Starting phenix.real_space_refine on Sat Aug 23 11:49:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r3g_18864/08_2025/8r3g_18864.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r3g_18864/08_2025/8r3g_18864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r3g_18864/08_2025/8r3g_18864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r3g_18864/08_2025/8r3g_18864.map" model { file = "/net/cci-nas-00/data/ceres_data/8r3g_18864/08_2025/8r3g_18864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r3g_18864/08_2025/8r3g_18864.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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: 6 Type Number sf(0) Gaussians Se 48 7.20 5 P 82 5.49 5 S 8 5.16 5 C 7285 2.51 5 N 2090 2.21 5 O 2472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11985 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 324} Chain breaks: 1 Chain: "F" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 837 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "E" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 844 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 324} Chain breaks: 1 Restraints were copied for chains: D, C Time building chain proxies: 3.60, per 1000 atoms: 0.30 Number of scatterers: 11985 At special positions: 0 Unit cell: (146.316, 130.698, 88.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Se 48 33.99 S 8 16.00 P 82 15.00 O 2472 8.00 N 2090 7.00 C 7285 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 472.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2480 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 12 sheets defined 61.3% alpha, 13.1% beta 38 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'C' and resid 1 through 12 Processing helix chain 'C' and resid 12 through 33 Processing helix chain 'C' and resid 36 through 44 Processing helix chain 'C' and resid 47 through 61 Processing helix chain 'C' and resid 74 through 92 removed outlier: 5.160A pdb=" N ASP C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N THR C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL C 91 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 105 Processing helix chain 'C' and resid 121 through 139 removed outlier: 4.160A pdb=" N LYS C 125 " --> pdb=" O PRO C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 160 Processing helix chain 'C' and resid 185 through 198 Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 221 through 233 removed outlier: 3.704A pdb=" N VAL C 227 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 Processing helix chain 'C' and resid 254 through 264 Processing helix chain 'C' and resid 291 through 298 removed outlier: 3.704A pdb=" N ASP C 296 " --> pdb=" O ASP C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 310 through 318 Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.683A pdb=" N LYS A 10 " --> pdb=" O GLN A 6 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 33 Processing helix chain 'A' and resid 36 through 45 Processing helix chain 'A' and resid 47 through 61 Processing helix chain 'A' and resid 74 through 92 removed outlier: 3.695A pdb=" N ASP A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 removed outlier: 3.651A pdb=" N LEU A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 139 removed outlier: 4.160A pdb=" N LYS A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 160 Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 211 through 221 Processing helix chain 'A' and resid 221 through 233 removed outlier: 3.704A pdb=" N VAL A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.704A pdb=" N ASP A 296 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 318 Processing helix chain 'A' and resid 330 through 338 Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 12 through 33 Processing helix chain 'B' and resid 36 through 44 Processing helix chain 'B' and resid 47 through 61 Processing helix chain 'B' and resid 74 through 92 removed outlier: 5.159A pdb=" N ASP B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N THR B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 91 " --> pdb=" O THR B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 105 Processing helix chain 'B' and resid 121 through 139 removed outlier: 4.160A pdb=" N LYS B 125 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 160 Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 221 through 233 removed outlier: 3.705A pdb=" N VAL B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.705A pdb=" N ASP B 296 " --> pdb=" O ASP B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 310 through 318 Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.682A pdb=" N LYS D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU D 11 " --> pdb=" O ALA D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 33 Processing helix chain 'D' and resid 36 through 45 Processing helix chain 'D' and resid 47 through 61 Processing helix chain 'D' and resid 74 through 92 removed outlier: 3.695A pdb=" N ASP D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 105 removed outlier: 3.651A pdb=" N LEU D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 139 removed outlier: 4.161A pdb=" N LYS D 125 " --> pdb=" O PRO