Starting phenix.real_space_refine on Wed Sep 17 12:25:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xog_38528/09_2025/8xog_38528_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xog_38528/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xog_38528/09_2025/8xog_38528_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xog_38528/09_2025/8xog_38528_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xog_38528/09_2025/8xog_38528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xog_38528/09_2025/8xog_38528.map" } resolution = 2.9 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= 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'TYR: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: {'ARG:plan': 2, 'GLN:plan1': 1, 'TYR: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: 2.41, per 1000 atoms: 0.28 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: 0.87 Conformation dependent library (CDL) restraints added in 514.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.26 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: 1.50 Time building geometry restraints manager: 1.14 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: 1.380 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.210 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.830 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (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 ARG 0.009 0.000 ARG B 219 TYR 0.009 0.001 TYR A 391 PHE 0.023 0.001 PHE R 326 TRP 0.015 0.001 TRP A 234 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8882) covalent geometry : angle 0.56125 (12033) hydrogen bonds : bond 0.18232 ( 460) hydrogen bonds : angle 7.01214 ( 1293) *********************** 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 : 0.341 Fit side-chains revert: symmetry clash 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: 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: 0.5471 time to fit residues: 69.1119 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 : 0.350 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 0.0010 overall best weight: 0.8188 ------------------------------------------------------------------------------- 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 = 0.4381 r_free = 0.4381 target = 0.218738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.138292 restraints weight = 9461.224| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.44 r_work: 0.3298 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1213 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= 0.134 Angle : 0.575 8.592 12033 Z= 0.307 Chirality : 0.043 0.189 1374 Planarity : 0.004 0.068 1529 Dihedral : 4.782 58.272 1205 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.03 % Allowed : 15.58 % Favored : 82.39 % 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 aren not related in a simple way. whole: 1.13 (0.26), residues: 1091 helix: 1.59 (0.25), residues: 400 sheet: 0.31 (0.32), residues: 260 loop : 0.40 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.012 0.001 TYR E 190 PHE 0.017 0.001 PHE R 326 TRP 0.021 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8882) covalent geometry : angle 0.57498 (12033) hydrogen bonds : bond 0.04512 ( 460) hydrogen bonds : angle 5.05797 ( 1293) *********************** 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 130 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7630 (mt-10) REVERT: A 213 GLN cc_start: 0.7585 (tt0) cc_final: 0.6948 (mt0) REVERT: A 391 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.6540 (m-80) REVERT: B 153 ASP cc_start: 0.6906 (m-30) cc_final: 0.6682 (t70) REVERT: B 165 THR cc_start: 0.8274 (p) cc_final: 0.7986 (t) REVERT: G 58 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7115 (mt-10) REVERT: R 141 MET cc_start: 0.7338 (ptp) cc_final: 0.6730 (tmt) outliers start: 19 outliers final: 6 residues processed: 123 average time/residue: 0.5342 time to fit residues: 70.7114 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 : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 165 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 76 optimal weight: 30.0000 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 B 175 GLN R 140 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.216692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.143377 restraints weight = 9431.065| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.97 r_work: 0.3429 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8882 Z= 0.147 Angle : 0.557 10.136 12033 Z= 0.295 Chirality : 0.042 0.159 1374 Planarity : 0.004 0.055 1529 Dihedral : 4.744 57.964 1205 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.99 % Allowed : 15.69 % Favored : 81.32 % 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 aren not related in a simple way. whole: 1.19 (0.26), residues: 1091 helix: 1.70 (0.25), residues: 402 sheet: 0.33 (0.32), residues: 260 loop : 0.35 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.010 