Starting phenix.real_space_refine on Fri Jul 3 03:30:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r3g_18864/07_2026/8r3g_18864.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r3g_18864/07_2026/8r3g_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_18864/07_2026/8r3g_18864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r3g_18864/07_2026/8r3g_18864.map" model { file = "/net/cci-nas-00/data/ceres_data/8r3g_18864/07_2026/8r3g_18864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r3g_18864/07_2026/8r3g_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-dev-6108/lib/python3.11/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: 3.02, per 1000 atoms: 0.25 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: 0.91 Conformation dependent library (CDL) restraints added in 358.1 milliseconds 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: 1.94 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: 2.43 Time building geometry restraints manager: 1.16 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: 14582 2.15 - 4.30: 2079 4.30 - 6.45: 212 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: 1269 0.084 - 0.169: 553 0.169 - 0.253: 108 0.253 - 0.337: 39 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: 4.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.800 Find NCS groups from input model: 0.220 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:1.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5176 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= 0.855 Angle : 1.533 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 are 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/Z covalent geometry : bond 0.01334 / 0.85 (12304) covalent geometry : angle 1.53304 / 1.07 (16923) hydrogen bonds : bond 0.18693 / 12.29 ( 694) hydrogen bonds : angle 7.14085 / 5.11 ( 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 : 0.282 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: 0.6906 (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: 0.7345 (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: 0.5087 (mtp) cc_final: 0.4762 (ttp) REVERT: D 145 VAL cc_start: 0.7442 (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: 0.1141 time to fit residues: 61.5468 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 : 0.384 ------------------------------------------------------------------------------- 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: 20.0000 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... 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 = 0.4106 r_free = 0.4106 target = 0.091656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.074087 restraints weight = 51852.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.076913 restraints weight = 33184.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.079140 restraints weight = 23224.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.080916 restraints weight = 17288.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.082066 restraints weight = 13475.272| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12304 Z= 0.193 Angle : 0.760 8.476 16923 Z= 0.413 Chirality : 0.049 0.237 1980 Planarity : 0.006 0.074 1878 Dihedral : 21.098 168.784 2326 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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 are not related in a simple way. whole: 0.40 (0.23), residues: 1324 helix: 0.75 (0.18), residues: 748 sheet: -0.67 (0.37), residues: 164 loop : 0.05 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 49 TYR 0.026 0.002 TYR C 274 PHE 0.038 0.004 PHE A 139 TRP 0.004 0.001 TRP C 122 HIS 0.003 0.001 HIS D 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (12304) covalent geometry : angle 0.75997 / 0.41 (16923) hydrogen bonds : bond 0.06175 / 4.19 ( 694) hydrogen bonds : angle 4.97025 / 3.63 ( 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 244 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.436 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: C 16 LEU cc_start: 0.9031 (mm) cc_final: 0.8471 (mm) REVERT: C 20 GLN cc_start: 0.8548 (mt0) cc_final: 0.7957 (mm110) REVERT: C 35 ILE cc_start: 0.7369 (mm) cc_final: 0.6993 (mm) REVERT: C 201 TYR cc_start: 0.6097 (p90) cc_final: 0.5719 (p90) REVERT: A 145 VAL cc_start: 0.8452 (t) cc_final: 0.7857 (t) REVERT: A 175 ARG cc_start: 0.8701 (mmm-85) cc_final: 0.8388 (tpp80) REVERT: A 274 TYR cc_start: 0.6784 (m-80) cc_final: 0.6448 (m-80) REVERT: A 326 LEU cc_start: 0.6016 (tp) cc_final: 0.5778 (tt) REVERT: B 171 PHE cc_start: 0.5517 (m-80) cc_final: 0.4990 (m-10) REVERT: B 201 TYR cc_start: 0.5754 (p90) cc_final: 0.5485 (p90) REVERT: D 12 LEU cc_start: 0.8888 (mt) cc_final: 