D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 160 Processing helix chain 'D' and resid 185 through 198 Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 221 through 233 removed outlier: 3.704A pdb=" N VAL D 227 " --> pdb=" O SER D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 Processing helix chain 'D' and resid 254 through 264 Processing helix chain 'D' and resid 291 through 298 removed outlier: 3.704A pdb=" N ASP D 296 " --> pdb=" O ASP D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 309 No H-bonds generated for 'chain 'D' and resid 307 through 309' Processing helix chain 'D' and resid 310 through 318 Processing helix chain 'D' and resid 330 through 338 Processing sheet with id=AA1, first strand: chain 'C' and resid 64 through 67 Processing sheet with id=AA2, first strand: chain 'C' and resid 109 through 113 removed outlier: 6.555A pdb=" N ASP C 109 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR C 328 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE C 111 " --> pdb=" O THR C 328 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE C 301 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL C 327 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA C 303 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ASP C 329 " --> pdb=" O ALA C 303 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU C 237 " --> pdb=" O ILE C 302 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL C 304 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N HIS C 239 " --> pdb=" O VAL C 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 242 through 243 removed outlier: 6.768A pdb=" N PHE C 275 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU C 269 " --> pdb=" O TYR C 273 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR C 273 " --> pdb=" O GLU C 269 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASN C 276 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL C 281 " --> pdb=" O ASN C 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 64 through 67 Processing sheet with id=AA5, first strand: chain 'A' and resid 109 through 113 removed outlier: 6.555A pdb=" N ASP A 109 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR A 328 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE A 111 " --> pdb=" O THR A 328 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A 301 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL A 327 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ASP A 329 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 237 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL A 304 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N HIS A 239 " --> pdb=" O VAL A 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 242 through 243 removed outlier: 6.767A pdb=" N PHE A 275 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU A 269 " --> pdb=" O TYR A 273 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN A 276 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A 281 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 67 Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 113 removed outlier: 6.555A pdb=" N ASP B 109 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR B 328 " --> pdb=" O ASP B 109 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE B 111 " --> pdb=" O THR B 328 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE B 301 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL B 327 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA B 303 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ASP B 329 " --> pdb=" O ALA B 303 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU B 237 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL B 304 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N HIS B 239 " --> pdb=" O VAL B 304 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 242 through 243 removed outlier: 6.767A pdb=" N PHE B 275 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU B 269 " --> pdb=" O TYR B 273 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR B 273 " --> pdb=" O GLU B 269 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASN B 276 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 281 " --> pdb=" O ASN B 276 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 64 through 67 Processing sheet with id=AB2, first strand: chain 'D' and resid 109 through 113 removed outlier: 6.556A pdb=" N ASP D 109 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR D 328 " --> pdb=" O ASP D 109 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE D 111 " --> pdb=" O THR D 328 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE D 301 " --> pdb=" O VAL D 325 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL D 327 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA D 303 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ASP D 329 " --> pdb=" O ALA D 303 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU D 237 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL D 304 " --> pdb=" O LEU D 237 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N HIS D 239 " --> pdb=" O VAL D 304 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 242 through 243 removed outlier: 6.767A pdb=" N PHE D 275 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU D 269 " --> pdb=" O TYR D 273 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR D 273 " --> pdb=" O GLU D 269 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN D 276 " --> pdb=" O VAL D 281 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL D 281 " --> pdb=" O ASN D 276 " (cutoff:3.500A) 601 hydrogen bonds defined for protein. 