Starting phenix.real_space_refine on Tue Apr 29 12:11:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xog_38528/04_2025/8xog_38528_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xog_38528/04_2025/8xog_38528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xog_38528/04_2025/8xog_38528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xog_38528/04_2025/8xog_38528.map" model { file = "/net/cci-nas-00/data/ceres_data/8xog_38528/04_2025/8xog_38528_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xog_38528/04_2025/8xog_38528_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5535 2.51 5 N 1509 2.21 5 O 1611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8708 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1852 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2552 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1724 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 423 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2155 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 256} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 5.32, per 1000 atoms: 0.61 Number of scatterers: 8708 At special positions: 0 Unit cell: (94.76, 120.304, 124.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1611 8.00 N 1509 7.00 C 5535 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 985.3 milliseconds 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 40.1% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 16 through 40 removed outlier: 3.776A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.604A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.954A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.488A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.535A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.644A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 25 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 4.025A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 53 through 87 removed outlier: 4.624A pdb=" N PHE R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 88 through 91 Processing helix chain 'R' and resid 92 through 116 removed outlier: 3.510A pdb=" N LEU R 96 " --> pdb=" O THR R 92 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU R 113 " --> pdb=" O VAL R 109 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU R 115 " --> pdb=" O ASP R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 125 removed outlier: 4.186A pdb=" N ASP R 125 " --> pdb=" O GLU R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 161 Processing helix chain 'R' and resid 170 through 200 Proline residue: R 192 - end of helix Processing helix chain 'R' and resid 211 through 223 Processing helix chain 'R' and resid 223 through 246 Processing helix chain 'R' and resid 254 through 285 removed outlier: 3.600A pdb=" N VAL R 265 " --> pdb=" O ILE R 261 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU R 266 " --> pdb=" O LEU R 262 " (cutoff:3.500A) Proline residue: R 274 - end of helix Processing helix chain 'R' and resid 302 through 325 removed outlier: 3.623A pdb=" N ASN R 316 " --> pdb=" O ALA R 312 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER R 317 " --> pdb=" O ALA R 313 " (cutoff:3.500A) Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 328 through 342 removed outlier: 3.624A pdb=" N ARG R 332 " --> pdb=" O GLY R 328 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.939A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.029A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.532A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.651A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.724A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.892A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.501A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.440A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.695A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.548A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.840A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.746A pdb=" N GLN E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2795 1.34 - 1.45: 1219 1.45 - 1.57: 4792 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 8882 Sorted by residual: bond pdb=" N SER B 74 " pdb=" CA SER B 74 " ideal model delta sigma weight residual 1.455 1.421 0.033 1.29e-02 6.01e+03 6.62e+00 bond pdb=" C TYR B 289 " pdb=" N ASP B 290 " ideal model delta sigma weight residual 1.332 1.365 -0.033 1.52e-02 4.33e+03 4.68e+00 bond pdb=" N ASP B 290 " pdb=" CA ASP B 290 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.32e-02 5.74e+03 4.64e+00 bond pdb=" CA SER B 74 " pdb=" CB SER B 74 " ideal model delta sigma weight residual 1.535 1.497 0.039 1.90e-02 2.77e+03 4.12e+00 bond pdb=" CA SER B 74 " pdb=" C SER B 74 " ideal model delta sigma weight residual 1.522 1.497 0.025 1.24e-02 6.50e+03 4.06e+00 ... (remaining 8877 