Starting phenix.real_space_refine on Sat Jul 4 05:03:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ofu_70443/07_2026/9ofu_70443.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ofu_70443/07_2026/9ofu_70443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ofu_70443/07_2026/9ofu_70443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ofu_70443/07_2026/9ofu_70443.map" model { file = "/net/cci-nas-00/data/ceres_data/9ofu_70443/07_2026/9ofu_70443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ofu_70443/07_2026/9ofu_70443.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 P 66 5.49 5 S 71 5.16 5 C 6151 2.51 5 N 1775 2.21 5 O 1990 1.98 5 H 8591 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 18644 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 668 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "F" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 685 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "C" Number of atoms: 4609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 4609 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain breaks: 4 Chain: "D" Number of atoms: 4035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 4035 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain breaks: 7 Chain: "A" Number of atoms: 4640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 4640 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 4 Chain: "B" Number of atoms: 4007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 4007 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain breaks: 7 Time building chain proxies: 3.53, per 1000 atoms: 0.19 Number of scatterers: 18644 At special positions: 0 Unit cell: (121.18, 122.01, 116.2, 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) S 71 16.00 P 66 15.00 O 1990 8.00 N 1775 7.00 C 6151 6.00 H 8591 1.00 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: 1.66 Conformation dependent library (CDL) restraints added in 596.4 milliseconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2042 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 45.9% alpha, 22.7% beta 30 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'C' and resid 3 through 23 Processing helix chain 'C' and resid 26 through 31 removed outlier: 3.910A pdb=" N SER C 31 " --> pdb=" O HIS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 54 Processing helix chain 'C' and resid 65 through 68 Processing helix chain 'C' and resid 69 through 75 Processing helix chain 'C' and resid 94 through 99 removed outlier: 4.109A pdb=" N TYR C 98 " --> pdb=" O ASN C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 110 through 114 Processing helix chain 'C' and resid 120 through 128 Processing helix chain 'C' and resid 162 through 166 Processing helix chain 'C' and resid 208 through 212 removed outlier: 3.516A pdb=" N ILE C 212 " --> pdb=" O PRO C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 242 removed outlier: 3.690A pdb=" N LEU C 241 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 removed outlier: 3.651A pdb=" N LEU C 249 " --> pdb=" O GLU C 245 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 245 through 250' Processing helix chain 'C' and resid 254 through 258 Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.633A pdb=" N LEU C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N MET C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE C 274 " --> pdb=" O HIS C 270 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 275 " --> pdb=" O HIS C 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 26 removed outlier: 3.652A pdb=" N MET D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 53 Processing helix chain 'D' and resid 70 through 82 Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 110 through 115 removed outlier: 4.131A pdb=" N TRP D 114 " --> pdb=" O PRO D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 123 Processing helix chain 'D' and resid 124 through 126 No H-bonds generated for 'chain 'D' and resid 124 through 126' Processing helix chain 'D' and resid 127 through 135 Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 297 through 302 removed outlier: 3.581A pdb=" N LEU D 301 " --> pdb=" O GLN D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 329 removed outlier: 3.854A pdb=" N PHE D 322 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLN D 323 " --> pdb=" O ARG D 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 23 Processing helix chain 'A' and resid 26 through 33 removed outlier: 3.814A pdb=" N HIS A 32 " --> pdb=" O ASN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 54 removed outlier: 3.732A pdb=" N ALA A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 removed outlier: 