0.8492 (mp) REVERT: D 114 SER cc_start: 0.8327 (m) cc_final: 0.7648 (t) REVERT: D 145 VAL cc_start: 0.8493 (t) cc_final: 0.7905 (t) REVERT: D 175 ARG cc_start: 0.8708 (mmm-85) cc_final: 0.8157 (tpp80) REVERT: D 326 LEU cc_start: 0.6053 (tp) cc_final: 0.5800 (tt) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.0992 time to fit residues: 35.1614 Evaluate side-chains 165 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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: 3.9990 chunk 41 optimal weight: 3.9990 chunk 70 optimal weight: 30.0000 chunk 21 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.092568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.075657 restraints weight = 52025.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.078356 restraints weight = 33890.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.080420 restraints weight = 24010.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.081874 restraints weight = 18106.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.083073 restraints weight = 14513.028| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12304 Z= 0.157 Angle : 0.678 8.763 16923 Z= 0.371 Chirality : 0.044 0.238 1980 Planarity : 0.005 0.066 1878 Dihedral : 21.087 176.092 2326 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % 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 are not related in a simple way. whole: 0.43 (0.23), residues: 1324 helix: 0.78 (0.18), residues: 760 sheet: -0.13 (0.38), residues: 156 loop : -0.25 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 250 TYR 0.015 0.002 TYR D 215 PHE 0.023 0.003 PHE D 271 TRP 0.005 0.001 TRP B 122 HIS 0.004 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 (12304) covalent geometry : angle 0.67783 / 0.37 (16923) hydrogen bonds : bond 0.05113 / 3.44 ( 694) hydrogen bonds : angle 4.72832 / 3.44 ( 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 210 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.439 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 16 LEU cc_start: 0.9144 (mm) cc_final: 0.8284 (mm) REVERT: C 20 GLN cc_start: 0.8570 (mt0) cc_final: 0.7890 (mm110) REVERT: C 35 ILE cc_start: 0.7683 (mm) cc_final: 0.7414 (mm) REVERT: C 54 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8230 (mm-30) REVERT: C 132 VAL cc_start: 0.9357 (p) cc_final: 0.8571 (t) REVERT: C 201 TYR cc_start: 0.6352 (p90) cc_final: 0.5861 (p90) REVERT: C 327 VAL cc_start: 0.8648 (t) cc_final: 0.8413 (t) REVERT: A 114 SER cc_start: 0.8454 (m) cc_final: 0.7717 (t) REVERT: A 175 ARG cc_start: 0.8730 (mmm-85) cc_final: 0.8388 (tpp80) REVERT: B 54 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8293 (mm-30) REVERT: B 171 PHE cc_start: 0.7123 (m-80) cc_final: 0.6689 (m-10) REVERT: B 201 TYR cc_start: 0.6089 (p90) cc_final: 0.5797 (p90) REVERT: B 237 LEU cc_start: 0.9018 (tp) cc_final: 0.8713 (tp) REVERT: B 327 VAL cc_start: 0.8642 (t) cc_final: 0.8286 (t) REVERT: D 114 SER cc_start: 0.8468 (m) cc_final: 0.7737 (t) REVERT: D 175 ARG cc_start: 0.8762 (mmm-85) cc_final: 0.8282 (tpp80) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.0942 time to fit residues: 29.0727 Evaluate side-chains 158 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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: 1.9990 chunk 16 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 63 optimal weight: 0.4980 chunk 115 optimal weight: 0.9980 chunk 99 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 239 HIS B 6 GLN B 239 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.088796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.071635 restraints weight = 54523.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.074313 restraints weight = 34550.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.076371 restraints weight = 24303.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.077832 restraints weight = 18326.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.079092 restraints weight = 14688.177| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 12304 Z= 0.156 Angle : 0.664 16.323 16923 Z= 0.359 Chirality : 0.043 0.225 1980 Planarity : 0.004 0.064 1878 Dihedral : 21.084 178.791 2326 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % 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 are not related in a simple way. whole: 0.45 (0.23), residues: 1324 helix: 0.85 (0.19), residues: 754 sheet: -0.18 (0.37), residues: 162 loop : -0.32 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 167 TYR 0.023 0.002 TYR B 78 PHE 0.028 0.003 PHE A 318 TRP 0.004 0.001 TRP D 122 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (12304) covalent geometry : angle 0.66420 / 0.36 (16923) hydrogen