " --> pdb=" O ASN E 60 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 257 through 261 removed outlier: 4.310A pdb=" N THR E 277 " --> pdb=" O VAL E 305 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 8 removed outlier: 4.882A pdb=" N LEU D 166 " --> pdb=" O ARG D 201 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 36 through 41 removed outlier: 6.466A pdb=" N THR D 56 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP D 40 " --> pdb=" O GLN D 54 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLN D 54 " --> pdb=" O ASP D 40 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN D 116 " --> pdb=" O TYR D 172 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR D 172 " --> pdb=" O GLN D 116 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 225 through 227 removed outlier: 9.890A pdb=" N LYS D 256 " --> pdb=" O GLY D 276 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N GLY D 276 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU D 258 " --> pdb=" O PHE D 274 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY D 272 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR D 262 " --> pdb=" O TYR D 270 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TYR D 270 " --> pdb=" O THR D 262 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY D 276 " --> pdb=" O ARG D 316 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 246 through 247 removed outlier: 4.585A pdb=" N TYR F 250 " --> pdb=" O ARG D 247 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TYR F 250 " --> pdb=" O ALA F 241 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA F 241 " --> pdb=" O TYR F 250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY F 252 " --> pdb=" O ILE F 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 3 through 8 removed outlier: 5.719A pdb=" N ALA F 8 " --> pdb=" O THR F 98 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR F 98 " --> pdb=" O ALA F 8 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N PHE F 97 " --> pdb=" O ALA F 116 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA F 116 " --> pdb=" O PHE F 97 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N HIS F 110 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE F 125 " --> pdb=" O HIS F 110 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N HIS F 112 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL F 123 " --> pdb=" O HIS F 112 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU F 114 " --> pdb=" O ARG F 121 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ARG F 121 " --> pdb=" O GLU F 114 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLN F 139 " --> pdb=" O ARG F 177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 28 through 32 removed outlier: 5.031A pdb=" N THR F 29 " --> pdb=" O HIS F 40 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N HIS F 40 " --> pdb=" O THR F 29 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR F 45 " --> pdb=" O ASN F 60 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 257 through 261 removed outlier: 4.309A pdb=" N THR F 277 " --> pdb=" O VAL F 305 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1224 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: 1.97 Time building geometry restraints manager: 1.35 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: 4731 1.34 - 1.46: 2990 1.46 - 1.57: 7078 1.57 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 14868 Sorted by residual: bond pdb=" C ILE D 43 " pdb=" N PRO D 44 " ideal model delta sigma weight residual 1.329 1.346 -0.017 1.20e-02 6.94e+03 1.99e+00 bond pdb=" C ILE C 43 " pdb=" N PRO C 44 " ideal model delta sigma weight residual 1.329 1.345 -0.017 1.20e-02 6.94e+03 1.89e+00 bond pdb=" C ILE A 43 " pdb=" N PRO A 44 " ideal model delta sigma weight residual 1.329 1.345 -0.016 1.20e-02 6.94e+03 1.87e+00 bond pdb=" N GLU D 288 " pdb=" CA GLU D 288 " ideal model delta sigma weight residual 1.458 1.475 -0.017 1.37e-02 5.33e+03 1.53e+00 bond pdb=" CB TRP F 37 " pdb=" CG TRP F 37 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.48e+00 ... (remaining 14863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 19329 1.40 - 2.80: 822 2.80 - 4.20: 137 4.20 - 5.60: 25 5.60 - 7.00: 9 Bond angle restraints: 20322 Sorted by residual: angle pdb=" C ALA D 287 " pdb=" N GLU D 288 " pdb=" CA GLU D 288 " ideal model delta sigma weight residual 125.02 131.23 -6.21 1.76e+00 3.23e-01 1.25e+01 angle pdb=" C ALA C 287 " pdb=" N GLU C 288 " pdb=" CA GLU C 288 " ideal model delta sigma weight residual 125.02 131.21 -6.19 1.76e+00 3.23e-01 1.24e+01 angle pdb=" C ALA A 287 " pdb=" N GLU A 288 " pdb=" CA GLU A 288 " ideal model delta sigma weight residual 125.02 131.20 -6.18 1.76e+00 3.23e-01 1.23e+01 angle pdb=" CA GLU D 288 " pdb=" CB GLU D 288 " pdb=" CG GLU D 288 " ideal model delta sigma weight residual 114.10 120.17 -6.07 2.00e+00 2.50e-01 9.23e+00 angle pdb=" CA GLU C 288 " pdb=" CB GLU C 288 " pdb=" CG GLU C 288 " ideal model delta sigma weight residual 114.10 120.15 -6.05 2.00e+00 2.50e-01 9.16e+00 ... (remaining 20317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7901 17.96 - 35.92: 499 35.92 - 53.88: 90 53.88 - 71.84: 