1707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 2.34 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.35: 3703 1.35 - 1.51: 3821 1.51 - 1.67: 4676 1.67 - 1.84: 8 1.84 - 2.00: 96 Bond restraints: 12304 Sorted by residual: bond pdb=" N VAL D 206 " pdb=" CA VAL D 206 " ideal model delta sigma weight residual 1.460 1.494 -0.035 7.50e-03 1.78e+04 2.13e+01 bond pdb=" N VAL A 206 " pdb=" CA VAL A 206 " ideal model delta sigma weight residual 1.460 1.494 -0.034 7.50e-03 1.78e+04 2.10e+01 bond pdb=" N VAL C 206 " pdb=" CA VAL C 206 " ideal model delta sigma weight residual 1.460 1.493 -0.033 7.50e-03 1.78e+04 1.99e+01 bond pdb=" N VAL B 206 " pdb=" CA VAL B 206 " ideal model delta sigma weight residual 1.460 1.493 -0.033 7.50e-03 1.78e+04 1.99e+01 bond pdb=" N LEU B 107 " pdb=" CA LEU B 107 " ideal model delta sigma weight residual 1.455 1.507 -0.052 1.25e-02 6.40e+03 1.75e+01 ... (remaining 12299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 14551 2.15 - 4.30: 2117 4.30 - 6.45: 205 6.45 - 8.60: 22 8.60 - 10.74: 28 Bond angle restraints: 16923 Sorted by residual: angle pdb=" C PHE C 205 " pdb=" N VAL C 206 " pdb=" CA VAL C 206 " ideal model delta sigma weight residual 122.59 114.90 7.69 7.20e-01 1.93e+00 1.14e+02 angle pdb=" C PHE B 205 " pdb=" N VAL B 206 " pdb=" CA VAL B 206 " ideal model delta sigma weight residual 122.59 114.90 7.69 7.20e-01 1.93e+00 1.14e+02 angle pdb=" C PHE D 205 " pdb=" N VAL D 206 " pdb=" CA VAL D 206 " ideal model delta sigma weight residual 122.59 116.43 6.16 7.20e-01 1.93e+00 7.31e+01 angle pdb=" C PHE A 205 " pdb=" N VAL A 206 " pdb=" CA VAL A 206 " ideal model delta sigma weight residual 122.59 116.46 6.13 7.20e-01 1.93e+00 7.24e+01 angle pdb=" N ARG B 175 " pdb=" CA ARG B 175 " pdb=" C ARG B 175 " ideal model delta sigma weight residual 110.53 99.79 10.74 1.32e+00 5.74e-01 6.62e+01 ... (remaining 16918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6931 35.97 - 71.93: 435 71.93 - 107.90: 18 107.90 - 143.87: 0 143.87 - 179.84: 2 Dihedral angle restraints: 7386 sinusoidal: 3546 harmonic: 3840 Sorted by residual: dihedral pdb=" C4' DC E 19 " pdb=" C3' DC E 19 " pdb=" O3' DC E 19 " pdb=" P DA E 20 " ideal model delta sinusoidal sigma weight residual 220.00 40.16 179.84 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC F 19 " pdb=" C3' DC F 19 " pdb=" O3' DC F 19 " pdb=" P DC F 20 " ideal model delta sinusoidal sigma weight residual 220.00 43.75 176.25 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C MSE D 88 " pdb=" N MSE D 88 " pdb=" CA MSE D 88 " pdb=" CB MSE D 88 " ideal model delta harmonic sigma weight residual -122.60 -132.12 9.52 0 2.50e+00 1.60e-01 1.45e+01 ... (remaining 7383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1275 0.084 - 0.169: 549 0.169 - 0.253: 107 0.253 - 0.337: 38 0.337 - 0.422: 11 Chirality restraints: 1980 Sorted by residual: chirality pdb=" CA VAL D 325 " pdb=" N VAL D 325 " pdb=" C VAL D 325 " pdb=" CB VAL D 325 " both_signs ideal model delta sigma weight residual False 2.44 2.86 -0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA VAL A 325 " pdb=" N VAL A 325 " pdb=" C VAL A 325 " pdb=" CB VAL A 325 " both_signs ideal model delta sigma weight residual False 2.44 2.86 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CA VAL C 325 " pdb=" N VAL C 325 " pdb=" C VAL C 325 " pdb=" CB VAL C 325 " both_signs ideal model delta sigma weight residual False 2.44 2.86 -0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 1977 not shown) Planarity restraints: 1878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 87 " 0.022 2.00e-02 2.50e+03 4.81e-02 2.31e+01 pdb=" C THR D 87 " -0.083 2.00e-02 2.50e+03 pdb=" O THR D 87 " 0.032 2.00e-02 2.50e+03 pdb=" N MSE D 88 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 87 " -0.022 2.00e-02 2.50e+03 4.81e-02 2.31e+01 pdb=" C THR A 87 " 0.083 2.00e-02 2.50e+03 pdb=" O THR A 87 " -0.032 2.00e-02 2.50e+03 pdb=" N MSE A 88 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 174 " 0.019 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C ALA A 174 " -0.069 2.00e-02 2.50e+03 pdb=" O ALA A 174 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG A 175 " 0.024 2.00e-02 2.50e+03 ... (remaining 1875 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1547 2.77 - 3.31: 11645 3.31 - 3.84: 20868 3.84 - 4.37: 26612 4.37 - 4.90: 39448 Nonbonded interactions: 100120 Sorted by model distance: nonbonded pdb=" OE2 GLU B 33 " pdb=" OH TYR B 78 " model vdw 2.243 3.040 nonbonded pdb=" OE2 GLU C 33 " pdb=" OH TYR C 78 " model vdw 2.243 3.040 nonbonded pdb=" NH2 ARG C 49 " pdb=" N6 DA E 28 " model vdw 2.253 3.200 nonbonded pdb=" OE2 GLU A 33 " pdb=" OH TYR A 78 " model vdw 2.259 3.040 nonbonded pdb=" OE2 GLU D 33 " pdb=" OH TYR D 78 " model vdw 2.259 3.040 ... (remaining 100115 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.910 