Starting phenix.real_space_refine on Fri May 16 07:42:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rk5_19260/05_2025/8rk5_19260.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rk5_19260/05_2025/8rk5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8rk5_19260/05_2025/8rk5_19260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rk5_19260/05_2025/8rk5_19260.map" model { file = "/net/cci-nas-00/data/ceres_data/8rk5_19260/05_2025/8rk5_19260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rk5_19260/05_2025/8rk5_19260.cif" } resolution = 4.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: E, F, C, D Time building chain proxies: 7.83, per 1000 atoms: 0.54 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: 4.17 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.11 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: 4.98 Time building geometry restraints manager: 4.62 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: 0.10 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.290 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4375 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 : 21.86 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (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 TRP 0.019 0.001 TRP B 189 HIS 0.003 0.001 HIS A 298 PHE 0.018 0.001 PHE A 128 TYR 0.019 0.002 TYR E 82 ARG 0.011 0.001 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.12721 ( 459) hydrogen bonds : angle 6.81945 ( 1224) SS BOND : bond 0.00546 ( 3) SS BOND : angle 2.12715 ( 6) covalent geometry : bond 0.00289 (14868) covalent geometry : angle 0.67393 (20322) Misc. bond : bond 0.48083 ( 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 62 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.246 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: 0.1366 time to fit residues: 10.1290 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 : 0.260 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 : 0.270 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: 0.1428 time to fit residues: 11.2347 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 : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 76 optimal weight: 0.0980 chunk 47 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 74 optimal weight: 0.0040 chunk 143 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 166 optimal weight: 9.9990 overall best weight: 2.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 309 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 = 0.4039 r_free = 0.4039 target = 0.134315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.126112 restraints weight = 7823.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.128484 restraints weight = 4908.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.130222 restraints weight = 3190.748| |-----------------------------------------------------------------------------| r_work (final): 0.3974 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.128891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.119133 restraints weight = 7208.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.121636 restraints weight = 4650.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.123366 restraints weight = 3166.231| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4563 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 14881 Z= 0.225 Angle : 0.732 11.668 20328 Z= 0.390 Chirality : 0.048 0.202 2112 Planarity : 0.006 0.062 2694 Dihedral : 4.883 22.905 2079 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.18), residues: 1854 helix: 0.08 (0.38), residues: 138 sheet: 0.03 (0.20), residues: 576 loop : -1.27 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 127 HIS 0.003 0.001 HIS A 298 PHE 0.065 0.003 PHE B 264 TYR 0.021 0.002 TYR D 126 ARG 0.010 0.001 ARG C 268 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 459) hydrogen bonds : angle 6.59527 ( 1224) SS BOND : bond 0.00277 ( 3) SS BOND : angle 2.63673 ( 6) covalent geometry : bond 0.00417 (14868) covalent geometry : angle 0.73035 (20322) Misc. bond : bond 0.05418 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.265 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1174 time to fit residues: 6.9509 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 : 0.258 Evaluate side-chains 51 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.244 Fit side-chains REVERT: A 136 TRP cc_start: 0.6541 (m100) cc_final: 0.6190 (m100) REVERT: A 169 VAL cc_start: 0.5815 (p) cc_final: 0.5395 (p) REVERT: A 269 ARG cc_start: 0.6222 (ptp90) cc_final: 0.5716 (mmt90) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1563 time to fit residues: 9.4405 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 : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 104 optimal weight: 0.0370 chunk 169 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 9.9990 chunk 92 optimal weight: 0.0000 chunk 8 optimal weight: 0.0870 chunk 93 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 overall best weight: 0.3440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4041 r_free = 0.4041 target = 0.134245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.125609 restraints weight = 7762.