6 71.84 - 89.80: 9 Dihedral angle restraints: 8505 sinusoidal: 3201 harmonic: 5304 Sorted by residual: dihedral pdb=" CA TRP F 37 " pdb=" C TRP F 37 " pdb=" N LEU F 38 " pdb=" CA LEU F 38 " ideal model delta harmonic sigma weight residual 180.00 162.92 17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA TRP E 37 " pdb=" C TRP E 37 " pdb=" N LEU E 38 " pdb=" CA LEU E 38 " ideal model delta harmonic sigma weight residual 180.00 162.94 17.06 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA TRP B 37 " pdb=" C TRP B 37 " pdb=" N LEU B 38 " pdb=" CA LEU B 38 " ideal model delta harmonic sigma weight residual 180.00 162.96 17.04 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 8502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1098 0.027 - 0.054: 654 0.054 - 0.082: 181 0.082 - 0.109: 117 0.109 - 0.136: 62 Chirality restraints: 2112 Sorted by residual: chirality pdb=" CA ILE D 144 " pdb=" N ILE D 144 " pdb=" C ILE D 144 " pdb=" CB ILE D 144 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE A 144 " pdb=" N ILE A 144 " pdb=" C ILE A 144 " pdb=" CB ILE A 144 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE F 125 " pdb=" N ILE F 125 " pdb=" C ILE F 125 " pdb=" CB ILE F 125 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 2109 not shown) Planarity restraints: 2694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 204 " -0.039 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO B 205 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 205 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 205 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 204 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO F 205 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO F 205 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 205 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 204 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO E 205 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 205 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 205 " 0.033 5.00e-02 4.00e+02 ... (remaining 2691 not shown) Histogram of nonbonded interaction distances: 0.55 - 1.42: 69 1.42 - 2.29: 236 2.29 - 3.16: 13060 3.16 - 4.03: 36671 4.03 - 4.90: 68628 Warning: very small nonbonded interaction distances. Nonbonded interactions: 118664 Sorted by model distance: nonbonded pdb=" OE1 GLN B 245 " pdb=" CA ALA C 79 " model vdw 0.555 3.470 nonbonded pdb=" CD ARG A 306 " pdb=" CB VAL C 183 " model vdw 0.573 3.870 nonbonded pdb=" CA ALA A 79 " pdb=" CD GLN E 245 " model vdw 0.605 3.700 nonbonded pdb=" N PRO A 99 " pdb=" NH1 ARG F 286 " model vdw 0.652 3.200 nonbonded pdb=" CA ALA A 79 " pdb=" OE1 GLN E 245 " model vdw 0.664 3.470 ... (remaining 118659 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 12.250 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4351 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 : 0.013 1.030 14881 Z= 1.256 Angle : 0.675 7.003 20328 Z= 0.391 Chirality : 0.044 0.136 2112 Planarity : 0.006 0.060 2694 Dihedral : 12.152 89.798 5160 Min Nonbonded Distance : 0.555 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.18), residues: 1854 helix: 0.02 (0.38), residues: 153 sheet: 0.08 (0.20), residues: 597 loop : -1.23 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 179 TYR 0.019 0.002 TYR E 82 PHE 0.018 0.001 PHE A 128 TRP 0.019 0.001 TRP B 189 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (14868) covalent geometry : angle 0.67393 / 0.39 (20322) SS BOND : bond 0.00546 / 0.24 ( 3) SS BOND : angle 2.12715 / 1.21 ( 6) hydrogen bonds : bond 0.12721 / 9.41 ( 459) hydrogen bonds : angle 6.81945 / 4.66 ( 1224) Misc. bond : bond 0.48083 / 35.47 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 TRP cc_start: 0.6618 (m100) cc_final: 0.6279 (m100) REVERT: A 200 LEU cc_start: 0.8144 (tp) cc_final: 0.7925 (tp) REVERT: A 260 PHE cc_start: 0.7328 (m-80) cc_final: 0.6391 (m-80) REVERT: A 269 ARG cc_start: 0.6735 (ptp90) cc_final: 0.6003 (ttm170) REVERT: A 288 GLU cc_start: 0.4162 (pp20) cc_final: 0.3907 (pp20) REVERT: A 318 ASP cc_start: 0.7451 (t70) cc_final: 0.7221 (t0) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0561 time to fit residues: 4.3997 Evaluate side-chains 46 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.067 Evaluate side-chains 62 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 70 ASN cc_start: 0.7275 (p0) cc_final: 0.7062 (t0) REVERT: B 286 ARG cc_start: 0.3551 (ttt-90) cc_final: 0.3028 (tpt170) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0428 time to fit residues: 3.2969 Evaluate side-chains 40 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.0470 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN A 309 ASN ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.129625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.119694 restraints weight = 7374.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.122085 restraints weight = 4779.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.123934 restraints weight = 3280.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.125233 restraints weight = 2334.