0.001 TYR A 339 PHE 0.015 0.001 PHE R 326 TRP 0.018 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8882) covalent geometry : angle 0.55740 (12033) hydrogen bonds : bond 0.04355 ( 460) hydrogen bonds : angle 4.76738 ( 1293) *********************** 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 133 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7423 (mt-10) REVERT: A 213 GLN cc_start: 0.7562 (tt0) cc_final: 0.6891 (mt0) REVERT: A 391 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.6543 (m-80) REVERT: B 153 ASP cc_start: 0.7029 (m-30) cc_final: 0.6734 (t70) REVERT: B 165 THR cc_start: 0.8165 (p) cc_final: 0.7870 (t) REVERT: E 230 MET cc_start: 0.2136 (ttp) cc_final: 0.1853 (mpt) REVERT: G 58 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7093 (mt-10) REVERT: R 141 MET cc_start: 0.7337 (ptp) cc_final: 0.6659 (tmt) outliers start: 28 outliers final: 15 residues processed: 122 average time/residue: 0.5083 time to fit residues: 67.0242 Evaluate side-chains 114 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 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 243 THR Chi-restraints excluded: chain E residue 155 VAL 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 Chi-restraints excluded: chain R residue 311 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 2 optimal weight: 2.9990 chunk 100 optimal weight: 0.0980 chunk 89 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- 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 R 140 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.217999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.145633 restraints weight = 9516.832| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.92 r_work: 0.3464 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1807 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= 0.116 Angle : 0.518 7.748 12033 Z= 0.274 Chirality : 0.041 0.153 1374 Planarity : 0.004 0.046 1529 Dihedral : 4.554 58.010 1205 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.88 % Allowed : 16.12 % Favored : 81.00 % 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 aren not related in a simple way. whole: 1.25 (0.26), residues: 1091 helix: 1.83 (0.26), residues: 402 sheet: 0.28 (0.32), residues: 261 loop : 0.36 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.010 0.001 TYR B 289 PHE 0.015 0.001 PHE R 326 TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8882) covalent geometry : angle 0.51755 (12033) hydrogen bonds : bond 0.03873 ( 460) hydrogen bonds : angle 4.51935 ( 1293) *********************** 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 131 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7372 (mt-10) REVERT: A 213 GLN cc_start: 0.7581 (tt0) cc_final: 0.6913 (mt0) REVERT: A 299 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7420 (pm20) REVERT: A 391 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.6586 (m-80) REVERT: B 153 ASP cc_start: 0.6943 (m-30) cc_final: 0.6689 (t70) REVERT: B 165 THR cc_start: 0.8045 (p) cc_final: 0.7822 (t) REVERT: E 230 MET cc_start: 0.2275 (ttp) cc_final: 0.1909 (mpt) REVERT: G 58 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7037 (mt-10) REVERT: R 141 MET cc_start: 0.7306 (ptp) cc_final: 0.6648 (tmt) outliers start: 27 outliers final: 11 residues processed: 117 average time/residue: 0.5703 time to fit residues: 71.5195 Evaluate side-chains 112 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 96 optimal weight: 0.0770 chunk 47 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- 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 R 54 GLN ** R 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.217248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.144737 restraints weight = 9442.999| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.95 r_work: 0.3448 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1928 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= 0.126 Angle : 0.536 14.286 12033 Z= 0.279 Chirality : 0.042 0.151 1374 Planarity : 0.004 0.042 1529 Dihedral : 4.552 58.249 1205 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.31 % Allowed : 16.33 % Favored : 80.36 % 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 aren not related in a simple way. whole: 1.25 (0.26), residues: 1091 helix: 1.85 (0.26), residues: 402 sheet: 0.24 (0.32), residues: 263 loop : 0.37 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.009 0.001 TYR B 289 PHE 0.016 0.001 PHE R 326 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8882) covalent geometry : angle 0.53580 (12033) hydrogen bonds : bond 0.03891 ( 460) hydrogen bonds : angle 4.43874 ( 1293) *********************** 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 138 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.7611 (tt0) cc_final: 0.6922 (mt0) REVERT: A 299 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7454 (pm20) REVERT: A 391 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.6482 (m-80) REVERT: B 153 ASP cc_start: 0.7002 (m-30) cc_final: 0.6733 (t70) REVERT: B 165 THR cc_start: 0.8041 (p) cc_final: 0.7794 (t) REVERT: B 215 GLU cc_start: 0.7174 (tt0) cc_final: 0.6901 (tt0) REVERT: B 251 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7974 (mmt-90) REVERT: B 260 GLU cc_start: 0.8105 (tt0) cc_final: 0.7834 (tt0) REVERT: E 230 MET cc_start: 0.2244 (ttp) cc_final: 0.1887 (mpt) REVERT: G 58 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7039 (mt-10) REVERT: R 141 MET cc_start: 0.7355 (ptp) cc_final: 0.6664 (tmt) REVERT: R 334 LYS cc_start: 0.6794 (tttp) cc_final: 0.6564 (tttp) outliers start: 31 outliers final: 15 residues processed: 128 average time/residue: 0.5560 time to fit residues: 76.4169 Evaluate side-chains 120 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 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 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 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 94 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 30.0000 chunk 44 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.4391 r_free = 0.4391 target = 0.217000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137294 restraints weight = 9435.531| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.51 r_work: 0.3443 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2076 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= 0.134 Angle : 0.545 14.813 12033 Z= 0.281 Chirality : 0.042 0.168 1374 Planarity : 0.004 0.039 1529 Dihedral : 4.537 58.445 1205 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.09 % Allowed : 17.72 % Favored : 79.19 % 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 aren not related in a simple way. whole: 1.23 (0.26), residues: 1091 helix: 1.91 (0.26), residues: 397 sheet: 0.24 (0.32), residues: 263 loop : 0.29 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 27 TYR 0.009 0.001 TYR R 156 PHE 0.016 0.001 PHE R 326 TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8882) covalent geometry : angle 0.54522 (12033) hydrogen bonds : bond 0.03883 ( 460) hydrogen bonds : angle 4.41951 ( 1293) *********************** 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 132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7317 (mt-10) REVERT: A 213 GLN cc_start: 0.7614 (tt0) cc_final: 0.6900 (mt0) REVERT: A 232 ARG cc_start: 0.8110 (ttm170) cc_final: 0.7799 (ttp-170) REVERT: A 299 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: A 370 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: A 391 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.6556 (m-80) REVERT: B 153 ASP cc_start: 0.6997 (m-30) cc_final: 0.6728 (t70) REVERT: B 165 THR cc_start: 0.8033 (p) cc_final: 0.7764 (t) REVERT: B 251 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7958 (mmt-90) REVERT: B 260 GLU cc_start: 0.8084 (tt0) cc_final: 0.7808 (tt0) REVERT: E 34 MET cc_start: 0.4357 (mmm) cc_final: 0.3721 (mmm) REVERT: E 230 MET cc_start: 0.2319 (ttp) cc_final: 0.1849 (mpt) REVERT: G 58 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6953 (mt-10) REVERT: R 141 MET cc_start: 0.7328 (ptp) cc_final: 0.6601 (tmt) REVERT: R 334 LYS cc_start: 0.6733 (tttp) cc_final: 0.6505 (tttp) outliers start: 29 outliers final: 15 residues processed: 120 average time/residue: 0.5798 time to fit residues: 74.4468 Evaluate side-chains 120 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 247 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 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 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 Chi-restraints excluded: chain R residue 311 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4397 r_free = 0.4397 target = 0.217625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143351 restraints weight = 9540.426| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.88 r_work: 0.3459 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8882 Z= 0.119 Angle : 0.557 15.740 12033 Z= 0.280 Chirality : 0.041 0.158 1374 Planarity : 0.004 0.038 1529 Dihedral : 4.469 58.586 1205 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.35 % Allowed : 19.42 % Favored : 78.23 % 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 aren not related in a simple way. whole: 1.27 (0.26), residues: 1091 helix: 1.98 (0.26), residues: 397 sheet: 0.24 (0.32), residues: 270 loop : 0.29 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 27 TYR 0.009 0.001 TYR B 289 PHE 0.015 0.001 PHE R 326 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8882) covalent geometry : angle 0.55739 (12033) hydrogen bonds : bond 0.03709 ( 460) hydrogen bonds : angle 4.33803 ( 1293) *********************** 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 130 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7365 (mt-10) REVERT: A 213 GLN cc_start: 0.7600 (tt0) cc_final: 0.6901 (mt0) REVERT: A 232 ARG cc_start: 0.8121 (ttm170) cc_final: 0.7882 (ttp-170) REVERT: A 299 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7426 (pm20) REVERT: A 310 ASP cc_start: 0.6581 (OUTLIER) cc_final: 0.6098 (t0) REVERT: A 391 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.6528 (m-80) REVERT: B 165 THR cc_start: 0.8011 (p) cc_final: 0.7762 (t) REVERT: B 251 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7982 (mmt-90) REVERT: B 260 GLU cc_start: 0.8114 (tt0) cc_final: 0.7875 (tt0) REVERT: E 34 MET cc_start: 0.4434 (mmm) cc_final: 0.4073 (mmm) REVERT: E 230 MET cc_start: 0.2284 (ttp) cc_final: 0.1853 (mpt) REVERT: G 58 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6923 (mt-10) REVERT: R 141 MET cc_start: 0.7386 (ptp) cc_final: 0.6624 (tmt) REVERT: R 334 LYS cc_start: 0.6800 (tttp) cc_final: 0.6575 (tttp) outliers start: 22 outliers final: 16 residues processed: 124 average time/residue: 0.5527 time to fit residues: 73.4441 Evaluate side-chains 122 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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 190 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain E residue 71 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 165 CYS 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 11 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 56 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4408 r_free = 0.4408 target = 0.218742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.139603 restraints weight = 9457.438| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.50 r_work: 0.3474 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8882 Z= 0.107 Angle : 0.539 14.985 12033 Z= 0.273 Chirality : 0.041 0.165 1374 Planarity : 0.003 0.036 1529 Dihedral : 4.373 58.716 1205 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.13 % Allowed : 20.60 % Favored : 77.27 % 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 aren not related in a simple way. whole: 1.30 (0.26), residues: 1091 helix: 2.08 (0.26), residues: 397 sheet: 0.26 (0.32), residues: 267 loop : 0.23 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 27 TYR 0.010 0.001 TYR B 289 PHE 0.016 0.001 PHE R 326 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 8882) covalent geometry : angle 0.53862 (12033) hydrogen bonds : bond 0.03583 ( 460) hydrogen bonds : angle 4.28505 ( 1293) *********************** 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 128 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7341 (mt-10) REVERT: A 209 GLU cc_start: 0.7571 (tt0) cc_final: 0.7097 (mt-10) REVERT: A 213 GLN cc_start: 0.7562 (tt0) cc_final: 0.6868 (mt0) REVERT: A 299 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7436 (pm20) REVERT: A 310 ASP cc_start: 0.6581 (OUTLIER) cc_final: 0.6089 (t0) REVERT: A 391 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.6531 (m-80) REVERT: B 38 ASP cc_start: 0.8108 (t70) cc_final: 0.7842 (t0) REVERT: B 165 THR cc_start: 0.7936 (p) cc_final: 0.7709 (t) REVERT: B 175 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7389 (pt0) REVERT: B 215 GLU cc_start: 0.7100 (tt0) cc_final: 0.6875 (tt0) REVERT: B 251 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7972 (mmt-90) REVERT: E 34 MET cc_start: 0.4512 (mmm) cc_final: 0.3923 (mmm) REVERT: E 230 MET cc_start: 0.2398 (ttp) cc_final: 0.1916 (mpt) REVERT: R 141 MET cc_start: 0.7323 (ptp) cc_final: 0.6607 (tmt) REVERT: R 334 LYS cc_start: 0.6812 (tttp) cc_final: 0.6600 (tttp) outliers start: 20 outliers final: 15 residues processed: 123 average time/residue: 0.5684 time to fit residues: 74.8750 Evaluate side-chains 120 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 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 190 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain E residue 71 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 60 optimal weight: 0.0470 overall best weight: 0.9482 ------------------------------------------------------------------------------- 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 266 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.217722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.145453 restraints weight = 9455.261| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.98 r_work: 0.3459 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2401 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= 0.124 Angle : 0.565 16.392 12033 Z= 0.284 Chirality : 0.042 0.165 1374 Planarity : 0.003 0.036 1529 Dihedral : 4.434 58.626 1205 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.92 % Allowed : 21.