4.301A pdb=" N CYS A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 69' Processing helix chain 'A' and resid 69 through 75 removed outlier: 4.147A pdb=" N LYS A 73 " --> pdb=" O CYS A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.899A pdb=" N TYR A 98 " --> pdb=" O ASN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.514A pdb=" N LEU A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.554A pdb=" N ILE A 212 " --> pdb=" O PRO A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 243 Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.862A pdb=" N LEU A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 245 through 250' Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.790A pdb=" N LEU A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 37 through 53 Processing helix chain 'B' and resid 70 through 82 Processing helix chain 'B' and resid 102 through 108 removed outlier: 3.554A pdb=" N VAL B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.821A pdb=" N TRP B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 305 through 310 removed outlier: 4.256A pdb=" N PHE B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 329 removed outlier: 3.734A pdb=" N VAL B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N VAL B 326 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS B 327 " --> pdb=" O GLN B 323 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 80 through 81 removed outlier: 3.619A pdb=" N VAL C 200 " --> pdb=" O HIS C 176 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS C 176 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C 175 " --> pdb=" O ARG C 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 231 through 234 removed outlier: 5.899A pdb=" N ARG C 224 " --> pdb=" O SER C 232 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N CYS C 234 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU C 222 " --> pdb=" O CYS C 234 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 223 " --> pdb=" O CYS C 316 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS C 316 " --> pdb=" O SER C 223 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLY C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA C 288 " --> pdb=" O GLY C 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 231 through 234 removed outlier: 5.899A pdb=" N ARG C 224 " --> pdb=" O SER C 232 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N CYS C 234 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU C 222 " --> pdb=" O CYS C 234 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 223 " --> pdb=" O CYS C 316 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS C 316 " --> pdb=" O SER C 223 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS C 313 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 96 through 99 removed outlier: 3.507A pdb=" N ALA D 249 " --> pdb=" O PHE D 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 272 through 275 removed outlier: 3.664A pdb=" N PHE D 273 " --> pdb=" O ASN D 371 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN D 371 " --> pdb=" O PHE D 273 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER D 275 " --> pdb=" O CYS D 369 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 336 through 337 removed outlier: 3.713A pdb=" N MET D 349 " --> pdb=" O PHE D 337 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 88 through 91 removed outlier: 6.499A pdb=" N MET A 88 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N THR A 83 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 90 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS A 203 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET A 196 " --> pdb=" O TYR A 180 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 200 " --> pdb=" O HIS A 176 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 174 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU A 204 " --> pdb=" O HIS A 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 231 through 234 removed outlier: 6.292A pdb=" N ARG A 224 " --> pdb=" O SER A 232 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N CYS A 234 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A 222 " --> pdb=" O CYS A 234 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 231 through 234 removed outlier: 6.292A pdb=" N ARG A 224 " --> pdb=" O SER A 232 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N CYS A 234 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A 222 " --> pdb=" O CYS A 234 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET A 286 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 84 through 87 Processing sheet with id=AB2, first strand: chain 'B' and resid 285 through 286 removed outlier: 