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.126246 restraints weight = 1717.581| |-----------------------------------------------------------------------------| r_work (final): 0.3890 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.135020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.126854 restraints weight = 7934.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.129285 restraints weight = 4960.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.130781 restraints weight = 3217.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.132044 restraints weight = 2224.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.132887 restraints weight = 1523.877| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4476 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 14881 Z= 0.222 Angle : 0.727 11.258 20328 Z= 0.387 Chirality : 0.048 0.191 2112 Planarity : 0.006 0.067 2694 Dihedral : 4.843 21.875 2079 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.18), residues: 1854 helix: 0.10 (0.38), residues: 138 sheet: 0.05 (0.20), residues: 606 loop : -1.23 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 268 TYR 0.021 0.002 TYR D 126 PHE 0.061 0.003 PHE B 264 TRP 0.024 0.002 TRP D 127 HIS 0.003 0.001 HIS E 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (14868) covalent geometry : angle 0.72615 / 0.39 (20322) SS BOND : bond 0.00313 / 0.14 ( 3) SS BOND : angle 2.61674 / 1.48 ( 6) hydrogen bonds : bond 0.03764 / 2.60 ( 459) hydrogen bonds : angle 6.56540 / 4.49 ( 1224) Misc. bond : bond 0.05503 / 2.65 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.091 Fit side-chains REVERT: A 120 TRP cc_start: 0.6768 (p90) cc_final: 0.5266 (p90) REVERT: A 136 TRP cc_start: 0.6560 (m100) cc_final: 0.6181 (m100) REVERT: A 169 VAL cc_start: 0.5774 (p) cc_final: 0.5365 (p) REVERT: A 180 TRP cc_start: 0.6467 (p-90) cc_final: 0.4766 (p-90) REVERT: A 269 ARG cc_start: 0.6225 (ptp90) cc_final: 0.5823 (mmt90) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0527 time to fit residues: 3.1489 Evaluate side-chains 41 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.055 Evaluate side-chains 48 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.080 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0381 time to fit residues: 2.2742 Evaluate side-chains 33 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 0.0020 chunk 16 optimal weight: 3.9990 chunk 148 optimal weight: 0.0980 chunk 162 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 115 optimal weight: 0.0270 chunk 87 optimal weight: 0.0060 overall best weight: 0.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 54 GLN ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.130809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.121076 restraints weight = 7446.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.123458 restraints weight = 4777.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.125206 restraints weight = 3238.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.126481 restraints weight = 2304.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.127384 restraints weight = 1689.026| |-----------------------------------------------------------------------------| r_work (final): 0.3894 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.136745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.128815 restraints weight = 7975.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.131209 restraints weight = 5056.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.133001 restraints weight = 3340.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.134065 restraints weight = 2242.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.134782 restraints weight = 1509.703| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4405 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 14881 Z= 0.202 Angle : 0.660 8.890 20328 Z= 0.352 Chirality : 0.046 0.158 2112 Planarity : 0.008 0.140 2694 Dihedral : 4.732 19.072 2079 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.20 % Allowed : 3.43 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.18), residues: 1854 helix: -0.22 (0.40), residues: 138 sheet: 0.04 (0.20), residues: 615 loop : -1.43 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 268 TYR 0.014 0.001 TYR F 82 PHE 0.066 0.002 PHE B 264 TRP 0.015 0.001 TRP F 278 HIS 0.012 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (14868) covalent geometry : angle 0.65888 / 0.35 (20322) SS BOND : bond 0.00077 / 0.03 ( 3) SS BOND : angle 2.76965 / 1.58 ( 6) hydrogen bonds : bond 0.03452 / 2.35 ( 459) hydrogen bonds : angle 6.31347 / 4.37 ( 1224) Misc. bond : bond 0.05288 / 2.62 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: A 120 TRP cc_start: 0.6742 (p90) cc_final: 0.6135 (p90) REVERT: A 136 TRP cc_start: 0.6701 (m100) cc_final: 0.6445 (m100) REVERT: A 169 VAL cc_start: 0.5586 (p) cc_final: 0.5124 (p) REVERT: A 180 TRP cc_start: 0.6726 (p-90) cc_final: 0.5336 (p-90) REVERT: A 190 ILE cc_start: 0.6331 (mt) cc_final: 0.6059 (tt) REVERT: A 252 LYS cc_start: 0.6959 (mttt) cc_final: 0.5976 (tptt) REVERT: A 318 ASP cc_start: 0.7382 (t70) cc_final: 0.7137 (t0) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.0389 