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.26), residues: 1091 helix: 2.05 (0.26), residues: 396 sheet: 0.25 (0.31), residues: 272 loop : 0.26 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 27 TYR 0.015 0.001 TYR A 318 PHE 0.015 0.001 PHE R 326 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8882) covalent geometry : angle 0.56499 (12033) hydrogen bonds : bond 0.03711 ( 460) hydrogen bonds : angle 4.29402 ( 1293) *********************** 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 120 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7353 (mt-10) REVERT: A 213 GLN cc_start: 0.7582 (tt0) cc_final: 0.6932 (mt0) REVERT: A 299 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: A 310 ASP cc_start: 0.6571 (OUTLIER) cc_final: 0.6096 (t0) REVERT: A 391 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.6534 (m-80) REVERT: B 38 ASP cc_start: 0.8126 (t70) cc_final: 0.7865 (t0) REVERT: B 165 THR cc_start: 0.8005 (p) cc_final: 0.7755 (t) REVERT: B 175 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7440 (pt0) REVERT: B 215 GLU cc_start: 0.7148 (tt0) cc_final: 0.6903 (tt0) REVERT: B 251 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7974 (mmt-90) REVERT: E 34 MET cc_start: 0.4291 (mmm) cc_final: 0.4052 (mmm) REVERT: E 230 MET cc_start: 0.2197 (ttp) cc_final: 0.1813 (mpt) REVERT: R 141 MET cc_start: 0.7323 (ptp) cc_final: 0.6644 (tmt) REVERT: R 334 LYS cc_start: 0.6799 (tttp) cc_final: 0.6589 (tttp) outliers start: 18 outliers final: 14 residues processed: 115 average time/residue: 0.5957 time to fit residues: 73.3088 Evaluate side-chains 118 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 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 190 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain E residue 71 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 59 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 46 optimal weight: 8.9990 chunk 93 optimal weight: 0.0060 chunk 10 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.4410 r_free = 0.4410 target = 0.218970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.142239 restraints weight = 9390.565| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 3.07 r_work: 0.3452 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 8882 Z= 0.109 Angle : 0.558 16.205 12033 Z= 0.278 Chirality : 0.041 0.153 1374 Planarity : 0.003 0.035 1529 Dihedral : 4.350 58.785 1205 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.03 % Allowed : 21.45 % Favored : 76.52 % 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 aren not related in a simple way. whole: 1.31 (0.26), residues: 1091 helix: 2.06 (0.26), residues: 396 sheet: 0.26 (0.31), residues: 277 loop : 0.27 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 27 TYR 0.013 0.001 TYR A 318 PHE 0.014 0.001 PHE R 326 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8882) covalent geometry : angle 0.55830 (12033) hydrogen bonds : bond 0.03618 ( 460) hydrogen bonds : angle 4.25598 ( 1293) ********************** 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 123 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7107 (mt-10) REVERT: A 209 GLU cc_start: 0.7453 (tt0) cc_final: 0.7058 (mt-10) REVERT: A 213 GLN cc_start: 0.7528 (tt0) cc_final: 0.6818 (mt0) REVERT: A 299 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7564 (pm20) REVERT: A 310 ASP cc_start: 0.6747 (OUTLIER) cc_final: 0.6279 (t0) REVERT: A 391 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.6452 (m-80) REVERT: B 38 ASP cc_start: 0.8144 (t70) cc_final: 0.7893 (t0) REVERT: B 165 THR cc_start: 0.7871 (p) cc_final: 0.7670 (t) REVERT: B 175 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7531 (pt0) REVERT: B 251 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7909 (mmt-90) REVERT: E 34 MET cc_start: 0.4476 (mmm) cc_final: 0.3852 (mmm) REVERT: E 230 MET cc_start: 0.2513 (ttp) cc_final: 0.1965 (mpt) REVERT: R 141 MET cc_start: 0.7001 (ptp) cc_final: 0.6416 (tmt) outliers start: 19 outliers final: 14 residues processed: 119 average time/residue: 0.5734 time to fit residues: 73.2184 Evaluate side-chains 122 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 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 190 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain E residue 71 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 92 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.218294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.140596 restraints weight = 9407.556| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.69 r_work: 0.3454 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8882 Z= 0.121 Angle : 0.571 16.022 12033 Z= 0.285 Chirality : 0.041 0.151 1374 Planarity : 0.003 0.036 1529 Dihedral : 4.401 58.702 1205 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.92 % Allowed : 21.13 % Favored : 76.95 % 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 aren not related in a simple way. whole: 1.31 (0.26), residues: 1091 helix: 2.03 (0.26), residues: 396 sheet: 0.32 (0.31), residues: 277 loop : 0.24 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 27 TYR 0.015 0.001 TYR A 318 PHE 0.014 0.001 PHE R 326 TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8882) covalent geometry : angle 0.57054 (12033) hydrogen bonds : bond 0.03680 ( 460) hydrogen bonds : angle 4.26263 ( 1293) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4337.97 seconds wall clock time: 74 minutes 36.97 seconds (4476.97 seconds total)