3.511A pdb=" N PHE B 285 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS B 369 " --> pdb=" O SER B 275 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 338 removed outlier: 3.683A pdb=" N PHE B 337 " --> pdb=" O MET B 349 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1062 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 4.13 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 8562 1.02 - 1.21: 31 1.21 - 1.41: 4350 1.41 - 1.61: 5931 1.61 - 1.81: 113 Bond restraints: 18987 Sorted by residual: bond pdb=" NE ARG B 276 " pdb=" HE ARG B 276 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C3' DC E 14 " pdb=" C2' DC E 14 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C3' DC E 10 " pdb=" C2' DC E 10 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.84e+00 bond pdb=" C3' DC F 52 " pdb=" C2' DC F 52 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.67e+00 bond pdb=" C3' DA F 37 " pdb=" C2' DA F 37 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.83e+00 ... (remaining 18982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.03: 33732 6.03 - 12.07: 3 12.07 - 18.10: 0 18.10 - 24.13: 2 24.13 - 30.17: 4 Bond angle restraints: 33741 Sorted by residual: angle pdb="HG22 THR A 102 " pdb=" CG2 THR A 102 " pdb="HG23 THR A 102 " ideal model delta sigma weight residual 109.00 78.83 30.17 3.00e+00 1.11e-01 1.01e+02 angle pdb="HG21 THR A 102 " pdb=" CG2 THR A 102 " pdb="HG22 THR A 102 " ideal model delta sigma weight residual 109.00 78.92 30.08 3.00e+00 1.11e-01 1.01e+02 angle pdb=" CB THR A 102 " pdb=" CG2 THR A 102 " pdb="HG23 THR A 102 " ideal model delta sigma weight residual 110.00 81.87 28.13 3.00e+00 1.11e-01 8.79e+01 angle pdb=" CB THR A 102 " pdb=" CG2 THR A 102 " pdb="HG21 THR A 102 " ideal model delta sigma weight residual 110.00 81.98 28.02 3.00e+00 1.11e-01 8.73e+01 angle pdb=" CB THR A 102 " pdb=" CG2 THR A 102 " pdb="HG22 THR A 102 " ideal model delta sigma weight residual 110.00 132.45 -22.45 3.00e+00 1.11e-01 5.60e+01 ... (remaining 33736 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.36: 8120 27.36 - 54.73: 716 54.73 - 82.09: 101 82.09 - 109.46: 7 109.46 - 136.82: 1 Dihedral angle restraints: 8945 sinusoidal: 5173 harmonic: 3772 Sorted by residual: dihedral pdb=" C THR C 83 " pdb=" N THR C 83 " pdb=" CA THR C 83 " pdb=" CB THR C 83 " ideal model delta harmonic sigma weight residual -122.00 -132.14 10.14 0 2.50e+00 1.60e-01 1.64e+01 dihedral pdb=" C4' DC F 52 " pdb=" C3' DC F 52 " pdb=" O3' DC F 52 " pdb=" P DA F 53 " ideal model delta sinusoidal sigma weight residual 220.00 83.18 136.82 1 3.50e+01 8.16e-04 1.36e+01 dihedral pdb=" CA PRO A 117 " pdb=" C PRO A 117 " pdb=" N CYS A 118 " pdb=" CA CYS A 118 " ideal model delta harmonic sigma weight residual 180.00 162.90 17.10 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 8942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1377 0.064 - 0.127: 208 0.127 - 0.191: 12 0.191 - 0.254: 0 0.254 - 0.318: 1 Chirality restraints: 1598 Sorted by residual: chirality pdb=" CA THR C 83 " pdb=" N THR C 83 " pdb=" C THR C 83 " pdb=" CB THR C 83 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA ILE C 91 " pdb=" N ILE C 91 " pdb=" C ILE C 91 " pdb=" CB ILE C 91 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CA ILE C 202 " pdb=" N ILE C 202 " pdb=" C ILE C 202 " pdb=" CB ILE C 202 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 1595 not shown) Planarity restraints: 2579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN C 283 " -0.188 2.00e-02 2.50e+03 4.00e-01 2.41e+03 pdb=" CD GLN C 283 " 0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN C 283 " 0.177 2.00e-02 2.50e+03 pdb=" NE2 GLN C 283 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN C 283 " 0.671 2.00e-02 2.50e+03 pdb="HE22 GLN C 283 " -0.667 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 103 " -0.161 2.00e-02 2.50e+03 1.83e-01 5.03e+02 pdb=" CD GLN A 103 " 0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN A 103 " 0.158 2.00e-02 2.50e+03 pdb=" NE2 GLN A 103 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 103 " 0.274 2.00e-02 2.50e+03 pdb="HE22 GLN A 103 " -0.275 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 299 " -0.072 2.00e-02 2.50e+03 7.22e-02 7.81e+01 pdb=" CD GLN A 299 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLN A 299 " 0.056 2.00e-02 2.50e+03 pdb=" NE2 GLN A 299 " 0.008 2.00e-02 2.50e+03 pdb="HE21 GLN A 299 " -0.112 2.00e-02 2.50e+03 pdb="HE22 GLN A 299 " 0.099 2.00e-02 2.50e+03 ... (remaining 2576 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 451 2.11 - 2.73: 30984 2.73 - 3.36: 50753 3.36 - 3.98: 64554 3.98 - 4.60: 100961 Nonbonded interactions: 247703 Sorted by model distance: nonbonded