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.128044 restraints weight = 4983.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.129822 restraints weight = 3335.297| |-----------------------------------------------------------------------------| r_work (final): 0.3969 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.129383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.120177 restraints weight = 7820.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.122347 restraints weight = 5163.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.123969 restraints weight = 3562.298| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4539 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 14881 Z= 0.278 Angle : 0.884 13.397 20328 Z= 0.479 Chirality : 0.053 0.357 2112 Planarity : 0.015 0.295 2694 Dihedral : 5.426 39.344 2079 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.40 % Allowed : 4.04 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.17), residues: 1854 helix: -0.75 (0.37), residues: 135 sheet: 0.01 (0.21), residues: 534 loop : -1.60 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP D 127 HIS 0.021 0.003 HIS B 215 PHE 0.069 0.005 PHE B 264 TYR 0.039 0.003 TYR C 35 ARG 0.044 0.003 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.05050 ( 459) hydrogen bonds : angle 6.92818 ( 1224) SS BOND : bond 0.00295 ( 3) SS BOND : angle 2.52352 ( 6) covalent geometry : bond 0.00541 (14868) covalent geometry : angle 0.88288 (20322) Misc. bond : bond 0.05450 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 240 TYR cc_start: 0.5498 (m-80) cc_final: 0.5266 (m-80) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0876 time to fit residues: 4.8464 Evaluate side-chains 35 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.269 Evaluate side-chains 45 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 136 TRP cc_start: 0.6398 (m100) cc_final: 0.6194 (m100) REVERT: A 169 VAL cc_start: 0.5663 (p) cc_final: 0.5248 (p) outliers start: 2 outliers final: 0 residues processed: 45 average time/residue: 0.1589 time to fit residues: 8.5355 Evaluate side-chains 35 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 145 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 chunk 108 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 170 optimal weight: 0.0040 overall best weight: 2.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4041 r_free = 0.4041 target = 0.134071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.125902 restraints weight = 7692.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.128353 restraints weight = 4835.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.130044 restraints weight = 3161.894| |-----------------------------------------------------------------------------| r_work (final): 0.3977 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.130654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.120478 restraints weight = 7616.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.122999 restraints weight = 4927.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.124849 restraints weight = 3368.160| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4532 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.029 2.292 14881 Z= 2.905 Angle : 0.898 13.397 20328 Z= 0.491 Chirality : 0.053 0.358 2112 Planarity : 0.015 0.295 2694 Dihedral : 5.427 39.240 2079 Min Nonbonded Distance : 0.134 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.17), residues: 1854 helix: -0.75 (0.37), residues: 135 sheet: 0.01 (0.21), residues: 534 loop : -1.60 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP D 127 HIS 0.021 0.003 HIS B 215 PHE 0.063 0.005 PHE F 264 TYR 0.039 0.003 TYR C 35 ARG 0.044 0.003 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.05049 ( 459) hydrogen bonds : angle 6.93017 ( 1224) SS BOND : bond 0.01153 ( 3) SS BOND : angle 3.30198 ( 6) covalent geometry : bond 0.00570 (14868) covalent geometry : angle 0.89638 (20322) Misc. bond : bond 1.11625 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0875 time to fit residues: 4.7285 Evaluate side-chains 35 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.258 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 : 0.246 Fit side-chains revert: symmetry clash REVERT: A 169 VAL cc_start: 0.5648 (p) cc_final: 0.5235 (p) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1217 time to fit residues: 6.3826 Evaluate side-chains 34 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 34 optimal weight: 20.0000 chunk 161 optimal weight: 8.9990 chunk 134 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 144 optimal weight: 6.9990 chunk 165 optimal weight: 0.0000 chunk 135 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 149 optimal weight: 0.0870 chunk 107 optimal weight: 0.2980 chunk 182 optimal weight: 0.8980 overall best weight: 0.