time to fit residues: 2.5411 Evaluate side-chains 40 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.073 Evaluate side-chains 50 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: B 218 VAL cc_start: 0.7510 (t) cc_final: 0.7236 (t) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0305 time to fit residues: 1.9749 Evaluate side-chains 36 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 88 optimal weight: 0.0010 chunk 138 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 82 optimal weight: 0.0030 chunk 84 optimal weight: 9.9990 chunk 170 optimal weight: 6.9990 chunk 111 optimal weight: 0.3980 chunk 103 optimal weight: 6.9990 chunk 74 optimal weight: 0.0060 chunk 59 optimal weight: 0.5980 chunk 165 optimal weight: 0.9990 overall best weight: 0.2012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.132096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.121689 restraints weight = 7177.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.124335 restraints weight = 4514.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.126225 restraints weight = 3019.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.127587 restraints weight = 2121.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.128600 restraints weight = 1548.494| |-----------------------------------------------------------------------------| r_work (final): 0.3910 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.139498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.131318 restraints weight = 7633.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.133815 restraints weight = 4816.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.135560 restraints weight = 3145.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.136665 restraints weight = 2082.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.137377 restraints weight = 1408.130| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4375 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 14881 Z= 0.206 Angle : 0.655 7.634 20328 Z= 0.354 Chirality : 0.046 0.172 2112 Planarity : 0.007 0.078 2694 Dihedral : 4.869 31.919 2079 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.20 % Allowed : 2.42 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.18), residues: 1854 helix: -0.20 (0.40), residues: 141 sheet: 0.03 (0.20), residues: 576 loop : -1.49 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 268 TYR 0.014 0.001 TYR A 126 PHE 0.149 0.004 PHE B 264 TRP 0.012 0.001 TRP A 180 HIS 0.005 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (14868) covalent geometry : angle 0.65372 / 0.35 (20322) SS BOND : bond 0.00224 / 0.10 ( 3) SS BOND : angle 2.55413 / 1.46 ( 6) hydrogen bonds : bond 0.03201 / 2.15 ( 459) hydrogen bonds : angle 6.05138 / 4.21 ( 1224) Misc. bond : bond 0.05087 / 2.61 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 TRP cc_start: 0.6739 (m100) cc_final: 0.6494 (m100) REVERT: A 169 VAL cc_start: 0.5608 (p) cc_final: 0.4774 (p) REVERT: A 197 SER cc_start: 0.5173 (t) cc_final: 0.4385 (m) REVERT: A 252 LYS cc_start: 0.6971 (mttt) cc_final: 0.5975 (tptt) REVERT: A 269 ARG cc_start: 0.7025 (ptp90) cc_final: 0.5935 (mmt90) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0452 time to fit residues: 3.1194 Evaluate side-chains 42 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.081 Evaluate side-chains 44 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: B 218 VAL cc_start: 0.7088 (t) cc_final: 0.6839 (t) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.0338 time to fit residues: 1.9123 Evaluate side-chains 29 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 36 optimal weight: 9.9990 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 GLN B 40 HIS ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.128299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.117656 restraints weight = 7505.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.120492 restraints weight = 4658.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.122578 restraints weight = 3089.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.124000 restraints weight = 2136.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.125020 restraints weight = 1533.041| |-----------------------------------------------------------------------------| r_work (final): 0.3880 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.132611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.125252 restraints weight = 8108.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.127545 restraints weight = 4965.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.129093 restraints weight = 3183.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.130178 restraints weight = 2083.