pdb=" HE3 MET A 99 " pdb=" HB3 MET A 150 " model vdw 1.490 2.440 nonbonded pdb=" HB3 LEU A 261 " pdb="HH21 ARG A 285 " model vdw 1.495 2.270 nonbonded pdb=" HD1 HIS A 259 " pdb=" H LEU A 261 " model vdw 1.508 2.100 nonbonded pdb=" HE2 MET A 99 " pdb=" HE1 MET A 150 " model vdw 1.512 2.440 nonbonded pdb="HG22 VAL C 81 " pdb=" HB ILE C 89 " model vdw 1.541 2.440 ... (remaining 247698 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' and (resid 1 through 54 or resid 65 through 129 or resid 141 through \ 180 or resid 195 through 324)) selection = (chain 'C' and (resid 1 through 180 or resid 195 through 212 or resid 218 throug \ h 324)) } ncs_group { reference = (chain 'B' and (resid 6 through 177 or resid 210 through 253 or resid 271 throug \ h 309 or resid 313 through 373)) selection = (chain 'D' and (resid 6 through 27 or resid 35 through 88 or resid 93 through 13 \ 4 or resid 171 through 221 or resid 247 through 253 or resid 271 through 373)) } 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: 4.540 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: 0.130 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.990 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 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 : 0.005 0.036 10396 Z= 0.330 Angle : 0.680 7.976 14304 Z= 0.463 Chirality : 0.044 0.318 1598 Planarity : 0.004 0.043 1575 Dihedral : 20.090 136.820 4005 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 16.23 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.28), residues: 1014 helix: 1.01 (0.28), residues: 353 sheet: -2.03 (0.32), residues: 244 loop : -0.02 (0.33), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 276 TYR 0.018 0.002 TYR C 180 PHE 0.014 0.001 PHE D 283 TRP 0.031 0.002 TRP D 348 HIS 0.007 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.33 (10396) covalent geometry : angle 0.68005 / 0.46 (14304) hydrogen bonds : bond 0.18120 / 19.81 ( 449) hydrogen bonds : angle 8.36695 / 10.92 ( 1216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.503 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 145 SER cc_start: 0.7951 (t) cc_final: 0.7557 (m) REVERT: C 161 MET cc_start: 0.7075 (tpp) cc_final: 0.6862 (tpp) REVERT: D 49 MET cc_start: 0.7313 (mmm) cc_final: 0.6629 (mmm) REVERT: A 72 LEU cc_start: 0.6784 (tp) cc_final: 0.6529 (tp) REVERT: A 310 GLN cc_start: 0.6407 (mm110) cc_final: 0.5587 (pm20) REVERT: B 23 SER cc_start: 0.8719 (p) cc_final: 0.8276 (m) REVERT: B 25 MET cc_start: 0.8195 (tpp) cc_final: 0.7992 (tpp) REVERT: B 274 ILE cc_start: 0.8127 (tp) cc_final: 0.7789 (tp) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2117 time to fit residues: 79.0322 Evaluate side-chains 193 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS C 270 HIS A 208 HIS ** B 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.202106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.165239 restraints weight = 37210.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.167890 restraints weight = 32802.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.169702 restraints weight = 25998.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.170147 restraints weight = 18910.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.170521 restraints weight = 17656.164| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10396 Z= 0.176 Angle : 0.599 6.768 14304 Z= 0.338 Chirality : 0.041 0.195 1598 Planarity : 0.005 0.058 1575 Dihedral : 21.780 133.408 1862 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.93 % Allowed : 18.97 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 1014 helix: 1.05 (0.27), residues: 355 sheet: -2.00 (0.30), residues: 255 loop : -0.08 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 49 TYR 0.020 0.002 TYR C 180 PHE 0.014 0.002 PHE B 322 TRP 0.014 0.001 TRP D 348 HIS 0.007 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (10396) covalent geometry : angle 0.59876 / 0.34 (14304) hydrogen bonds : bond 0.05094 / 5.48 ( 449) hydrogen bonds : angle 6.44501 / 8.07 ( 1216) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 0.534 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: 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 145 SER cc_start: 0.7940 (t) cc_final: 0.7631 (m) REVERT: A 72 LEU cc_start: 0.6910 (tp) cc_final: 0.6597 (tp) REVERT: B 287 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7341 (m-30) outliers start: 19 outliers final: 12 residues processed: 213 average time/residue: 0.2201 time to fit residues: 65.6462 Evaluate side-chains 202 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 354 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 43 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 85 optimal weight: 0.3980 chunk 75 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 41 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS C 270 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.201063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.163926 restraints weight = 37068.