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 11810 1.69 - 3.38: 190 3.38 - 5.07: 24 5.07 - 6.76: 7 6.76 - 8.45: 2 Bond angle restraints: 12033 Sorted by residual: angle pdb=" N ASP B 290 " pdb=" CA ASP B 290 " pdb=" C ASP B 290 " ideal model delta sigma weight residual 113.20 107.58 5.62 1.21e+00 6.83e-01 2.16e+01 angle pdb=" CA PRO R 192 " pdb=" N PRO R 192 " pdb=" CD PRO R 192 " ideal model delta sigma weight residual 112.00 106.53 5.47 1.40e+00 5.10e-01 1.53e+01 angle pdb=" C SER R 325 " pdb=" N PHE R 326 " pdb=" CA PHE R 326 " ideal model delta sigma weight residual 122.86 117.29 5.57 1.53e+00 4.27e-01 1.32e+01 angle pdb=" CA SER B 74 " pdb=" CB SER B 74 " pdb=" OG SER B 74 " ideal model delta sigma weight residual 111.10 105.40 5.70 2.00e+00 2.50e-01 8.13e+00 angle pdb=" N ASP B 290 " pdb=" CA ASP B 290 " pdb=" CB ASP B 290 " ideal model delta sigma weight residual 110.42 114.92 -4.50 1.62e+00 3.81e-01 7.71e+00 ... (remaining 12028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 4709 17.85 - 35.71: 430 35.71 - 53.56: 96 53.56 - 71.42: 19 71.42 - 89.27: 9 Dihedral angle restraints: 5263 sinusoidal: 2030 harmonic: 3233 Sorted by residual: dihedral pdb=" CA PHE R 326 " pdb=" C PHE R 326 " pdb=" N LEU R 327 " pdb=" CA LEU R 327 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA PHE R 223 " pdb=" C PHE R 223 " pdb=" N ILE R 224 " pdb=" CA ILE R 224 " ideal model delta harmonic sigma weight residual -180.00 -161.08 -18.92 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ILE A 207 " pdb=" C ILE A 207 " pdb=" N PHE A 208 " pdb=" CA PHE A 208 " ideal model delta harmonic sigma weight residual 180.00 161.68 18.32 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 5260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1050 0.042 - 0.083: 227 0.083 - 0.125: 82 0.125 - 0.166: 14 0.166 - 0.208: 1 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CA ASP B 290 " pdb=" N ASP B 290 " pdb=" C ASP B 290 " pdb=" CB ASP B 290 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA TYR A 391 " pdb=" N TYR A 391 " pdb=" C TYR A 391 " pdb=" CB TYR A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA VAL E 2 " pdb=" N VAL E 2 " pdb=" C VAL E 2 " pdb=" CB VAL E 2 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1371 not shown) Planarity restraints: 1529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 191 " -0.078 5.00e-02 4.00e+02 1.15e-01 2.13e+01 pdb=" N PRO R 192 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO R 192 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO R 192 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 219 " -0.156 9.50e-02 1.11e+02 7.03e-02 3.28e+00 pdb=" NE ARG B 219 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 219 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 219 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 219 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 73 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C ALA B 73 " -0.031 2.00e-02 2.50e+03 pdb=" O ALA B 73 " 0.012 2.00e-02 2.50e+03 pdb=" N SER B 74 " 0.010 2.00e-02 2.50e+03 ... (remaining 1526 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2092 2.79 - 3.32: 8526 3.32 - 3.84: 14308 3.84 - 4.37: 17360 4.37 - 4.90: 29977 Nonbonded interactions: 72263 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.263 3.040 nonbonded pdb=" OG SER E 17 " pdb=" O THR E 84 " model vdw 2.264 3.040 nonbonded pdb=" O ASN A 239 " pdb=" OD1 ASP A 240 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASP B 170 " pdb=" OG1 THR B 173 " model vdw 2.285 3.040 nonbonded pdb=" O ASN A 392 " pdb=" ND2 ASN A 392 " model vdw 2.325 3.120 ... (remaining 72258 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.580 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:10.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 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 : 0.003 0.060 8882 Z= 0.168 Angle : 0.561 8.446 12033 Z= 0.318 Chirality : 0.041 0.208 1374 Planarity : 0.005 0.115 1529 Dihedral : 14.841 89.272 3167 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.21 % Allowed : 14.41 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1091 helix: 1.40 (0.26), residues: 401 sheet: -0.07 (0.31), residues: 274 loop : 0.24 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.004 0.001 HIS B 91 PHE 0.023 0.001 PHE R 326 TYR 0.009 0.001 TYR A 391 ARG 0.009 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.18232 ( 460) hydrogen bonds : angle 7.01214 ( 1293) covalent geometry : bond 0.00340 ( 8882) covalent geometry : angle 0.56125 (12033) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 213 GLN cc_start: 0.7248 (tt0) cc_final: 0.6554 (mt0) REVERT: A 232 ARG cc_start: 0.7934 (ttm170) cc_final: 0.7684 (ttp-170) REVERT: A 391 TYR cc_start: 0.8359 (OUTLIER) cc_final: 0.6070 (m-80) REVERT: G 58 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6937 (mt-10) REVERT: R 