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5193 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 0.099 12304 Z= 0.853 Angle : 1.540 10.744 16923 Z= 1.067 Chirality : 0.100 0.422 1980 Planarity : 0.007 0.048 1878 Dihedral : 19.042 179.837 4906 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.18 % Allowed : 5.16 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.21), residues: 1324 helix: -0.91 (0.16), residues: 732 sheet: -0.59 (0.35), residues: 156 loop : -0.21 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG B 167 TYR 0.049 0.010 TYR A 317 PHE 0.028 0.006 PHE B 57 TRP 0.010 0.005 TRP C 122 HIS 0.015 0.005 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.01344 (12304) covalent geometry : angle 1.54038 (16923) hydrogen bonds : bond 0.18693 ( 694) hydrogen bonds : angle 7.14085 ( 1893) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 393 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 20 GLN cc_start: 0.8013 (mt0) cc_final: 0.7503 (mm-40) REVERT: C 132 VAL cc_start: 0.8206 (t) cc_final: 0.7907 (p) REVERT: C 152 THR cc_start: 0.8581 (m) cc_final: 0.8272 (p) REVERT: C 173 PRO cc_start: 0.6274 (Cg_endo) cc_final: 0.5881 (Cg_exo) REVERT: C 304 VAL cc_start: 0.7403 (t) cc_final: 0.7123 (m) REVERT: A 145 VAL cc_start: 0.7381 (t) cc_final: 0.6907 (t) REVERT: B 29 ILE cc_start: 0.8635 (mt) cc_final: 0.8279 (mm) REVERT: B 35 ILE cc_start: 0.8725 (tt) cc_final: 0.8216 (tp) REVERT: B 101 LEU cc_start: 0.7635 (tp) cc_final: 0.7323 (tp) REVERT: B 132 VAL cc_start: 0.8259 (t) cc_final: 0.7993 (p) REVERT: B 152 THR cc_start: 0.8727 (m) cc_final: 0.8385 (p) REVERT: B 304 VAL cc_start: 0.7346 (t) cc_final: 0.7090 (m) REVERT: D 12 LEU cc_start: 0.8142 (mt) cc_final: 0.6583 (mt) REVERT: D 19 MSE cc_start: 0.5088 (mtp) cc_final: 0.4762 (ttp) REVERT: D 145 VAL cc_start: 0.7443 (t) cc_final: 0.7094 (t) REVERT: D 295 ILE cc_start: 0.8004 (pt) cc_final: 0.7693 (pt) outliers start: 2 outliers final: 0 residues processed: 395 average time/residue: 0.1370 time to fit residues: 73.3955 Evaluate side-chains 203 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.0070 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN A 252 ASN B 3 GLN B 6 GLN D 252 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.090539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.072846 restraints weight = 51134.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.075583 restraints weight = 32748.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.077761 restraints weight = 22941.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.079421 restraints weight = 17138.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.080725 restraints weight = 13494.964| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12304 Z= 0.169 Angle : 0.672 9.248 16923 Z= 0.367 Chirality : 0.044 0.192 1980 Planarity : 0.005 0.087 1878 Dihedral : 20.686 179.195 2326 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.23), residues: 1324 helix: 0.95 (0.18), residues: 764 sheet: -0.27 (0.36), residues: 156 loop : -0.07 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 52 TYR 0.015 0.002 TYR C 274 PHE 0.032 0.003 PHE D 139 TRP 0.003 0.001 TRP B 122 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00360 (12304) covalent geometry : angle 0.67204 (16923) hydrogen bonds : bond 0.04736 ( 694) hydrogen bonds : angle 4.64472 ( 1893) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 LEU cc_start: 0.8745 (mp) cc_final: 0.8078 (mp) REVERT: C 35 ILE cc_start: 0.7510 (mm) cc_final: 0.7157 (mm) REVERT: C 54 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8307 (mm-30) REVERT: C 78 TYR cc_start: 0.7165 (m-80) cc_final: 0.6892 (m-80) REVERT: C 201 TYR cc_start: 0.6192 (p90) cc_final: 0.5889 (p90) REVERT: C 304 VAL cc_start: 0.8769 (t) cc_final: 0.8015 (m) REVERT: C 327 VAL cc_start: 0.9005 (t) cc_final: 0.8608 (t) REVERT: A 12 LEU cc_start: 0.9354 (mp) cc_final: 0.9000 (mp) REVERT: A 175 ARG cc_start: 0.8709 (mmm-85) cc_final: 0.8411 (tpp80) REVERT: B 54 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8414 (mm-30) REVERT: B 78 TYR cc_start: 0.7134 (m-80) cc_final: 0.6819 (m-80) REVERT: B 304 VAL cc_start: 0.8631 (t) cc_final: 0.7766 (m) REVERT: B 327 VAL cc_start: 0.8929 (t) cc_final: 0.8418 (t) REVERT: D 12 LEU cc_start: 0.8981 (mt) cc_final: 0.8704 (mp) REVERT: D 175 ARG cc_start: 0.8694 (mmm-85) cc_final: 0.8256 (tpp80) REVERT: D 201 TYR cc_start: 0.7589 (p90) cc_final: 0.7387 (p90) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.1089 time to fit residues: 38.6079 Evaluate side-chains 171 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 115 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 42 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.087623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.070181 restraints weight = 53645.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.072861 restraints weight = 33645.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.074986 restraints weight = 23312.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.076474 restraints weight = 17327.