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 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 = 0.4053 r_free = 0.4053 target = 0.135410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.126551 restraints weight = 8056.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.129087 restraints weight = 5117.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.130746 restraints weight = 3395.361| |-----------------------------------------------------------------------------| r_work (final): 0.3981 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.131559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.121111 restraints weight = 7096.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.123837 restraints weight = 4464.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.125743 restraints weight = 3003.785| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4547 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.256 14881 Z= 0.290 Angle : 0.822 10.855 20328 Z= 0.451 Chirality : 0.053 0.253 2112 Planarity : 0.012 0.243 2694 Dihedral : 5.266 26.598 2079 Min Nonbonded Distance : 1.514 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.85 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.17), residues: 1854 helix: -1.22 (0.35), residues: 135 sheet: -0.22 (0.21), residues: 528 loop : -1.77 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP A 120 HIS 0.009 0.002 HIS C 298 PHE 0.185 0.006 PHE F 264 TYR 0.039 0.003 TYR A 35 ARG 0.043 0.003 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 459) hydrogen bonds : angle 6.98896 ( 1224) SS BOND : bond 0.00235 ( 3) SS BOND : angle 2.46937 ( 6) covalent geometry : bond 0.00630 (14868) covalent geometry : angle 0.82139 (20322) Misc. bond : bond 0.05873 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.276 Fit side-chains revert: symmetry clash REVERT: B 218 VAL cc_start: 0.7142 (t) cc_final: 0.6856 (t) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0809 time to fit residues: 4.4091 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 : 0.250 Evaluate side-chains 51 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 TRP cc_start: 0.7011 (p90) cc_final: 0.6062 (p90) REVERT: A 188 ARG cc_start: 0.4844 (ptm160) cc_final: 0.4638 (ptm160) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1389 time to fit residues: 8.5509 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 : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 84 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 141 optimal weight: 0.0870 chunk 1 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 HIS A 298 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.133936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.125675 restraints weight = 7714.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.128122 restraints weight = 4849.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.129917 restraints weight = 3198.429| |-----------------------------------------------------------------------------| r_work (final): 0.3968 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.132779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.123238 restraints weight = 6935.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.125689 restraints weight = 4361.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.127494 restraints weight = 2933.810| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4555 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 14881 Z= 0.230 Angle : 0.860 19.895 20328 Z= 0.450 Chirality : 0.051 0.258 2112 Planarity : 0.011 0.216 2694 Dihedral : 5.364 33.009 2079 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.61 % Allowed : 2.83 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.17), residues: 1854 helix: -1.31 (0.34), residues: 135 sheet: -0.35 (0.21), residues: 528 loop : -1.88 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP C 127 HIS 0.072 0.005 HIS C 298 PHE 0.162 0.005 PHE C 129 TYR 0.033 0.003 TYR D 145 ARG 0.042 0.003 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 459) hydrogen bonds : angle 6.99933 ( 1224) SS BOND : bond 0.00212 ( 3) SS BOND : angle 2.57235 ( 6) covalent geometry : bond 0.00451 (14868) covalent geometry : angle 0.85947 (20322) Misc. bond : bond 0.05459 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: B 218 VAL cc_start: 0.7138 (t) cc_final: 0.6876 (t) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0841 time to fit residues: 4.6865 Evaluate side-chains 34 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.283 Evaluate side-chains 50 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 120 TRP cc_start: 0.6851 (p90) cc_final: 0.6543 (p90) REVERT: A 197 SER cc_start: 0.5011 (t) cc_final: 0.4315 (m) REVERT: A 270 TYR cc_start: 0.5711 (t80) cc_final: 0.5480 (t80) outliers start: 3 outliers final: 0 residues processed: 48 average time/residue: 0.1020 time to fit residues: 6.2596 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 : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 75 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 52 optimal weight: 0.3980 chunk 146 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 HIS ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 HIS A 309 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 = 0.3949 r_free = 0.3949 target = 0.127994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.120380 restraints weight = 7741.