bonds : bond 0.04494 / 3.03 ( 694) hydrogen bonds : angle 4.54765 / 3.31 ( 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 209 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.349 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 35 ILE cc_start: 0.7669 (mm) cc_final: 0.7310 (mm) REVERT: C 54 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8328 (mm-30) REVERT: C 125 LYS cc_start: 0.8457 (mtpt) cc_final: 0.8152 (tttt) REVERT: C 201 TYR cc_start: 0.6350 (p90) cc_final: 0.5907 (p90) REVERT: C 290 MSE cc_start: 0.5159 (mmp) cc_final: 0.4158 (mmp) REVERT: A 159 MSE cc_start: 0.5416 (mmm) cc_final: 0.5198 (mmm) REVERT: A 175 ARG cc_start: 0.8603 (mmm-85) cc_final: 0.8257 (tpp80) REVERT: B 54 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8383 (mm-30) REVERT: B 101 LEU cc_start: 0.9209 (tp) cc_final: 0.8830 (tp) REVERT: B 148 THR cc_start: 0.8566 (t) cc_final: 0.8241 (t) REVERT: B 237 LEU cc_start: 0.8995 (tp) cc_final: 0.8773 (tp) REVERT: B 241 ILE cc_start: 0.8315 (mm) cc_final: 0.8085 (mm) REVERT: B 327 VAL cc_start: 0.8905 (t) cc_final: 0.8556 (t) REVERT: D 175 ARG cc_start: 0.8672 (mmm-85) cc_final: 0.8244 (tpp80) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.0981 time to fit residues: 29.5568 Evaluate side-chains 155 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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: 20.0000 chunk 121 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 53 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 0.0980 chunk 64 optimal weight: 7.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.086697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.069884 restraints weight = 55223.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.072316 restraints weight = 35987.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.074253 restraints weight = 25618.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.075638 restraints weight = 19567.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.076707 restraints weight = 15903.547| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12304 Z= 0.178 Angle : 0.658 7.407 16923 Z= 0.363 Chirality : 0.042 0.229 1980 Planarity : 0.005 0.072 1878 Dihedral : 21.065 179.489 2326 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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 are not related in a simple way. whole: 0.54 (0.23), residues: 1324 helix: 0.97 (0.19), residues: 756 sheet: -0.09 (0.37), residues: 160 loop : -0.43 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 30 TYR 0.025 0.002 TYR C 78 PHE 0.045 0.004 PHE D 139 TRP 0.007 0.002 TRP C 122 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (12304) covalent geometry : angle 0.65790 / 0.36 (16923) hydrogen bonds : bond 0.04517 / 3.06 ( 694) hydrogen bonds : angle 4.64934 / 3.38 ( 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 198 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.307 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 16 LEU cc_start: 0.8768 (mm) cc_final: 0.8022 (mm) REVERT: C 54 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8296 (mm-30) REVERT: C 132 VAL cc_start: 0.9636 (t) cc_final: 0.9398 (p) REVERT: C 201 TYR cc_start: 0.6615 (p90) cc_final: 0.6196 (p90) REVERT: C 290 MSE cc_start: 0.5258 (mmp) cc_final: 0.4531 (mmp) REVERT: A 12 LEU cc_start: 0.9316 (mp) cc_final: 0.9114 (mt) REVERT: A 51 LEU cc_start: 0.9140 (tp) cc_final: 0.8686 (mt) REVERT: A 175 ARG cc_start: 0.8650 (mmm-85) cc_final: 0.8256 (tpp80) REVERT: A 204 LEU cc_start: 0.8547 (mt) cc_final: 0.8326 (mt) REVERT: B 15 LEU cc_start: 0.9020 (mp) cc_final: 0.7829 (mp) REVERT: B 54 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8314 (mm-30) REVERT: B 88 MSE cc_start: 0.7378 (tpp) cc_final: 0.6872 (tpp) REVERT: B 92 LEU cc_start: 0.7062 (mt) cc_final: 0.6792 (mt) REVERT: B 120 SER cc_start: 0.8041 (m) cc_final: 0.7834 (m) REVERT: B 237 LEU cc_start: 0.8987 (tp) cc_final: 0.8783 (tp) REVERT: B 241 ILE cc_start: 0.8504 (mm) cc_final: 0.8262 (mm) REVERT: D 12 LEU cc_start: 0.8930 (mt) cc_final: 0.8700 (mp) REVERT: D 51 LEU cc_start: 0.9149 (tp) cc_final: 0.8659 (mt) REVERT: D 175 ARG cc_start: 0.8791 (mmm-85) cc_final: 0.8360 (tpp80) REVERT: D 204 LEU cc_start: 0.8565 (mt) cc_final: 0.8341 (mt) REVERT: D 327 VAL cc_start: 0.8193 (p) cc_final: 0.7945 (m) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1061 time to fit residues: 30.3802 Evaluate side-chains 147 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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: 4.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 79 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 HIS B 6 GLN B 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.084479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.067573 restraints weight = 56128.