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.130919 restraints weight = 1391.699| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4591 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 14881 Z= 0.205 Angle : 0.644 7.717 20328 Z= 0.340 Chirality : 0.045 0.219 2112 Planarity : 0.008 0.131 2694 Dihedral : 4.835 20.674 2079 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.85 % Favored : 94.98 % Rotamer: Outliers : 0.20 % Allowed : 2.02 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.18), residues: 1854 helix: -0.33 (0.38), residues: 141 sheet: -0.28 (0.21), residues: 552 loop : -1.47 (0.17), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 268 TYR 0.015 0.002 TYR B 82 PHE 0.067 0.003 PHE E 264 TRP 0.014 0.002 TRP A 120 HIS 0.005 0.002 HIS F 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (14868) covalent geometry : angle 0.64255 / 0.34 (20322) SS BOND : bond 0.00204 / 0.09 ( 3) SS BOND : angle 2.53383 / 1.44 ( 6) hydrogen bonds : bond 0.03459 / 2.31 ( 459) hydrogen bonds : angle 6.30541 / 4.34 ( 1224) Misc. bond : bond 0.05168 / 2.75 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.068 Fit side-chains REVERT: A 169 VAL cc_start: 0.5610 (p) cc_final: 0.5337 (p) REVERT: A 190 ILE cc_start: 0.6086 (mm) cc_final: 0.5880 (mm) REVERT: A 197 SER cc_start: 0.5300 (t) cc_final: 0.4447 (m) REVERT: A 213 ASP cc_start: 0.8188 (t0) cc_final: 0.7957 (t0) REVERT: A 252 LYS cc_start: 0.7179 (mttt) cc_final: 0.5849 (tptt) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.0461 time to fit residues: 3.0290 Evaluate side-chains 39 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.115 Evaluate side-chains 36 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: B 110 HIS cc_start: 0.6166 (m170) cc_final: 0.5230 (m170) REVERT: B 218 VAL cc_start: 0.7514 (t) cc_final: 0.7225 (t) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0281 time to fit residues: 1.4242 Evaluate side-chains 24 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 43 optimal weight: 0.0030 chunk 36 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 140 optimal weight: 0.4980 chunk 17 optimal weight: 0.0060 chunk 20 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 chunk 117 optimal weight: 0.0470 chunk 121 optimal weight: 0.0010 overall best weight: 0.1110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 HIS ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 HIS ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.130800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.120185 restraints weight = 7532.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.123125 restraints weight = 4585.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.125205 restraints weight = 2995.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.126633 restraints weight = 2043.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.127612 restraints weight = 1437.982| |-----------------------------------------------------------------------------| r_work (final): 0.3921 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.135046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.126467 restraints weight = 8033.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.128954 restraints weight = 5098.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.130817 restraints weight = 3402.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.131948 restraints weight = 2269.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.132875 restraints weight = 1562.621| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4549 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 14881 Z= 0.177 Angle : 0.657 8.350 20328 Z= 0.354 Chirality : 0.046 0.161 2112 Planarity : 0.007 0.094 2694 Dihedral : 5.120 38.832 2079 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.85 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.18), residues: 1854 helix: -0.00 (0.40), residues: 141 sheet: -0.36 (0.20), residues: 570 loop : -1.45 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 268 TYR 0.021 0.002 TYR A 104 PHE 0.164 0.004 PHE E 264 TRP 0.016 0.001 TRP A 136 HIS 0.004 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (14868) covalent geometry : angle 0.65572 / 0.35 (20322) SS BOND : bond 0.00156 / 0.07 ( 3) SS BOND : angle 2.66488 / 1.52 ( 6) hydrogen bonds : bond 0.03412 / 2.34 ( 459) hydrogen bonds : angle 6.10795 / 4.22 ( 1224) Misc. bond : bond 0.04310 / 2.37 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: A 252 LYS cc_start: 0.7051 (mttt) cc_final: 0.5806 (tptt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0454 time to fit residues: 2.7837 Evaluate side-chains 37 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.085 Evaluate side-chains 38 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 48 PHE cc_start: 0.5184 (m-80) cc_final: 0.4858 (t80) REVERT: B 189 TRP cc_start: 0.5543 (m100) cc_final: 0.5050 (m100) REVERT: B 218 VAL cc_start: 0.7205 (t) cc_final: 0.6991 (t) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0349 time to fit residues: 1.8229 Evaluate side-chains 27 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 163 optimal weight: 8.9990 chunk 51 optimal weight: 0.0060 chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 182 optimal weight: 0.0270 chunk 146 optimal weight: 6.9990 chunk 139 optimal weight: 0.0010 chunk 76 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 overall best weight: 0.2660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 GLN ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.131019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.120600 restraints weight = 7456.