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.077798 restraints weight = 13750.888| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12304 Z= 0.144 Angle : 0.588 9.532 16923 Z= 0.325 Chirality : 0.040 0.133 1980 Planarity : 0.005 0.067 1878 Dihedral : 20.532 178.811 2326 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.23), residues: 1324 helix: 1.28 (0.19), residues: 758 sheet: -0.19 (0.36), residues: 160 loop : -0.24 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 49 TYR 0.018 0.002 TYR B 201 PHE 0.022 0.002 PHE A 271 TRP 0.012 0.001 TRP C 122 HIS 0.003 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00305 (12304) covalent geometry : angle 0.58816 (16923) hydrogen bonds : bond 0.03928 ( 694) hydrogen bonds : angle 4.32415 ( 1893) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8462 (mm-30) REVERT: C 78 TYR cc_start: 0.7449 (m-80) cc_final: 0.7177 (m-80) REVERT: C 201 TYR cc_start: 0.7145 (p90) cc_final: 0.6932 (p90) REVERT: A 12 LEU cc_start: 0.9347 (mp) cc_final: 0.8969 (mt) REVERT: A 51 LEU cc_start: 0.9166 (tp) cc_final: 0.8602 (mt) REVERT: A 175 ARG cc_start: 0.8654 (mmm-85) cc_final: 0.8309 (tpp80) REVERT: A 204 LEU cc_start: 0.8539 (mt) cc_final: 0.8297 (mt) REVERT: B 54 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8342 (mm-30) REVERT: B 78 TYR cc_start: 0.7405 (m-80) cc_final: 0.7165 (m-80) REVERT: B 101 LEU cc_start: 0.9193 (tp) cc_final: 0.8820 (tp) REVERT: B 132 VAL cc_start: 0.9436 (t) cc_final: 0.9207 (p) REVERT: B 237 LEU cc_start: 0.8977 (tp) cc_final: 0.8764 (tp) REVERT: B 241 ILE cc_start: 0.8410 (mm) cc_final: 0.8201 (mm) REVERT: D 51 LEU cc_start: 0.9128 (tp) cc_final: 0.8570 (mt) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1183 time to fit residues: 36.9158 Evaluate side-chains 149 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 HIS B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.082396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.065726 restraints weight = 54916.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.068317 restraints weight = 33756.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.070254 restraints weight = 23223.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.071636 restraints weight = 17376.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.072790 restraints weight = 13901.193| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.6142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12304 Z= 0.165 Angle : 0.597 6.884 16923 Z= 0.332 Chirality : 0.040 0.145 1980 Planarity : 0.005 0.066 1878 Dihedral : 20.453 176.740 2326 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.23), residues: 1324 helix: 1.33 (0.18), residues: 756 sheet: 0.08 (0.37), residues: 160 loop : -0.40 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 175 TYR 0.018 0.002 TYR B 201 PHE 0.020 0.002 PHE D 271 TRP 0.011 0.002 TRP C 122 HIS 0.003 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00353 (12304) covalent geometry : angle 0.59745 (16923) hydrogen bonds : bond 0.03926 ( 694) hydrogen bonds : angle 4.51573 ( 1893) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 132 VAL cc_start: 0.9420 (p) cc_final: 0.9142 (t) REVERT: C 201 TYR cc_start: 0.7112 (p90) cc_final: 0.6890 (p90) REVERT: A 19 MSE cc_start: 0.6123 (ptm) cc_final: 0.5888 (ptp) REVERT: A 154 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8767 (mt-10) REVERT: A 175 ARG cc_start: 0.8618 (mmm-85) cc_final: 0.7840 (ttm-80) REVERT: A 327 VAL cc_start: 0.8680 (p) cc_final: 0.8341 (m) REVERT: B 59 LYS cc_start: 0.9410 (ttmt) cc_final: 0.9209 (ttmm) REVERT: B 132 VAL cc_start: 0.9483 (t) cc_final: 0.9001 (t) REVERT: B 160 MSE cc_start: 0.4228 (tpp) cc_final: 0.3474 (tpp) REVERT: D 12 LEU cc_start: 0.9150 (mt) cc_final: 0.8797 (mp) REVERT: D 154 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8722 (mt-10) REVERT: D 327 VAL cc_start: 0.8557 (p) cc_final: 0.7764 (m) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1023 time to fit residues: 28.7955 Evaluate side-chains 141 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 72 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 64 optimal weight: 0.0020 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 239 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.083784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.067045 restraints weight = 54827.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.069568 restraints weight = 34095.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.071557 restraints weight = 23612.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.072946 restraints weight = 17683.