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.070107 restraints weight = 35519.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.072073 restraints weight = 25012.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.073438 restraints weight = 18923.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.074591 restraints weight = 15317.044| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12304 Z= 0.191 Angle : 0.670 13.258 16923 Z= 0.368 Chirality : 0.042 0.225 1980 Planarity : 0.005 0.073 1878 Dihedral : 21.039 178.706 2326 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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 are not related in a simple way. whole: 0.48 (0.23), residues: 1324 helix: 0.89 (0.18), residues: 760 sheet: 0.09 (0.38), residues: 158 loop : -0.48 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 175 TYR 0.017 0.002 TYR B 201 PHE 0.041 0.003 PHE A 139 TRP 0.009 0.002 TRP C 122 HIS 0.003 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.19 (12304) covalent geometry : angle 0.66985 / 0.37 (16923) hydrogen bonds : bond 0.04467 / 2.99 ( 694) hydrogen bonds : angle 4.64236 / 3.36 ( 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 184 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.466 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: A 51 LEU cc_start: 0.9084 (tp) cc_final: 0.8783 (mt) REVERT: A 88 MSE cc_start: 0.6930 (ptp) cc_final: 0.6448 (ptp) REVERT: A 175 ARG cc_start: 0.8687 (mmm-85) cc_final: 0.8282 (tpp80) REVERT: B 15 LEU cc_start: 0.8953 (mp) cc_final: 0.7948 (mp) REVERT: B 88 MSE cc_start: 0.7542 (tpp) cc_final: 0.7164 (tpp) REVERT: B 92 LEU cc_start: 0.7054 (mt) cc_final: 0.6664 (mt) REVERT: B 160 MSE cc_start: 0.4932 (ptm) cc_final: 0.4664 (ptp) REVERT: B 237 LEU cc_start: 0.9081 (tp) cc_final: 0.8869 (tp) REVERT: D 51 LEU cc_start: 0.9100 (tp) cc_final: 0.8704 (mt) REVERT: D 327 VAL cc_start: 0.8275 (p) cc_final: 0.8005 (m) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.0945 time to fit residues: 26.0873 Evaluate side-chains 138 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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: 4.9990 chunk 70 optimal weight: 30.0000 chunk 54 optimal weight: 0.0980 chunk 137 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.083995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.066959 restraints weight = 56478.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.069567 restraints weight = 35498.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.071545 restraints weight = 24760.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.073011 restraints weight = 18684.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.073972 restraints weight = 14930.908| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12304 Z= 0.164 Angle : 0.616 8.244 16923 Z= 0.343 Chirality : 0.041 0.225 1980 Planarity : 0.004 0.072 1878 Dihedral : 20.988 178.385 2326 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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 are not related in a simple way. whole: 0.61 (0.23), residues: 1324 helix: 1.06 (0.18), residues: 754 sheet: 0.00 (0.38), residues: 158 loop : -0.51 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 175 TYR 0.021 0.002 TYR B 201 PHE 0.042 0.003 PHE D 139 TRP 0.008 0.001 TRP B 122 HIS 0.004 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (12304) covalent geometry : angle 0.61630 / 0.34 (16923) hydrogen bonds : bond 0.04137 / 2.81 ( 694) hydrogen bonds : angle 4.57726 / 3.32 ( 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 180 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.426 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 201 TYR cc_start: 0.5994 (p90) cc_final: 0.5332 (p90) REVERT: A 51 LEU cc_start: 0.9210 (tp) cc_final: 0.8694 (mt) REVERT: A 175 ARG cc_start: 0.8710 (mmm-85) cc_final: 0.8160 (tpp80) REVERT: A 204 LEU cc_start: 0.8697 (mt) cc_final: 0.8481 (mt) REVERT: A 327 VAL cc_start: 0.8352 (p) cc_final: 0.7625 (m) REVERT: B 54 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8371 (mm-30) REVERT: B 88 MSE cc_start: 0.7735 (tpp) cc_final: 0.7384 (tpp) REVERT: B 92 LEU cc_start: 0.7099 (mt) cc_final: 0.6754 (mt) REVERT: D 51 LEU cc_start: 0.9084 (tp) cc_final: 0.8689 (mt) REVERT: D 175 ARG cc_start: 0.9033 (mmm-85) cc_final: 0.8276 (tpp80) REVERT: D 204 LEU cc_start: 0.8663 (mt) cc_final: 0.8446 (mt) REVERT: D 327 VAL cc_start: 0.8278 (p) cc_final: 0.7558 (m) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.0957 time to fit residues: 26.0595 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 : 0.417 ------------------------------------------------------------------------------- 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: 1.9990 chunk 92 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 chunk 113 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 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 = 0.3942 r_free = 0.3942 target = 0.083429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.066478 restraints weight = 52554.