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.165399 restraints weight = 32812.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.167259 restraints weight = 29838.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.167803 restraints weight = 22362.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.168541 restraints weight = 19764.495| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10396 Z= 0.150 Angle : 0.546 7.607 14304 Z= 0.306 Chirality : 0.039 0.177 1598 Planarity : 0.004 0.049 1575 Dihedral : 21.794 130.798 1862 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.93 % Allowed : 19.47 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 1014 helix: 1.13 (0.28), residues: 364 sheet: -1.85 (0.30), residues: 242 loop : -0.33 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 276 TYR 0.013 0.001 TYR C 90 PHE 0.012 0.001 PHE A 221 TRP 0.009 0.001 TRP D 348 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (10396) covalent geometry : angle 0.54624 / 0.31 (14304) hydrogen bonds : bond 0.04472 / 4.79 ( 449) hydrogen bonds : angle 5.98373 / 7.52 ( 1216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.640 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 145 SER cc_start: 0.8072 (t) cc_final: 0.7688 (m) REVERT: C 299 GLN cc_start: 0.8203 (tt0) cc_final: 0.7597 (tm-30) REVERT: D 99 VAL cc_start: 0.8539 (p) cc_final: 0.8181 (t) REVERT: A 72 LEU cc_start: 0.6908 (tp) cc_final: 0.6632 (tp) REVERT: A 99 MET cc_start: 0.6950 (mmm) cc_final: 0.6598 (mmm) REVERT: B 287 ASP cc_start: 0.7645 (m-30) cc_final: 0.7441 (m-30) outliers start: 19 outliers final: 16 residues processed: 205 average time/residue: 0.2006 time to fit residues: 59.2194 Evaluate side-chains 201 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain B residue 355 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 53 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 265 HIS C 270 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.196985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.158873 restraints weight = 37436.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.161373 restraints weight = 35062.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.163128 restraints weight = 27870.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.163542 restraints weight = 20555.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.163994 restraints weight = 19127.717| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10396 Z= 0.194 Angle : 0.579 7.160 14304 Z= 0.323 Chirality : 0.040 0.179 1598 Planarity : 0.005 0.048 1575 Dihedral : 21.847 128.872 1862 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.35 % Allowed : 20.28 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.77 (0.27), residues: 1014 helix: 0.94 (0.27), residues: 371 sheet: -2.06 (0.29), residues: 253 loop : -0.64 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 276 TYR 0.012 0.002 TYR B 120 PHE 0.015 0.002 PHE A 221 TRP 0.007 0.001 TRP D 348 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (10396) covalent geometry : angle 0.57878 / 0.32 (14304) hydrogen bonds : bond 0.04160 / 4.47 ( 449) hydrogen bonds : angle 5.80976 / 7.23 ( 1216) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 0.499 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: symmetry clash revert: symmetry clash REVERT: C 42 THR cc_start: 0.7679 (OUTLIER) cc_final: 0.7434 (t) REVERT: C 88 MET cc_start: 0.8226 (mmm) cc_final: 0.7226 (mtt) REVERT: C 145 SER cc_start: 0.8351 (t) cc_final: 0.7890 (m) REVERT: C 299 GLN cc_start: 0.8587 (tt0) cc_final: 0.8059 (tm-30) REVERT: D 99 VAL cc_start: 0.8543 (p) cc_final: 0.8205 (t) REVERT: A 72 LEU cc_start: 0.6966 (tp) cc_final: 0.6717 (tp) REVERT: B 287 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7423 (m-30) outliers start: 33 outliers final: 28 residues processed: 209 average time/residue: 0.1912 time to fit residues: 58.1143 Evaluate side-chains 207 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain B residue 355 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 4 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 0.0470 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS C 270 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.198511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.160561 restraints weight = 37106.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.162126 restraints weight = 33460.