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.074152 restraints weight = 14218.410| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.6474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12304 Z= 0.123 Angle : 0.549 6.248 16923 Z= 0.303 Chirality : 0.039 0.145 1980 Planarity : 0.004 0.065 1878 Dihedral : 20.399 178.685 2326 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.23), residues: 1324 helix: 1.49 (0.19), residues: 764 sheet: 0.40 (0.38), residues: 154 loop : -0.54 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 175 TYR 0.008 0.001 TYR B 78 PHE 0.025 0.002 PHE D 139 TRP 0.008 0.001 TRP C 122 HIS 0.002 0.000 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00261 (12304) covalent geometry : angle 0.54852 (16923) hydrogen bonds : bond 0.03421 ( 694) hydrogen bonds : angle 4.31023 ( 1893) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 TYR cc_start: 0.7757 (m-80) cc_final: 0.7410 (m-80) REVERT: A 108 LYS cc_start: 0.7162 (ttmm) cc_final: 0.6836 (tptt) REVERT: A 154 GLU cc_start: 0.9146 (tm-30) cc_final: 0.8709 (mt-10) REVERT: A 175 ARG cc_start: 0.8521 (mmm-85) cc_final: 0.8085 (tpp80) REVERT: A 200 THR cc_start: 0.6836 (t) cc_final: 0.6609 (t) REVERT: A 327 VAL cc_start: 0.8440 (p) cc_final: 0.7991 (m) REVERT: D 12 LEU cc_start: 0.9125 (mt) cc_final: 0.8785 (mp) REVERT: D 201 TYR cc_start: 0.8474 (p90) cc_final: 0.8091 (p90) REVERT: D 274 TYR cc_start: 0.7286 (m-80) cc_final: 0.7042 (m-80) REVERT: D 327 VAL cc_start: 0.7823 (p) cc_final: 0.6973 (p) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.0994 time to fit residues: 28.2235 Evaluate side-chains 139 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 120 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN B 6 GLN B 61 GLN D 192 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.082860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.066387 restraints weight = 55349.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.068764 restraints weight = 35136.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.070651 restraints weight = 24673.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.071908 restraints weight = 18675.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.072934 restraints weight = 15243.758| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.6872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12304 Z= 0.148 Angle : 0.574 9.090 16923 Z= 0.316 Chirality : 0.039 0.137 1980 Planarity : 0.004 0.065 1878 Dihedral : 20.327 177.394 2326 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.23), residues: 1324 helix: 1.51 (0.19), residues: 758 sheet: 0.11 (0.38), residues: 162 loop : -0.51 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.008 0.001 TYR B 273 PHE 0.019 0.002 PHE D 271 TRP 0.020 0.002 TRP C 122 HIS 0.003 0.000 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00326 (12304) covalent geometry : angle 0.57382 (16923) hydrogen bonds : bond 0.03654 ( 694) hydrogen bonds : angle 4.41234 ( 1893) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 MSE cc_start: 0.5886 (mtm) cc_final: 0.5674 (mtp) REVERT: C 78 TYR cc_start: 0.7989 (m-80) cc_final: 0.7686 (m-80) REVERT: C 120 SER cc_start: 0.8600 (p) cc_final: 0.8204 (m) REVERT: C 237 LEU cc_start: 0.8899 (tp) cc_final: 0.8679 (tp) REVERT: A 154 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8701 (mt-10) REVERT: A 175 ARG cc_start: 0.8597 (mmm-85) cc_final: 0.8150 (tpp80) REVERT: B 120 SER cc_start: 0.8237 (p) cc_final: 0.7623 (m) REVERT: B 122 TRP cc_start: 0.7694 (p90) cc_final: 0.7099 (p90) REVERT: B 144 ILE cc_start: 0.6767 (mp) cc_final: 0.6466 (mp) REVERT: D 135 MSE cc_start: 0.6879 (tpp) cc_final: 0.6650 (tpp) REVERT: D 201 TYR cc_start: 0.8462 (p90) cc_final: 0.8037 (p90) REVERT: D 236 MSE cc_start: 0.3381 (mtt) cc_final: 0.2774 (mtt) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.0991 time to fit residues: 26.1364 Evaluate side-chains 136 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 94 optimal weight: 0.2980 chunk 70 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 92 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.081494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.065372 restraints weight = 56511.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.067680 restraints weight = 35799.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.069484 restraints weight = 25281.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.070797 restraints weight = 19205.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.071646 restraints weight = 15580.194| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.7345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12304 Z= 0.152 Angle : 0.578 6.473 16923 Z= 0.321 Chirality : 0.039 0.149 1980 Planarity : 0.004 0.068 1878 Dihedral : 20.312 178.330 2326 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.23), residues: 1324 helix: 1.55 (0.19), residues: 758 sheet: 0.12 (0.39), residues: 154 loop : -0.66 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 250 TYR 0.008 0.001 TYR D 28 PHE 0.020 0.002 PHE D 271 TRP 0.015 0.002 TRP C 122 HIS 0.003 0.000 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00329 (12304) covalent geometry : angle 0.57849 (16923) hydrogen bonds : bond 0.03702 ( 694) hydrogen bonds : angle 4.46750 ( 1893) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 63 LEU cc_start: 0.9193 (tp) cc_final: 0.8985 (tp) REVERT: C 78 TYR cc_start: 0.8006 (m-80) cc_final: 0.7758 (m-80) REVERT: C 120 SER cc_start: 0.8594 (p) cc_final: 0.8205 (m) REVERT: C 237 LEU cc_start: 0.8892 (tp) cc_final: 0.8647 (tp) REVERT: A 108 LYS cc_start: 0.7524 (ttmm) cc_final: 0.7068 (tptt) REVERT: A 175 ARG cc_start: 0.8632 (mmm-85) cc_final: 0.8103 (tpp80) REVERT: A 274 TYR cc_start: 0.7814 (m-80) cc_final: 0.7423 (m-80) REVERT: B 62 ASN cc_start: 0.9048 (m110) cc_final: 0.8825 (t0) REVERT: B 63 LEU cc_start: 0.9200 (tp) cc_final: 0.8931 (tp) REVERT: B 122 TRP cc_start: 