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.069013 restraints weight = 32688.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.070976 restraints weight = 22723.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.072427 restraints weight = 17074.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.073373 restraints weight = 13694.766| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12304 Z= 0.145 Angle : 0.621 7.975 16923 Z= 0.344 Chirality : 0.041 0.226 1980 Planarity : 0.004 0.073 1878 Dihedral : 20.949 178.169 2326 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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 are not related in a simple way. whole: 0.55 (0.23), residues: 1324 helix: 1.06 (0.19), residues: 754 sheet: 0.00 (0.38), residues: 158 loop : -0.64 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 129 TYR 0.022 0.002 TYR B 201 PHE 0.041 0.003 PHE D 139 TRP 0.005 0.001 TRP C 122 HIS 0.005 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (12304) covalent geometry : angle 0.62113 / 0.34 (16923) hydrogen bonds : bond 0.04012 / 2.71 ( 694) hydrogen bonds : angle 4.61352 / 3.34 ( 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 183 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.435 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: A 154 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8662 (mt-10) REVERT: A 175 ARG cc_start: 0.8689 (mmm-85) cc_final: 0.8154 (tpp80) REVERT: A 204 LEU cc_start: 0.8671 (mt) cc_final: 0.8469 (mt) REVERT: B 54 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8375 (mm-30) REVERT: B 88 MSE cc_start: 0.7813 (tpp) cc_final: 0.7607 (tpp) REVERT: B 92 LEU cc_start: 0.7245 (mt) cc_final: 0.7023 (mt) REVERT: D 175 ARG cc_start: 0.8980 (mmm-85) cc_final: 0.8294 (tpp80) REVERT: D 204 LEU cc_start: 0.8647 (mt) cc_final: 0.8428 (mt) REVERT: D 327 VAL cc_start: 0.7831 (p) cc_final: 0.7414 (t) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.0838 time to fit residues: 23.5794 Evaluate side-chains 138 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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: 2.9990 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 0.0370 chunk 109 optimal weight: 0.0980 chunk 95 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN D 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.084923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.067567 restraints weight = 54821.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.070234 restraints weight = 34319.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.072262 restraints weight = 23928.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.073826 restraints weight = 17943.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.074900 restraints weight = 14316.334| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.6276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12304 Z= 0.135 Angle : 0.625 9.840 16923 Z= 0.341 Chirality : 0.042 0.229 1980 Planarity : 0.004 0.074 1878 Dihedral : 20.909 177.887 2326 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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 are not related in a simple way. whole: 0.57 (0.23), residues: 1324 helix: 1.10 (0.19), residues: 754 sheet: 0.13 (0.38), residues: 148 loop : -0.75 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 52 TYR 0.009 0.001 TYR C 273 PHE 0.040 0.003 PHE A 139 TRP 0.006 0.001 TRP C 122 HIS 0.002 0.000 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (12304) covalent geometry : angle 0.62476 / 0.34 (16923) hydrogen bonds : bond 0.03894 / 2.67 ( 694) hydrogen bonds : angle 4.58445 / 3.33 ( 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 183 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.376 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: A 175 ARG cc_start: 0.8598 (mmm-85) cc_final: 0.8111 (tpp80) REVERT: A 204 LEU cc_start: 0.8611 (mt) cc_final: 0.8402 (mt) REVERT: B 54 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8284 (mm-30) REVERT: B 120 SER cc_start: 0.8570 (p) cc_final: 0.8127 (m) REVERT: B 144 ILE cc_start: 0.6726 (mp) cc_final: 0.6460 (mp) REVERT: B 201 TYR cc_start: 0.5879 (p90) cc_final: 0.5182 (p90) REVERT: D 175 ARG cc_start: 0.8896 (mmm-85) cc_final: 0.8285 (tpp80) REVERT: D 201 TYR cc_start: 0.8490 (p90) cc_final: 0.8090 (p90) REVERT: D 327 VAL cc_start: 0.8029 (p) cc_final: 0.7220 (t) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.0913 time to fit residues: 25.3261 Evaluate side-chains 143 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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: 5.9990 chunk 79 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 91 optimal weight: 0.0170 chunk 37 optimal weight: 0.5980 chunk 77 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.083513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.066666 restraints weight = 52826.