141 MET cc_start: 0.6606 (ptp) cc_final: 0.5929 (tmt) outliers start: 2 outliers final: 0 residues processed: 118 average time/residue: 1.1097 time to fit residues: 140.6815 Evaluate side-chains 108 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 175 GLN B 259 GLN E 194 ASN E 232 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.215027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.134655 restraints weight = 9354.583| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.39 r_work: 0.3314 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8882 Z= 0.215 Angle : 0.642 10.547 12033 Z= 0.339 Chirality : 0.046 0.174 1374 Planarity : 0.005 0.072 1529 Dihedral : 5.064 57.644 1205 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.31 % Allowed : 14.94 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1091 helix: 1.29 (0.25), residues: 401 sheet: 0.25 (0.32), residues: 267 loop : 0.35 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.007 0.001 HIS B 91 PHE 0.019 0.002 PHE R 227 TYR 0.013 0.001 TYR A 339 ARG 0.005 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.05063 ( 460) hydrogen bonds : angle 5.21841 ( 1293) covalent geometry : bond 0.00501 ( 8882) covalent geometry : angle 0.64235 (12033) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7647 (mt-10) REVERT: A 213 GLN cc_start: 0.7614 (tt0) cc_final: 0.6927 (mt0) REVERT: A 391 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.6564 (m-80) REVERT: G 58 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7101 (mt-10) REVERT: R 141 MET cc_start: 0.7554 (ptp) cc_final: 0.6782 (tmt) outliers start: 31 outliers final: 12 residues processed: 128 average time/residue: 1.0099 time to fit residues: 140.1097 Evaluate side-chains 109 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 266 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 34 optimal weight: 0.3980 chunk 29 optimal weight: 0.1980 chunk 79 optimal weight: 5.9990 chunk 81 optimal weight: 0.4980 chunk 88 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 77 optimal weight: 30.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 294 GLN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.218249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139104 restraints weight = 9494.519| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.52 r_work: 0.3480 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8882 Z= 0.115 Angle : 0.536 10.022 12033 Z= 0.284 Chirality : 0.041 0.153 1374 Planarity : 0.004 0.052 1529 Dihedral : 4.665 58.191 1205 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.56 % Allowed : 15.69 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.26), residues: 1091 helix: 1.62 (0.25), residues: 402 sheet: 0.22 (0.32), residues: 262 loop : 0.37 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.010 0.001 TYR B 289 ARG 0.004 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 460) hydrogen bonds : angle 4.72393 ( 1293) covalent geometry : bond 0.00245 ( 8882) covalent geometry : angle 0.53645 (12033) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7358 (mt-10) REVERT: A 213 GLN cc_start: 0.7546 (tt0) cc_final: 0.6873 (mt0) REVERT: A 391 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.6561 (m-80) REVERT: B 153 ASP cc_start: 0.6972 (m-30) cc_final: 0.6639 (t70) REVERT: B 165 THR cc_start: 0.8039 (p) cc_final: 0.7828 (t) REVERT: E 230 MET cc_start: 0.2185 (ttp) cc_final: 0.1853 (mpt) REVERT: G 58 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7020 (mt-10) REVERT: R 141 MET cc_start: 0.7212 (ptp) cc_final: 0.6531 (tmt) outliers start: 24 outliers final: 6 residues processed: 122 average time/residue: 1.1128 time to fit residues: 147.5055 Evaluate side-chains 105 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 163 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 294 GLN A 387 ASN R 140 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.213740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.139175 restraints weight = 9472.028| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.81 r_work: 0.3387 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8882 Z= 0.224 Angle : 0.604 9.624 12033 Z= 0.319 Chirality : 0.045 0.186 1374 Planarity : 0.004 0.050 1529 Dihedral : 4.942 58.200 1205 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.42 % Allowed : 16.01 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1091 helix: 1.50 (0.26), residues: 397 sheet: 0.16 (0.32), residues: 267 loop : 0.36 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.019 0.002 PHE R 326 TYR 0.014 0.002 TYR A 339 ARG 0.003 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04613 ( 460) hydrogen bonds : angle 4.78754 ( 1293) covalent geometry : bond 0.00530 ( 8882) covalent geometry : angle 0.60369 (12033) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7435 (mt-10) REVERT: A 213 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.6910 (mt0) REVERT: A 266 LEU cc_start: 0.8487 (mt) cc_final: 0.8174 (mm) REVERT: A 299 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7431 (pm20) REVERT: A 391 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.6629 (m-80) REVERT: B 251 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7916 (mmt-90) REVERT: B 260 GLU cc_start: 0.8119 (tt0) cc_final: 0.7709 (tt0) REVERT: G 58 GLU cc_start: 0.7464 (mm-30) cc_final: 0.6986 (mt-10) REVERT: R 141 MET cc_start: 0.7515 (ptp) cc_final: 0.6665 (tmt) REVERT: R 247 HIS cc_start: 0.6667 (OUTLIER) cc_final: 0.6447 (m-70) outliers start: 32 outliers final: 12 residues processed: 117 average time/residue: 1.1036 time to fit residues: 138.9764 Evaluate side-chains 112 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 247 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 91 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 76 optimal weight: 30.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.215601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.141866 restraints weight = 9360.770| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.89 r_work: 0.3417 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8882 Z= 0.149 Angle : 0.579 15.361 12033 Z= 0.297 Chirality : 0.043 0.166 1374 Planarity : 0.004 0.043 1529 Dihedral : 4.761 58.672 1205 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.88 % Allowed : 17.18 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1091 helix: 1.66 (0.26), residues: 397 sheet: 0.05 (0.32), residues: 269 loop : 0.33 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.010 0.001 TYR B 289 ARG 0.004 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 460) hydrogen bonds : angle 4.61063 ( 1293) covalent geometry : bond 0.00341 ( 8882) covalent geometry : angle 0.57928 (12033) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7394 (mt-10) REVERT: A 266 LEU cc_start: 0.8466 (mt) cc_final: 0.8152 (mm) REVERT: A 299 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7448 (pm20) REVERT: A 391 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.6526 (m-80) REVERT: B 251 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7971 (mmt-90) REVERT: B 260 GLU cc_start: 0.8120 (tt0) cc_final: 0.7742 (tt0) REVERT: E 188 LEU cc_start: 0.3889 (mt) cc_final: 0.3494 (pt) REVERT: E 230 MET cc_start: 0.2303 (ttp) cc_final: 0.1859 (mpt) REVERT: G 58 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6867 (mt-10) REVERT: R 141 MET cc_start: 0.7460 (ptp) cc_final: 0.6595 (tmt) REVERT: R 247 HIS cc_start: 0.6747 (OUTLIER) cc_final: 0.6540 (m-70) outliers start: 27 outliers final: 13 residues processed: 116 average time/residue: 1.0448 time to fit residues: 130.6725 Evaluate side-chains 110 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 247 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 85 optimal weight: 0.2980 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 0.4980 chunk 59 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 50 optimal weight: 0.0870 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.218345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.146463 restraints weight = 9362.799| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.99 r_work: 0.3468 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8882 Z= 0.107 Angle : 0.533 14.509 12033 Z= 0.274 Chirality : 0.041 0.152 1374 Planarity : 0.004 0.039 1529 Dihedral : 4.504 58.795 1205 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.35 % Allowed : 19.00 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.26), residues: 1091 helix: 1.92 (0.26), residues: 397 sheet: 0.14 (0.32), residues: 265 loop : 0.23 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE R 326 TYR 0.015 0.001 TYR A 318 ARG 0.004 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 460) hydrogen bonds : angle 4.38599 ( 1293) covalent geometry : bond 0.00228 ( 8882) covalent geometry : angle 0.53298 (12033) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.7577 (tt0) cc_final: 0.6885 (mt0) REVERT: A 232 ARG cc_start: 0.8091 (ttm170) cc_final: 0.7766 (ttp-170) REVERT: A 299 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7357 (pm20) REVERT: A 391 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.6495 (m-80) REVERT: B 153 ASP cc_start: 0.7061 (m-30) cc_final: 0.6710 (t70) REVERT: B 251 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7968 (mmt-90) REVERT: B 260 GLU cc_start: 0.8100 (tt0) cc_final: 0.7758 (tt0) REVERT: E 34 MET cc_start: 0.4399 (mmm) cc_final: 0.3771 (mmm) REVERT: E 230 MET cc_start: 0.2269 (ttp) cc_final: 0.1873 (mpt) REVERT: R 141 MET cc_start: 0.7391 (ptp) cc_final: 0.6619 (tmt) REVERT: R 334 LYS cc_start: 0.6745 (tttp) cc_final: 0.6419 (tttp) outliers start: 22 outliers final: 11 residues processed: 119 average time/residue: 1.1072 time to fit residues: 141.5777 Evaluate side-chains 108 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 