0.7517 (p90) cc_final: 0.7150 (p90) REVERT: D 135 MSE cc_start: 0.7139 (tpp) cc_final: 0.6935 (tpp) REVERT: D 139 PHE cc_start: 0.8882 (m-10) cc_final: 0.8558 (m-10) REVERT: D 154 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8620 (mt-10) REVERT: D 170 LEU cc_start: 0.9226 (tp) cc_final: 0.8883 (mm) REVERT: D 201 TYR cc_start: 0.8372 (p90) cc_final: 0.8041 (p90) REVERT: D 236 MSE cc_start: 0.3336 (mtt) cc_final: 0.3131 (mtt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.0949 time to fit residues: 24.5620 Evaluate side-chains 134 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.0470 chunk 92 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 101 optimal weight: 0.2980 chunk 73 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN D 192 HIS D 286 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.083247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.067026 restraints weight = 53651.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.069414 restraints weight = 34139.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.071326 restraints weight = 24014.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.072702 restraints weight = 18121.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.073733 restraints weight = 14514.647| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.7539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12304 Z= 0.130 Angle : 0.582 12.326 16923 Z= 0.316 Chirality : 0.039 0.194 1980 Planarity : 0.004 0.068 1878 Dihedral : 20.278 178.495 2326 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.24), residues: 1324 helix: 1.69 (0.19), residues: 760 sheet: -0.01 (0.39), residues: 152 loop : -0.63 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 250 TYR 0.010 0.001 TYR B 317 PHE 0.031 0.002 PHE A 139 TRP 0.011 0.001 TRP C 122 HIS 0.003 0.000 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00281 (12304) covalent geometry : angle 0.58179 (16923) hydrogen bonds : bond 0.03551 ( 694) hydrogen bonds : angle 4.37293 ( 1893) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 TYR cc_start: 0.7989 (m-80) cc_final: 0.7720 (m-80) REVERT: C 120 SER cc_start: 0.8426 (p) cc_final: 0.7896 (m) REVERT: A 108 LYS cc_start: 0.7573 (ttmm) cc_final: 0.7122 (tptt) REVERT: A 175 ARG cc_start: 0.8509 (mmm-85) cc_final: 0.8011 (tpp80) REVERT: A 274 TYR cc_start: 0.7589 (m-80) cc_final: 0.7255 (m-80) REVERT: A 290 MSE cc_start: 0.3913 (mmt) cc_final: 0.3614 (mmt) REVERT: B 62 ASN cc_start: 0.9148 (m110) cc_final: 0.8810 (t0) REVERT: B 63 LEU cc_start: 0.9251 (tp) cc_final: 0.9024 (tp) REVERT: B 122 TRP cc_start: 0.7828 (p90) cc_final: 0.7103 (p90) REVERT: B 335 LYS cc_start: 0.9088 (tppp) cc_final: 0.8542 (tttt) REVERT: D 108 LYS cc_start: 0.7587 (ttmm) cc_final: 0.7119 (tptt) REVERT: D 135 MSE cc_start: 0.7085 (tpp) cc_final: 0.6880 (tpp) REVERT: D 139 PHE cc_start: 0.8804 (m-10) cc_final: 0.8580 (m-10) REVERT: D 170 LEU cc_start: 0.9224 (tp) cc_final: 0.8853 (mm) REVERT: D 201 TYR cc_start: 0.8314 (p90) cc_final: 0.7910 (p90) REVERT: D 236 MSE cc_start: 0.3426 (mtt) cc_final: 0.3160 (mtt) REVERT: D 274 TYR cc_start: 0.7312 (m-80) cc_final: 0.6997 (m-80) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.0864 time to fit residues: 23.0019 Evaluate side-chains 136 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.082856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.066673 restraints weight = 53912.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.069090 restraints weight = 34257.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.070924 restraints weight = 24050.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.072276 restraints weight = 18252.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.073282 restraints weight = 14691.361| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.7762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12304 Z= 0.129 Angle : 0.573 8.007 16923 Z= 0.316 Chirality : 0.039 0.130 1980 Planarity : 0.004 0.069 1878 Dihedral : 20.229 177.884 2326 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.24), residues: 1324 helix: 1.66 (0.19), residues: 760 sheet: -0.17 (0.39), residues: 156 loop : -0.63 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 250 TYR 0.007 0.001 TYR D 215 PHE 0.018 0.002 PHE D 271 TRP 0.006 0.001 TRP D 122 HIS 0.004 0.001 HIS D 286 Details of bonding type rmsd covalent geometry : bond 0.00279 (12304) covalent geometry : angle 0.57277 (16923) hydrogen bonds : bond 0.03535 ( 694) hydrogen bonds : angle 4.48662 ( 1893) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 THR cc_start: 0.8635 (p) cc_final: 0.8321 (p) REVERT: C 120 SER cc_start: 0.8318 (p) cc_final: 0.7733 (m) REVERT: A 108 LYS cc_start: 0.7602 (ttmm) cc_final: 0.7234 (tptt) REVERT: A 170 LEU cc_start: 0.9219 (tp) cc_final: 0.8875 (mm) REVERT: A 175 ARG cc_start: 0.8480 (mmm-85) cc_final: 0.7976 (tpp80) REVERT: A 201 TYR cc_start: 0.8301 (p90) cc_final: 0.7791 (p90) REVERT: A 274 TYR cc_start: 0.7525 (m-80) cc_final: 0.7100 (m-80) REVERT: B 62 ASN cc_start: 0.9147 (m110) cc_final: 0.8886 (t0) REVERT: B 63 LEU cc_start: 0.9240 (tp) cc_final: 0.9039 (tp) REVERT: B 122 TRP cc_start: 0.7764 (p90) cc_final: 0.7229 (p90) REVERT: B 160 MSE