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.164433 restraints weight = 28341.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.164708 restraints weight = 20839.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.164980 restraints weight = 19387.465| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10396 Z= 0.130 Angle : 0.520 5.391 14304 Z= 0.290 Chirality : 0.039 0.174 1598 Planarity : 0.004 0.049 1575 Dihedral : 21.812 127.601 1862 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.14 % Allowed : 19.98 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.44 (0.27), residues: 1014 helix: 1.19 (0.28), residues: 364 sheet: -1.73 (0.30), residues: 239 loop : -0.59 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 276 TYR 0.012 0.001 TYR B 120 PHE 0.011 0.001 PHE A 221 TRP 0.005 0.001 TRP D 348 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (10396) covalent geometry : angle 0.51960 / 0.29 (14304) hydrogen bonds : bond 0.03684 / 3.93 ( 449) hydrogen bonds : angle 5.59448 / 7.00 ( 1216) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.497 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 THR cc_start: 0.7599 (OUTLIER) cc_final: 0.7305 (t) REVERT: C 88 MET cc_start: 0.8346 (mmm) cc_final: 0.7605 (mtt) REVERT: C 145 SER cc_start: 0.8343 (t) cc_final: 0.7913 (m) REVERT: C 299 GLN cc_start: 0.8462 (tt0) cc_final: 0.7983 (tm-30) REVERT: D 99 VAL cc_start: 0.8533 (p) cc_final: 0.8241 (t) REVERT: A 72 LEU cc_start: 0.6877 (tp) cc_final: 0.6613 (tp) outliers start: 31 outliers final: 23 residues processed: 203 average time/residue: 0.1817 time to fit residues: 54.3532 Evaluate side-chains 198 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 355 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 4 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 50 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.0010 chunk 76 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.197438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.159240 restraints weight = 37058.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.161311 restraints weight = 34238.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.163567 restraints weight = 27702.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.163739 restraints weight = 19889.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.164097 restraints weight = 18917.472| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10396 Z= 0.152 Angle : 0.535 7.190 14304 Z= 0.296 Chirality : 0.038 0.174 1598 Planarity : 0.004 0.050 1575 Dihedral : 21.818 125.649 1862 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.65 % Allowed : 19.88 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 1014 helix: 1.08 (0.28), residues: 371 sheet: -1.88 (0.30), residues: 247 loop : -0.56 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 276 TYR 0.011 0.001 TYR A 90 PHE 0.012 0.001 PHE A 221 TRP 0.005 0.001 TRP D 348 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (10396) covalent geometry : angle 0.53539 / 0.30 (14304) hydrogen bonds : bond 0.03619 / 3.84 ( 449) hydrogen bonds : angle 5.45072 / 6.86 ( 1216) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.621 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 THR cc_start: 0.7642 (OUTLIER) cc_final: 0.7406 (t) REVERT: C 88 MET cc_start: 0.8205 (mmm) cc_final: 0.7431 (mtt) REVERT: C 145 SER cc_start: 0.8410 (t) cc_final: 0.7973 (m) REVERT: C 299 GLN cc_start: 0.8600 (tt0) cc_final: 0.8048 (tm-30) REVERT: D 99 VAL cc_start: 0.8498 (p) cc_final: 0.8215 (t) REVERT: A 72 LEU cc_start: 0.6886 (tp) cc_final: 0.6617 (tp) outliers start: 36 outliers final: 31 residues processed: 196 average time/residue: 0.1909 time to fit residues: 54.8476 Evaluate side-chains 205 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain B residue 355 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 2.9990 chunk 17 optimal weight: 0.0370 chunk 32 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 58 optimal weight: 0.0570 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.192358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.153840 restraints weight = 38111.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.154084 restraints weight = 35278.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.156944 restraints weight = 30454.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.157155 restraints weight = 21425.