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.123097 restraints weight = 4795.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.125150 restraints weight = 3290.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.126546 restraints weight = 2292.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.127526 restraints weight = 1659.980| |-----------------------------------------------------------------------------| r_work (final): 0.3920 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.137440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.129121 restraints weight = 7604.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.131506 restraints weight = 4848.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.133155 restraints weight = 3233.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.134387 restraints weight = 2194.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.135125 restraints weight = 1500.575| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4487 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 14881 Z= 0.165 Angle : 0.621 9.176 20328 Z= 0.330 Chirality : 0.047 0.232 2112 Planarity : 0.006 0.074 2694 Dihedral : 4.847 33.058 2079 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.02 % Favored : 94.82 % Rotamer: Outliers : 0.20 % Allowed : 0.61 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.18), residues: 1854 helix: -0.61 (0.38), residues: 162 sheet: -0.39 (0.20), residues: 570 loop : -1.47 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 207 TYR 0.014 0.001 TYR A 69 PHE 0.091 0.003 PHE E 264 TRP 0.013 0.001 TRP D 136 HIS 0.014 0.002 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (14868) covalent geometry : angle 0.61936 / 0.33 (20322) SS BOND : bond 0.00167 / 0.07 ( 3) SS BOND : angle 2.43638 / 1.38 ( 6) hydrogen bonds : bond 0.03518 / 2.39 ( 459) hydrogen bonds : angle 6.11085 / 4.20 ( 1224) Misc. bond : bond 0.04189 / 2.31 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.068 Fit side-chains revert: symmetry clash REVERT: A 120 TRP cc_start: 0.6575 (p90) cc_final: 0.5213 (p90) REVERT: A 169 VAL cc_start: 0.5650 (p) cc_final: 0.5327 (p) REVERT: A 199 TYR cc_start: 0.7539 (m-10) cc_final: 0.7283 (m-80) REVERT: A 252 LYS cc_start: 0.7041 (mttt) cc_final: 0.5777 (tptt) REVERT: A 269 ARG cc_start: 0.6757 (ptp90) cc_final: 0.5882 (mmt-90) REVERT: A 288 GLU cc_start: 0.4771 (tm-30) cc_final: 0.4151 (tm-30) REVERT: A 317 LYS cc_start: 0.7735 (pptt) cc_final: 0.7285 (pptt) REVERT: A 318 ASP cc_start: 0.7711 (t70) cc_final: 0.7429 (t0) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0413 time to fit residues: 2.3559 Evaluate side-chains 39 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.086 Evaluate side-chains 46 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 189 TRP cc_start: 0.5533 (m100) cc_final: 0.5069 (m100) REVERT: B 262 MET cc_start: 0.4394 (mtt) cc_final: 0.3975 (mtt) outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.0422 time to fit residues: 2.4937 Evaluate side-chains 28 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 77 optimal weight: 0.2980 chunk 5 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 0.0270 chunk 18 optimal weight: 8.9990 chunk 102 optimal weight: 0.0870 chunk 111 optimal weight: 3.9990 chunk 86 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 152 optimal weight: 7.9990 overall best weight: 0.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS B 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.131075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.119892 restraints weight = 7644.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.122805 restraints weight = 4953.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.124868 restraints weight = 3307.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.126308 restraints weight = 2307.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.127370 restraints weight = 1669.154| |-----------------------------------------------------------------------------| r_work (final): 0.3922 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.138041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.129851 restraints weight = 8125.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.132275 restraints weight = 5164.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.133871 restraints weight = 3416.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.135046 restraints weight = 2320.