cc_start: 0.4113 (mtp) cc_final: 0.3454 (mtp) REVERT: B 335 LYS cc_start: 0.9096 (tppp) cc_final: 0.8526 (tttt) REVERT: D 108 LYS cc_start: 0.7598 (ttmm) cc_final: 0.7166 (tptt) REVERT: D 139 PHE cc_start: 0.8866 (m-10) cc_final: 0.8605 (m-10) REVERT: D 170 LEU cc_start: 0.9246 (tp) cc_final: 0.8879 (mm) REVERT: D 201 TYR cc_start: 0.8268 (p90) cc_final: 0.7882 (p90) REVERT: D 236 MSE cc_start: 0.3526 (mtt) cc_final: 0.3257 (mtt) REVERT: D 274 TYR cc_start: 0.7389 (m-80) cc_final: 0.7070 (m-80) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.0865 time to fit residues: 21.9463 Evaluate side-chains 134 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 54 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 95 optimal weight: 0.1980 chunk 124 optimal weight: 1.9990 chunk 91 optimal weight: 0.0270 chunk 37 optimal weight: 0.0270 chunk 77 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS A 286 HIS B 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.083384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.066567 restraints weight = 56820.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.069064 restraints weight = 35590.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.071005 restraints weight = 24790.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.072296 restraints weight = 18651.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.073426 restraints weight = 15118.015| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.7952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12304 Z= 0.126 Angle : 0.578 8.389 16923 Z= 0.315 Chirality : 0.039 0.180 1980 Planarity : 0.004 0.071 1878 Dihedral : 20.185 177.758 2326 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.24), residues: 1324 helix: 1.63 (0.19), residues: 760 sheet: -0.17 (0.39), residues: 156 loop : -0.63 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 250 TYR 0.007 0.001 TYR D 28 PHE 0.019 0.002 PHE D 271 TRP 0.009 0.001 TRP D 122 HIS 0.004 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00275 (12304) covalent geometry : angle 0.57815 (16923) hydrogen bonds : bond 0.03442 ( 694) hydrogen bonds : angle 4.47483 ( 1893) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 16 LEU cc_start: 0.9221 (mm) cc_final: 0.8911 (mm) REVERT: C 19 MSE cc_start: 0.6533 (mtm) cc_final: 0.5953 (mtp) REVERT: C 32 THR cc_start: 0.8650 (p) cc_final: 0.8355 (p) REVERT: C 120 SER cc_start: 0.8485 (p) cc_final: 0.7813 (m) REVERT: C 241 ILE cc_start: 0.8327 (mm) cc_final: 0.8110 (mm) REVERT: A 108 LYS cc_start: 0.7598 (ttmm) cc_final: 0.7212 (tptt) REVERT: A 135 MSE cc_start: 0.7249 (mmm) cc_final: 0.6736 (tpp) REVERT: A 139 PHE cc_start: 0.8904 (m-10) cc_final: 0.8576 (m-10) REVERT: A 154 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8531 (mt-10) REVERT: A 170 LEU cc_start: 0.9267 (tp) cc_final: 0.8876 (mm) REVERT: A 175 ARG cc_start: 0.8407 (mmm-85) cc_final: 0.7898 (tpp80) REVERT: A 201 TYR cc_start: 0.8322 (p90) cc_final: 0.7824 (p90) REVERT: A 291 GLN cc_start: 0.8949 (mt0) cc_final: 0.8438 (mp10) REVERT: B 62 ASN cc_start: 0.9228 (m110) cc_final: 0.8929 (t0) REVERT: B 63 LEU cc_start: 0.9281 (tp) cc_final: 0.9078 (tp) REVERT: B 160 MSE cc_start: 0.4000 (mtp) cc_final: 0.3355 (mtp) REVERT: B 335 LYS cc_start: 0.9100 (tppp) cc_final: 0.8525 (tttt) REVERT: D 108 LYS cc_start: 0.7513 (ttmm) cc_final: 0.7083 (tptt) REVERT: D 135 MSE cc_start: 0.6676 (tpp) cc_final: 0.6411 (tpp) REVERT: D 139 PHE cc_start: 0.8845 (m-10) cc_final: 0.8619 (m-10) REVERT: D 170 LEU cc_start: 0.9310 (tp) cc_final: 0.8926 (mm) REVERT: D 201 TYR cc_start: 0.8276 (p90) cc_final: 0.7892 (p90) REVERT: D 274 TYR cc_start: 0.7585 (m-80) cc_final: 0.7251 (m-80) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.0831 time to fit residues: 21.3866 Evaluate side-chains 136 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 134 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.077168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.061523 restraints weight = 58306.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.063753 restraints weight = 36442.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.065495 restraints weight = 25317.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.066755 restraints weight = 19139.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.067275 restraints weight = 15502.049| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.8357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 12304 Z= 0.242 Angle : 0.692 9.745 16923 Z= 0.380 Chirality : 0.041 0.166 1980 Planarity : 0.005 0.076 1878 Dihedral : 20.418 177.442 2326 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.23), residues: 1324 helix: 1.09 (0.18), residues: 780 sheet: -0.33 (0.40), residues: 152 loop : -0.80 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 52 TYR 0.011 0.002 TYR C 317 PHE 0.019 0.003 PHE D 271 TRP 0.015 0.002 TRP D 122 HIS 0.005 0.002 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00514 (12304) covalent geometry : angle 0.69165 (16923) hydrogen bonds : bond 0.04613 ( 694) hydrogen bonds : angle 4.89782 ( 1893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1929.42 seconds wall clock time: 34 minutes 12.29 seconds (2052.29 seconds total)