247 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 294 GLN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.218003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.146751 restraints weight = 9481.936| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.85 r_work: 0.3475 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8882 Z= 0.116 Angle : 0.549 15.499 12033 Z= 0.280 Chirality : 0.041 0.137 1374 Planarity : 0.004 0.037 1529 Dihedral : 4.478 58.745 1205 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.13 % Allowed : 20.38 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.26), residues: 1091 helix: 1.96 (0.26), residues: 397 sheet: 0.18 (0.31), residues: 272 loop : 0.23 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE R 326 TYR 0.015 0.001 TYR A 318 ARG 0.008 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 460) hydrogen bonds : angle 4.34431 ( 1293) covalent geometry : bond 0.00253 ( 8882) covalent geometry : angle 0.54859 (12033) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.7577 (tt0) cc_final: 0.6889 (mt0) REVERT: A 232 ARG cc_start: 0.8133 (ttm170) cc_final: 0.7889 (ttp-170) REVERT: A 299 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7435 (pm20) REVERT: A 391 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.6520 (m-80) REVERT: B 153 ASP cc_start: 0.7105 (m-30) cc_final: 0.6801 (t70) REVERT: B 251 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7984 (mmt-90) REVERT: B 260 GLU cc_start: 0.8100 (tt0) cc_final: 0.7742 (tt0) REVERT: E 34 MET cc_start: 0.4540 (mmm) cc_final: 0.3913 (mmm) REVERT: E 230 MET cc_start: 0.2271 (ttp) cc_final: 0.1846 (mpt) REVERT: R 141 MET cc_start: 0.7368 (ptp) cc_final: 0.6613 (tmt) REVERT: R 334 LYS cc_start: 0.6747 (tttp) cc_final: 0.6536 (tttp) outliers start: 20 outliers final: 11 residues processed: 112 average time/residue: 1.0894 time to fit residues: 131.1962 Evaluate side-chains 108 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 247 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 27 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 72 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 294 GLN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.217240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.144199 restraints weight = 9468.058| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.88 r_work: 0.3454 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8882 Z= 0.131 Angle : 0.560 16.532 12033 Z= 0.285 Chirality : 0.042 0.153 1374 Planarity : 0.004 0.038 1529 Dihedral : 4.537 58.697 1205 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.56 % Allowed : 20.28 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.26), residues: 1091 helix: 1.94 (0.26), residues: 397 sheet: 0.18 (0.31), residues: 278 loop : 0.25 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE R 326 TYR 0.010 0.001 TYR R 156 ARG 0.008 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 460) hydrogen bonds : angle 4.35619 ( 1293) covalent geometry : bond 0.00297 ( 8882) covalent geometry : angle 0.55978 (12033) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7568 (mt-10) REVERT: A 213 GLN cc_start: 0.7588 (tt0) cc_final: 0.6942 (mt0) REVERT: A 299 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7446 (pm20) REVERT: A 391 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.6512 (m-80) REVERT: B 153 ASP cc_start: 0.7145 (m-30) cc_final: 0.6813 (t70) REVERT: B 251 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7915 (mmt-90) REVERT: B 260 GLU cc_start: 0.8124 (tt0) cc_final: 0.7636 (tt0) REVERT: E 34 MET cc_start: 0.4429 (mmm) cc_final: 0.3794 (mmm) REVERT: E 140 MET cc_start: 0.1327 (ptp) cc_final: 0.0765 (ptm) REVERT: E 230 MET cc_start: 0.2253 (ttp) cc_final: 0.1786 (mpt) REVERT: R 141 MET cc_start: 0.7417 (ptp) cc_final: 0.6608 (tmt) REVERT: R 334 LYS cc_start: 0.6692 (tttp) cc_final: 0.6483 (tttp) outliers start: 24 outliers final: 14 residues processed: 117 average time/residue: 1.1430 time to fit residues: 144.1144 Evaluate side-chains 110 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 247 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 32 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 99 optimal weight: 0.5980 chunk 69 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 294 GLN B 175 GLN B 266 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.217340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.140103 restraints weight = 9432.037| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.81 r_work: 0.3440 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8882 Z= 0.133 Angle : 0.574 16.054 12033 Z= 0.290 Chirality : 0.042 0.157 1374 Planarity : 0.004 0.038 1529 Dihedral : 4.514 58.789 1205 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.81 % Allowed : 21.34 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.26), residues: 1091 helix: 1.90 (0.26), residues: 