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.135916 restraints weight = 1623.471| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4483 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 14881 Z= 0.180 Angle : 0.629 10.099 20328 Z= 0.327 Chirality : 0.046 0.175 2112 Planarity : 0.006 0.073 2694 Dihedral : 4.525 18.356 2079 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.50 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.18), residues: 1854 helix: -0.78 (0.37), residues: 162 sheet: -0.46 (0.20), residues: 573 loop : -1.44 (0.17), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 207 TYR 0.010 0.001 TYR A 162 PHE 0.077 0.003 PHE E 264 TRP 0.012 0.001 TRP D 136 HIS 0.009 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (14868) covalent geometry : angle 0.62812 / 0.33 (20322) SS BOND : bond 0.00228 / 0.10 ( 3) SS BOND : angle 2.28783 / 1.30 ( 6) hydrogen bonds : bond 0.03417 / 2.32 ( 459) hydrogen bonds : angle 6.15769 / 4.24 ( 1224) Misc. bond : bond 0.05106 / 2.65 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.064 Fit side-chains revert: symmetry clash REVERT: A 120 TRP cc_start: 0.6579 (p90) cc_final: 0.5387 (p90) REVERT: A 252 LYS cc_start: 0.7157 (mttt) cc_final: 0.5812 (tptt) REVERT: A 269 ARG cc_start: 0.6761 (ptp90) cc_final: 0.5791 (mmt-90) REVERT: A 288 GLU cc_start: 0.5173 (tm-30) cc_final: 0.4407 (tm-30) REVERT: A 317 LYS cc_start: 0.7654 (pptt) cc_final: 0.7172 (pptt) REVERT: A 318 ASP cc_start: 0.7768 (t70) cc_final: 0.7470 (t0) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0494 time to fit residues: 2.8073 Evaluate side-chains 37 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.052 Evaluate side-chains 38 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 189 TRP cc_start: 0.5584 (m100) cc_final: 0.5121 (m100) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0279 time to fit residues: 1.4689 Evaluate side-chains 26 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 38 optimal weight: 0.3980 chunk 130 optimal weight: 4.9990 chunk 56 optimal weight: 0.0040 chunk 147 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 103 optimal weight: 0.0670 chunk 181 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 108 optimal weight: 0.0000 overall best weight: 0.1334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.132218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.121974 restraints weight = 7443.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.124700 restraints weight = 4829.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.126674 restraints weight = 3249.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.128009 restraints weight = 2268.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.128880 restraints weight = 1628.545| |-----------------------------------------------------------------------------| r_work (final): 0.3952 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.140864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.132855 restraints weight = 7996.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.135213 restraints weight = 5111.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.136869 restraints weight = 3381.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.138036 restraints weight = 2278.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.138755 restraints weight = 1561.116| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4432 moved from start: 0.5680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 14881 Z= 0.172 Angle : 0.611 10.122 20328 Z= 0.319 Chirality : 0.046 0.178 2112 Planarity : 0.006 0.077 2694 Dihedral : 4.337 16.742 2079 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.85 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.18), residues: 1854 helix: -0.49 (0.39), residues: 159 sheet: -0.32 (0.20), residues: 564 loop : -1.42 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 207 TYR 0.010 0.001 TYR C 162 PHE 0.067 0.003 PHE B 264 TRP 0.013 0.001 TRP D 136 HIS 0.008 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (14868) covalent geometry : angle 0.60929 / 0.32 (20322) SS BOND : bond 0.00175 / 0.08 ( 3) SS BOND : angle 2.75707 / 1.58 ( 6) hydrogen bonds : bond 0.03395 / 2.32 ( 459) hydrogen bonds : angle 6.04689 / 4.17 ( 1224) Misc. bond : bond 0.04800 / 2.48 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.069 Fit side-chains revert: symmetry clash REVERT: A 120 TRP cc_start: 0.6429 (p90) cc_final: 0.5554 (p90) REVERT: A 190 ILE cc_start: 0.6293 (mm) cc_final: 0.6035 (mm) REVERT: A 252 LYS cc_start: 0.7124 (mttt) cc_final: 0.5829 (tptt) REVERT: A 269 ARG cc_start: 0.6839 (ptp90) cc_final: 0.5892 (mmt-90) REVERT: A 288 GLU cc_start: 0.5183 (tm-30) cc_final: 0.4420 (tm-30) REVERT: A 317 LYS cc_start: 0.7685 (pptt) cc_final: 0.7246 (pptt) REVERT: A 318 ASP cc_start: 0.7733 (t70) cc_final: 0.7414 (t0) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0458 time to fit residues: 2.8341 Evaluate side-chains 43 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.055 Evaluate side-chains 38 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 189 TRP cc_start: 0.5636 (m100) cc_final: 0.5269 (m100) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0390 time to fit residues: 1.9005 Evaluate side-chains 26 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 102 optimal weight: 0.0030 chunk 120 optimal weight: 0.4980 chunk 146 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.0050 chunk 163 optimal weight: 0.0000 chunk 151 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 22 optimal weight: 0.0050 overall best weight: 0.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 HIS ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.132751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.122320 restraints weight = 7229.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.125120 restraints weight = 4655.