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.069247 restraints weight = 32846.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.071253 restraints weight = 22660.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.072670 restraints weight = 16842.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.073892 restraints weight = 13422.305| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.6436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12304 Z= 0.133 Angle : 0.616 8.712 16923 Z= 0.337 Chirality : 0.041 0.230 1980 Planarity : 0.004 0.074 1878 Dihedral : 20.868 177.395 2326 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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 are not related in a simple way. whole: 0.56 (0.23), residues: 1324 helix: 1.09 (0.19), residues: 754 sheet: 0.10 (0.38), residues: 148 loop : -0.73 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 30 TYR 0.016 0.001 TYR C 274 PHE 0.040 0.003 PHE A 139 TRP 0.006 0.001 TRP C 122 HIS 0.002 0.000 HIS C 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (12304) covalent geometry : angle 0.61611 / 0.34 (16923) hydrogen bonds : bond 0.03865 / 2.63 ( 694) hydrogen bonds : angle 4.57096 / 3.32 ( 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 180 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.444 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: A 135 MSE cc_start: 0.6853 (tpp) cc_final: 0.6599 (mmt) REVERT: A 145 VAL cc_start: 0.8889 (t) cc_final: 0.8575 (t) REVERT: A 175 ARG cc_start: 0.8580 (mmm-85) cc_final: 0.8087 (tpp80) REVERT: A 204 LEU cc_start: 0.8611 (mt) cc_final: 0.8407 (mt) REVERT: A 236 MSE cc_start: 0.3571 (mtt) cc_final: 0.2882 (mtp) REVERT: B 54 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8387 (mm-30) REVERT: B 120 SER cc_start: 0.8639 (p) cc_final: 0.8230 (m) REVERT: D 175 ARG cc_start: 0.8881 (mmm-85) cc_final: 0.8249 (tpp80) REVERT: D 201 TYR cc_start: 0.8520 (p90) cc_final: 0.8134 (p90) REVERT: D 204 LEU cc_start: 0.8626 (mt) cc_final: 0.8384 (mt) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.0975 time to fit residues: 26.4969 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 : 0.430 ------------------------------------------------------------------------------- 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: 0.1980 chunk 123 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 70 optimal weight: 30.0000 chunk 67 optimal weight: 20.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 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 = 0.3962 r_free = 0.3962 target = 0.084116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.067012 restraints weight = 52635.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.069640 restraints weight = 32834.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.071631 restraints weight = 22761.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.072982 restraints weight = 16978.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.074172 restraints weight = 13634.367| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.6597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12304 Z= 0.138 Angle : 0.612 7.758 16923 Z= 0.338 Chirality : 0.041 0.231 1980 Planarity : 0.004 0.075 1878 Dihedral : 20.831 176.896 2326 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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 are not related in a simple way. whole: 0.55 (0.23), residues: 1324 helix: 1.13 (0.19), residues: 750 sheet: -0.08 (0.37), residues: 152 loop : -0.76 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 129 TYR 0.008 0.001 TYR B 273 PHE 0.038 0.003 PHE D 139 TRP 0.007 0.001 TRP C 122 HIS 0.003 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (12304) covalent geometry : angle 0.61232 / 0.34 (16923) hydrogen bonds : bond 0.03914 / 2.66 ( 694) hydrogen bonds : angle 4.55430 / 3.31 ( 1893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1956.18 seconds wall clock time: 34 minutes 40.95 seconds (2080.95 seconds total)