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.122594 restraints weight = 4836.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.124226 restraints weight = 3165.095| |-----------------------------------------------------------------------------| r_work (final): 0.3888 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.127795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.117925 restraints weight = 7568.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.120564 restraints weight = 4864.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.122485 restraints weight = 3278.184| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4765 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 14881 Z= 0.275 Angle : 0.849 11.876 20328 Z= 0.456 Chirality : 0.052 0.209 2112 Planarity : 0.010 0.157 2694 Dihedral : 5.601 21.617 2079 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.17), residues: 1854 helix: -1.40 (0.34), residues: 135 sheet: -0.56 (0.20), residues: 543 loop : -1.99 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.006 TRP A 105 HIS 0.023 0.004 HIS C 298 PHE 0.064 0.004 PHE E 264 TYR 0.042 0.004 TYR D 145 ARG 0.040 0.003 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 459) hydrogen bonds : angle 6.96877 ( 1224) SS BOND : bond 0.00262 ( 3) SS BOND : angle 2.84696 ( 6) covalent geometry : bond 0.00569 (14868) covalent geometry : angle 0.84760 (20322) Misc. bond : bond 0.05531 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: B 110 HIS cc_start: 0.5700 (m170) cc_final: 0.5402 (m170) REVERT: B 218 VAL cc_start: 0.7343 (t) cc_final: 0.6996 (t) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1219 time to fit residues: 6.0389 Evaluate side-chains 31 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.235 Evaluate side-chains 51 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.248 Fit side-chains REVERT: A 126 TYR cc_start: 0.4861 (p90) cc_final: 0.4284 (p90) REVERT: A 169 VAL cc_start: 0.5652 (p) cc_final: 0.5450 (p) REVERT: A 203 PRO cc_start: 0.6946 (Cg_exo) cc_final: 0.6728 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1126 time to fit residues: 7.2635 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 : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.2424 > 50: distance: 0 - 1: 22.510 distance: 1 - 2: 33.390 distance: 2 - 3: 32.774 distance: 2 - 4: 34.658 distance: 4 - 5: 18.140 distance: 5 - 6: 42.097 distance: 5 - 8: 33.825 distance: 6 - 7: 11.338 distance: 6 - 13: 32.410 distance: 8 - 9: 22.595 distance: 9 - 10: 15.725 distance: 10 - 11: 25.701 distance: 11 - 12: 14.041 distance: 13 - 14: 32.388 distance: 14 - 15: 27.964 distance: 14 - 17: 16.353 distance: 15 - 16: 52.359 distance: 15 - 24: 39.679 distance: 17 - 18: 14.599 distance: 18 - 19: 15.137 distance: 18 - 20: 9.692 distance: 19 - 21: 15.321 distance: 20 - 22: 4.747 distance: 21 - 23: 20.082 distance: 22 - 23: 19.793 distance: 24 - 25: 32.143 distance: 24 - 30: 45.337 distance: 25 - 26: 52.838 distance: 25 - 28: 49.197 distance: 26 - 27: 43.308 distance: 26 - 31: 46.924 distance: 28 - 29: 39.898 distance: 29 - 30: 56.141 distance: 31 - 32: 66.611 distance: 32 - 33: 29.265 distance: 32 - 35: 51.315 distance: 33 - 34: 28.055 distance: 33 - 39: 41.415 distance: 35 - 36: 45.286 distance: 36 - 37: 20.969 distance: 36 - 38: 23.000 distance: 39 - 40: 41.392 distance: 40 - 41: 9.174 distance: 40 - 43: 28.734 distance: 41 - 42: 11.654 distance: 41 - 48: 28.804 distance: 43 - 44: 13.403 distance: 44 - 45: 45.243 distance: 45 - 46: 27.487 distance: 46 - 47: 46.794 distance: 48 - 49: 33.692 distance: 49 - 50: 43.181 distance: 49 - 52: 49.302 distance: 50 - 51: 40.020 distance: 50 - 53: 16.183 distance: 53 - 54: 27.365 distance: 54 - 55: 31.266 distance: 54 - 57: 29.053 distance: 55 - 56: 22.622 distance: 55 - 61: 12.241 distance: 57 - 58: 24.644 distance: 58 - 59: 32.853 distance: 58 - 60: 13.595 distance: 61 - 62: 34.348 distance: 62 - 63: 25.735 distance: 62 - 65: 42.620 distance: 63 - 64: 40.438 distance: 63 - 70: 16.932 distance: 65 - 66: 19.873 distance: 66 - 67: 62.395 distance: 67 - 68: 49.030 distance: 67 - 69: 41.347 distance: 70 - 71: 12.432 distance: 71 - 72: 7.753 distance: 71 - 74: 5.846 distance: 72 - 73: 9.991 distance: 74 - 75: 7.978 distance: 75 - 76: 27.185 distance: 75 - 77: 10.298 distance: 76 - 78: 26.666 distance: 77 - 79: 12.337 distance: 78 - 80: 21.986 distance: 79 - 80: 10.993