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.127090 restraints weight = 3118.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.128341 restraints weight = 2184.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.129400 restraints weight = 1591.641| |-----------------------------------------------------------------------------| r_work (final): 0.3949 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.139979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.131199 restraints weight = 8198.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.133669 restraints weight = 5347.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.135079 restraints weight = 3614.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.136490 restraints weight = 2610.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.137338 restraints weight = 1840.987| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4415 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 14881 Z= 0.209 Angle : 0.732 15.391 20328 Z= 0.403 Chirality : 0.047 0.198 2112 Planarity : 0.008 0.129 2694 Dihedral : 4.962 43.877 2079 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.85 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.19), residues: 1854 helix: -0.42 (0.40), residues: 159 sheet: -0.45 (0.20), residues: 576 loop : -1.35 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 206 TYR 0.018 0.001 TYR C 111 PHE 0.239 0.005 PHE F 264 TRP 0.014 0.001 TRP D 136 HIS 0.007 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (14868) covalent geometry : angle 0.73132 / 0.40 (20322) SS BOND : bond 0.00182 / 0.08 ( 3) SS BOND : angle 2.44492 / 1.39 ( 6) hydrogen bonds : bond 0.03352 / 2.27 ( 459) hydrogen bonds : angle 5.99075 / 4.12 ( 1224) Misc. bond : bond 0.05075 / 2.81 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.053 Fit side-chains revert: symmetry clash REVERT: A 111 TYR cc_start: 0.7280 (p90) cc_final: 0.7070 (p90) REVERT: A 120 TRP cc_start: 0.6410 (p90) cc_final: 0.5464 (p90) REVERT: A 252 LYS cc_start: 0.7098 (mttt) cc_final: 0.5811 (tptt) REVERT: A 269 ARG cc_start: 0.7084 (ptp90) cc_final: 0.6100 (mmt90) REVERT: A 317 LYS cc_start: 0.7683 (pptt) cc_final: 0.7243 (pptt) REVERT: A 318 ASP cc_start: 0.7719 (t70) cc_final: 0.7390 (t0) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0565 time to fit residues: 3.3315 Evaluate side-chains 42 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.089 Evaluate side-chains 32 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 189 TRP cc_start: 0.5665 (m100) cc_final: 0.5262 (m100) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0413 time to fit residues: 1.7268 Evaluate side-chains 28 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 152 optimal weight: 7.9990 chunk 14 optimal weight: 0.0370 chunk 163 optimal weight: 0.0030 chunk 23 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 112 optimal weight: 0.1980 chunk 67 optimal weight: 10.0000 overall best weight: 0.6472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.133172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.122302 restraints weight = 7674.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.124996 restraints weight = 4984.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.126850 restraints weight = 3394.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.128302 restraints weight = 2447.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.129388 restraints weight = 1804.817| |-----------------------------------------------------------------------------| r_work (final): 0.3947 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.140137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.131820 restraints weight = 8127.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.133959 restraints weight = 5289.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.135763 restraints weight = 3655.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.137021 restraints weight = 2527.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.137857 restraints weight = 1763.271| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4400 moved from start: 0.6185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 14881 Z= 0.183 Angle : 0.656 10.807 20328 Z= 0.347 Chirality : 0.046 0.176 2112 Planarity : 0.007 0.100 2694 Dihedral : 5.011 44.873 2079 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.85 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.19), residues: 1854 helix: -0.35 (0.40), residues: 159 sheet: -0.48 (0.20), residues: 582 loop : -1.36 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 206 TYR 0.013 0.001 TYR A 145 PHE 0.146 0.004 PHE B 264 TRP 0.016 0.001 TRP D 105 HIS 0.005 0.001 HIS D 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (14868) covalent geometry : angle 0.65455 / 0.35 (20322) SS BOND : bond 0.00215 / 0.10 ( 3) SS BOND : angle 2.45320 / 1.40 ( 6) hydrogen bonds : bond 0.03348 / 2.26 ( 459) hydrogen bonds : angle 6.00966 / 4.14 ( 1224) Misc. bond : bond 0.04465 / 2.58 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1313.86 seconds wall clock time: 23 minutes 47.37 seconds (1427.37 seconds total)