397 sheet: 0.23 (0.31), residues: 269 loop : 0.09 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE R 326 TYR 0.010 0.001 TYR B 289 ARG 0.004 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 460) hydrogen bonds : angle 4.36055 ( 1293) covalent geometry : bond 0.00302 ( 8882) covalent geometry : angle 0.57413 (12033) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7330 (mt-10) REVERT: A 213 GLN cc_start: 0.7600 (tt0) cc_final: 0.6896 (mt0) REVERT: A 299 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7460 (pm20) REVERT: A 391 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.6421 (m-80) REVERT: B 153 ASP cc_start: 0.7047 (m-30) cc_final: 0.6747 (t70) REVERT: B 251 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7807 (mmt-90) REVERT: B 260 GLU cc_start: 0.7922 (tt0) cc_final: 0.7430 (tt0) REVERT: E 140 MET cc_start: 0.1459 (ptp) cc_final: 0.0891 (ptm) REVERT: E 230 MET cc_start: 0.2348 (ttp) cc_final: 0.1869 (mpt) REVERT: R 141 MET cc_start: 0.7146 (ptp) cc_final: 0.6419 (tmt) REVERT: R 334 LYS cc_start: 0.6754 (tttp) cc_final: 0.6453 (tttp) outliers start: 17 outliers final: 14 residues processed: 113 average time/residue: 1.1001 time to fit residues: 133.7269 Evaluate side-chains 116 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 247 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 80 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 0.0470 chunk 84 optimal weight: 0.3980 chunk 96 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 294 GLN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.219611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140387 restraints weight = 9383.121| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.54 r_work: 0.3495 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8882 Z= 0.103 Angle : 0.557 15.579 12033 Z= 0.277 Chirality : 0.041 0.135 1374 Planarity : 0.003 0.036 1529 Dihedral : 4.335 58.982 1205 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.71 % Allowed : 21.66 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.26), residues: 1091 helix: 2.04 (0.26), residues: 396 sheet: 0.24 (0.31), residues: 274 loop : 0.14 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE R 326 TYR 0.011 0.001 TYR B 289 ARG 0.004 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 460) hydrogen bonds : angle 4.22680 ( 1293) covalent geometry : bond 0.00221 ( 8882) covalent geometry : angle 0.55673 (12033) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7463 (mt-10) REVERT: A 209 GLU cc_start: 0.7574 (tt0) cc_final: 0.7142 (mt-10) REVERT: A 213 GLN cc_start: 0.7515 (tt0) cc_final: 0.6851 (mt0) REVERT: A 299 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7488 (pm20) REVERT: A 391 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.6435 (m-80) REVERT: B 153 ASP cc_start: 0.6986 (m-30) cc_final: 0.6748 (t70) REVERT: B 175 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7440 (pt0) REVERT: B 251 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7954 (mmt-90) REVERT: B 260 GLU cc_start: 0.8041 (tt0) cc_final: 0.7646 (tt0) REVERT: E 34 MET cc_start: 0.4642 (mmm) cc_final: 0.4027 (mmm) REVERT: E 230 MET cc_start: 0.2298 (ttp) cc_final: 0.1869 (mpt) REVERT: R 141 MET cc_start: 0.7258 (ptp) cc_final: 0.6548 (tmt) REVERT: R 334 LYS cc_start: 0.6730 (tttp) cc_final: 0.6430 (tttp) outliers start: 16 outliers final: 12 residues processed: 120 average time/residue: 1.0643 time to fit residues: 137.7287 Evaluate side-chains 120 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 247 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 39 optimal weight: 0.0470 chunk 26 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 7 optimal weight: 0.0050 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 overall best weight: 1.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 392 ASN ** R 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.215797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.136816 restraints weight = 9439.618| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.05 r_work: 0.3318 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8882 Z= 0.156 Angle : 0.607 15.678 12033 Z= 0.303 Chirality : 0.042 0.151 1374 Planarity : 0.004 0.037 1529 Dihedral : 4.588 58.962 1205 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.03 % Allowed : 21.34 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.26), residues: 1091 helix: 1.89 (0.26), residues: 396 sheet: 0.25 (0.31), residues: 278 loop : 0.14 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE R 326 TYR 0.012 0.001 TYR R 156 ARG 0.004 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 460) hydrogen bonds : angle 4.38698 ( 1293) covalent geometry : bond 0.00364 ( 8882) covalent geometry : angle 0.60717 (12033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8329.26 seconds wall clock time: 144 minutes 18.33 seconds (8658.33 seconds total)