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.157440 restraints weight = 20362.646| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10396 Z= 0.160 Angle : 0.534 6.035 14304 Z= 0.297 Chirality : 0.039 0.179 1598 Planarity : 0.004 0.051 1575 Dihedral : 21.851 122.353 1862 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.65 % Allowed : 19.88 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.59 (0.27), residues: 1014 helix: 1.08 (0.28), residues: 364 sheet: -1.76 (0.31), residues: 242 loop : -0.72 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 276 TYR 0.009 0.001 TYR A 90 PHE 0.026 0.002 PHE B 283 TRP 0.004 0.001 TRP D 348 HIS 0.007 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (10396) covalent geometry : angle 0.53438 / 0.30 (14304) hydrogen bonds : bond 0.03549 / 3.78 ( 449) hydrogen bonds : angle 5.42760 / 6.81 ( 1216) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.510 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 THR cc_start: 0.7625 (OUTLIER) cc_final: 0.7316 (t) REVERT: C 88 MET cc_start: 0.8344 (mmm) cc_final: 0.7606 (mtt) REVERT: C 122 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7260 (tm-30) REVERT: C 145 SER cc_start: 0.8453 (t) cc_final: 0.7931 (m) REVERT: D 99 VAL cc_start: 0.8529 (p) cc_final: 0.8227 (t) REVERT: D 355 THR cc_start: 0.7168 (OUTLIER) cc_final: 0.6803 (p) REVERT: A 72 LEU cc_start: 0.6836 (tp) cc_final: 0.6559 (tp) REVERT: A 198 CYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7894 (m) outliers start: 36 outliers final: 30 residues processed: 193 average time/residue: 0.1771 time to fit residues: 49.8206 Evaluate side-chains 202 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 355 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.192104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.154568 restraints weight = 37941.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.155450 restraints weight = 34718.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.158281 restraints weight = 29668.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.158188 restraints weight = 21301.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.158543 restraints weight = 19961.578| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10396 Z= 0.152 Angle : 0.527 5.430 14304 Z= 0.293 Chirality : 0.039 0.172 1598 Planarity : 0.004 0.051 1575 Dihedral : 21.845 119.180 1862 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.85 % Allowed : 20.69 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 1014 helix: 1.18 (0.28), residues: 364 sheet: -1.91 (0.30), residues: 248 loop : -0.65 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 276 TYR 0.023 0.001 TYR A 293 PHE 0.018 0.002 PHE B 283 TRP 0.010 0.001 TRP A 295 HIS 0.007 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (10396) covalent geometry : angle 0.52726 / 0.29 (14304) hydrogen bonds : bond 0.03457 / 3.67 ( 449) hydrogen bonds : angle 5.33870 / 6.71 ( 1216) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.364 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 THR cc_start: 0.7685 (OUTLIER) cc_final: 0.7467 (t) REVERT: C 88 MET cc_start: 0.8173 (mmm) cc_final: 0.7310 (mtt) REVERT: C 145 SER cc_start: 0.8453 (t) cc_final: 0.8007 (m) REVERT: D 99 VAL cc_start: 0.8503 (p) cc_final: 0.8212 (t) REVERT: D 355 THR cc_start: 0.7343 (OUTLIER) cc_final: 0.6989 (p) REVERT: A 72 LEU cc_start: 0.6787 (tp) cc_final: 0.6529 (tp) REVERT: A 198 CYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7871 (m) outliers start: 38 outliers final: 33 residues processed: 192 average time/residue: 0.1830 time to fit residues: 50.9213 Evaluate side-chains 205 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 355 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 101 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 109 optimal weight: 0.0570 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 270 HIS B 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.192806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.155059 restraints weight = 38005.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.155599 restraints weight = 33874.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.157673 restraints weight = 30613.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.158128 restraints weight = 22001.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.159166 restraints weight = 20321.884| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10396 Z= 0.129 Angle : 0.508 5.586 14304 Z= 0.281 Chirality : 0.038 0.169 1598 Planarity : 0.004 0.052 1575 Dihedral : 21.829 115.522 1862 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.45 % Allowed : 21.60 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 1014 helix: 1.31 (0.28), residues: 364 sheet: -1.74 (0.31), residues: 241 loop : -0.62 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 350 TYR 0.020 0.001 TYR D 120 PHE 0.015 0.001 PHE B 283 TRP 0.005 0.001 TRP A 295 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (10396) covalent geometry : angle 0.50813 / 0.28 (14304) hydrogen bonds : bond 0.03286 / 3.50 ( 449) hydrogen bonds : angle 5.25451 / 6.61 ( 1216) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.408 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: symmetry clash revert: symmetry clash REVERT: C 42 THR cc_start: 0.7673 (OUTLIER) cc_final: 0.7395 (t) REVERT: C 88 MET cc_start: 0.8301 (mmm) cc_final: 0.7514 (mtt) REVERT: C 145 SER cc_start: 0.8465 (t) cc_final: 0.8018 (m) REVERT: D 99 VAL cc_start: 0.8501 (p) cc_final: 0.8250 (t) REVERT: D 355 THR cc_start: 0.7210 (OUTLIER) cc_final: 0.6848 (p) REVERT: A 72 LEU cc_start: 0.6699 (tp) cc_final: 0.6451 (tp) REVERT: A 198 CYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7790 (m) REVERT: A 293 TYR cc_start: 0.6681 (p90) cc_final: 0.6437 (p90) outliers start: 34 outliers final: 28 residues processed: 194 average time/residue: 0.1962 time to fit residues: 54.4803 Evaluate side-chains 201 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 355 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.191381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.154255 restraints weight = 37968.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.154979 restraints weight = 34232.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.157957 restraints weight = 29404.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.157802 restraints weight = 20849.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.158187 restraints weight = 19772.807| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10396 Z= 0.160 Angle : 0.534 6.226 14304 Z= 0.298 Chirality : 0.039 0.168 1598 Planarity : 0.004 0.051 1575 Dihedral : 21.857 111.684 1862 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.85 % Allowed : 21.30 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.27), residues: 1014 helix: 1.35 (0.28), residues: 358 sheet: -1.69 (0.31), residues: 233 loop : -0.72 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 338 TYR 0.010 0.001 TYR C 45 PHE 0.016 0.002 PHE D 283 TRP 0.033 0.001 TRP D 346 HIS 0.010 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (10396) covalent geometry : angle 0.53412 / 0.30 (14304) hydrogen bonds : bond 0.03415 / 3.62 ( 449) hydrogen bonds : angle 5.27332 / 6.64 ( 1216) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 0.560 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 THR cc_start: 0.7723 (OUTLIER) cc_final: 0.7462 (t) REVERT: C 88 MET cc_start: 0.8136 (mmm) cc_final: 0.7263 (mtt) REVERT: C 145 SER cc_start: 0.8482 (t) cc_final: 0.8025 (m) REVERT: D 99 VAL cc_start: 0.8495 (p) cc_final: 0.8246 (t) REVERT: D 355 THR cc_start: 0.7344 (OUTLIER) cc_final: 0.6985 (p) REVERT: A 72 LEU cc_start: 0.6748 (tp) cc_final: 0.6498 (tp) REVERT: A 198 CYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7833 (m) REVERT: A 293 TYR cc_start: 0.6698 (p90) cc_final: 0.6495 (p90) REVERT: B 301 LEU cc_start: 0.6185 (mp) cc_final: 0.5677 (mp) outliers start: 38 outliers final: 33 residues processed: 194 average time/residue: 0.1878 time to fit residues: 53.6270 Evaluate side-chains 208 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 346 TRP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 355 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.0770 chunk 30 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.192983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.155729 restraints weight = 37774.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.155980 restraints weight = 33575.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.159236 restraints weight = 30071.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.159130 restraints weight = 20939.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.159474 restraints weight = 19751.612| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10396 Z= 0.118 Angle : 0.507 5.355 14304 Z= 0.280 Chirality : 0.038 0.168 1598 Planarity : 0.004 0.053 1575 Dihedral : 21.810 107.271 1862 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.14 % Allowed : 21.81 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.27), residues: 1014 helix: 1.42 (0.28), residues: 364 sheet: -1.59 (0.32), residues: 225 loop : -0.66 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 350 TYR 0.013 0.001 TYR C 45 PHE 0.015 0.001 PHE B 283 TRP 0.013 0.001 TRP D 346 HIS 0.010 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (10396) covalent geometry : angle 0.50742 / 0.28 (14304) hydrogen bonds : bond 0.03157 / 3.38 ( 449) hydrogen bonds : angle 5.15503 / 6.51 ( 1216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3123.37 seconds wall clock time: 54 minutes 15.16 seconds (3255.16 seconds total)