Starting phenix.real_space_refine on Wed Jan 15 17:59:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xog_38528/01_2025/8xog_38528_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xog_38528/01_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_38528/01_2025/8xog_38528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xog_38528/01_2025/8xog_38528.map" model { file = "/net/cci-nas-00/data/ceres_data/8xog_38528/01_2025/8xog_38528_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xog_38528/01_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-5571/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: 5.36, per 1000 atoms: 0.62 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.02 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: 2.71 Time building geometry restraints manager: 2.67 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: 1.500 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.720 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.940 ------------------------------------------------------------------------------- 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= 0.218 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 *********************** 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 : 1.072 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: 1.1191 time to fit residues: 142.4766 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 : 0.947 ------------------------------------------------------------------------------- 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 = 67)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.134764 restraints weight = 9354.583| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.37 r_work: 0.3315 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 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= 0.330 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 *********************** 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 : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7658 (mt-10) REVERT: A 213 GLN cc_start: 0.7618 (tt0) cc_final: 0.6933 (mt0) REVERT: A 391 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.6567 (m-80) REVERT: G 58 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7160 (mt-10) REVERT: R 141 MET cc_start: 0.7570 (ptp) cc_final: 0.6803 (tmt) outliers start: 31 outliers final: 12 residues processed: 128 average time/residue: 1.0190 time to fit residues: 141.1745 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 : 0.923 ------------------------------------------------------------------------------- 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: 1.9990 chunk 29 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 81 optimal weight: 0.0980 chunk 88 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 67 optimal weight: 0.0170 chunk 47 optimal weight: 1.9990 chunk 77 optimal weight: 30.0000 overall best weight: 0.5622 ------------------------------------------------------------------------------- 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 = 0.4407 r_free = 0.4407 target = 0.218582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139715 restraints weight = 9496.878| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.51 r_work: 0.3485 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8882 Z= 0.159 Angle : 0.533 10.332 12033 Z= 0.282 Chirality : 0.041 0.152 1374 Planarity : 0.004 0.053 1529 Dihedral : 4.633 58.126 1205 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.56 % Allowed : 15.58 % Favored : 81.86 % 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: 1.13 (0.26), residues: 1091 helix: 1.65 (0.25), residues: 402 sheet: 0.18 (0.32), residues: 268 loop : 0.44 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 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 *********************** 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 129 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7354 (mt-10) REVERT: A 213 GLN cc_start: 0.7543 (tt0) cc_final: 0.6875 (mt0) REVERT: A 232 ARG cc_start: 0.8049 (ttp-170) cc_final: 0.7834 (ttp-170) REVERT: A 391 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.6424 (m-80) REVERT: B 153 ASP cc_start: 0.6944 (m-30) cc_final: 0.6632 (t70) REVERT: E 230 MET cc_start: 0.2196 (ttp) cc_final: 0.1873 (mpt) REVERT: G 58 GLU cc_start: 0.7490 (mm-30) cc_final: 0.6998 (mt-10) REVERT: R 141 MET cc_start: 0.7180 (ptp) cc_final: 0.6499 (tmt) outliers start: 24 outliers final: 6 residues processed: 121 average time/residue: 1.0536 time to fit residues: 137.6452 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 : 0.930 ------------------------------------------------------------------------------- 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: 5.9990 chunk 19 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 66 optimal weight: 50.0000 chunk 81 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.4374 r_free = 0.4374 target = 0.215204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.142372 restraints weight = 9467.074| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.74 r_work: 0.3418 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8882 Z= 0.272 Angle : 0.577 9.148 12033 Z= 0.303 Chirality : 0.043 0.176 1374 Planarity : 0.004 0.048 1529 Dihedral : 4.801 58.128 1205 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.31 % Allowed : 15.58 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.07 (0.26), residues: 1091 helix: 1.62 (0.26), residues: 397 sheet: 0.12 (0.32), residues: 268 loop : 0.41 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.002 PHE R 326 TYR 0.012 0.001 TYR A 339 ARG 0.004 0.000 ARG G 27 *********************** 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 127 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7394 (mt-10) REVERT: A 213 GLN cc_start: 0.7594 (tt0) cc_final: 0.6899 (mt0) REVERT: A 266 LEU cc_start: 0.8491 (mt) cc_final: 0.8181 (mm) REVERT: A 299 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7451 (pm20) REVERT: A 391 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.6623 (m-80) REVERT: B 251 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7945 (mmt-90) REVERT: B 260 GLU cc_start: 0.8099 (tt0) cc_final: 0.7694 (tt0) REVERT: E 230 MET cc_start: 0.2292 (ttp) cc_final: 0.1900 (mpt) REVERT: G 58 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6987 (mt-10) REVERT: R 141 MET cc_start: 0.7472 (ptp) cc_final: 0.6675 (tmt) outliers start: 31 outliers final: 14 residues processed: 116 average time/residue: 1.2588 time to fit residues: 156.8028 Evaluate side-chains 109 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4395 r_free = 0.4395 target = 0.217377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.144968 restraints weight = 9369.251| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 3.00 r_work: 0.3447 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8882 Z= 0.175 Angle : 0.563 15.286 12033 Z= 0.284 Chirality : 0.042 0.156 1374 Planarity : 0.004 0.041 1529 Dihedral : 4.591 58.644 1205 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.35 % Allowed : 17.08 % 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: 1.13 (0.26), residues: 1091 helix: 1.71 (0.26), residues: 403 sheet: 0.11 (0.32), residues: 269 loop : 0.41 (0.32), residues: 419 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 A 212 TYR 0.010 0.001 TYR B 289 ARG 0.003 0.000 ARG G 27 *********************** 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: 22 poor density : 106 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 213 GLN cc_start: 0.7594 (tt0) cc_final: 0.6919 (mt0) REVERT: A 232 ARG cc_start: 0.8086 (ttp-170) cc_final: 0.7746 (ttp-170) REVERT: A 299 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7434 (pm20) REVERT: A 391 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.6598 (m-80) REVERT: B 153 ASP cc_start: 0.7060 (m-30) cc_final: 0.6699 (t70) REVERT: B 251 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7984 (mmt-90) REVERT: B 260 GLU cc_start: 0.8104 (tt0) cc_final: 0.7739 (tt0) REVERT: E 188 LEU cc_start: 0.3861 (mt) cc_final: 0.3469 (pt) REVERT: E 230 MET cc_start: 0.2294 (ttp) cc_final: 0.1840 (mpt) REVERT: R 141 MET cc_start: 0.7414 (ptp) cc_final: 0.6637 (tmt) outliers start: 22 outliers final: 11 residues processed: 121 average time/residue: 1.0707 time to fit residues: 139.6147 Evaluate side-chains 113 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 65 optimal weight: 0.0070 chunk 36 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 = 0.4402 r_free = 0.4402 target = 0.218320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140829 restraints weight = 9346.548| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.91 r_work: 0.3443 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8882 Z= 0.163 Angle : 0.543 14.329 12033 Z= 0.277 Chirality : 0.041 0.155 1374 Planarity : 0.004 0.039 1529 Dihedral : 4.484 58.597 1205 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.56 % Allowed : 19.10 % Favored : 78.34 % 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: 1.18 (0.26), residues: 1091 helix: 1.91 (0.26), residues: 397 sheet: 0.19 (0.31), residues: 270 loop : 0.24 (0.31), residues: 424 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 0.015 0.001 PHE R 326 TYR 0.016 0.001 TYR A 318 ARG 0.004 0.000 ARG G 27 *********************** 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 124 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7127 (mt-10) REVERT: A 213 GLN cc_start: 0.7565 (tt0) cc_final: 0.6862 (mt0) REVERT: A 232 ARG cc_start: 0.8009 (ttp-170) cc_final: 0.7709 (ttp-170) REVERT: A 299 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7464 (pm20) REVERT: A 370 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: A 391 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.6428 (m-80) REVERT: B 153 ASP cc_start: 0.6899 (m-30) cc_final: 0.6636 (t70) REVERT: B 251 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7868 (mmt-90) REVERT: B 260 GLU cc_start: 0.7967 (tt0) cc_final: 0.7626 (tt0) REVERT: E 34 MET cc_start: 0.4363 (mmm) cc_final: 0.3719 (mmm) REVERT: E 230 MET cc_start: 0.2287 (ttp) cc_final: 0.1861 (mpt) REVERT: R 141 MET cc_start: 0.7075 (ptp) cc_final: 0.6394 (tmt) REVERT: R 334 LYS cc_start: 0.6819 (tttp) cc_final: 0.6604 (tttp) outliers start: 24 outliers final: 13 residues processed: 118 average time/residue: 1.1687 time to fit residues: 148.3754 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 : 0.936 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 28 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 70 optimal weight: 20.0000 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.217989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.145239 restraints weight = 9475.065| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 3.01 r_work: 0.3454 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8882 Z= 0.170 Angle : 0.542 15.293 12033 Z= 0.277 Chirality : 0.041 0.148 1374 Planarity : 0.004 0.038 1529 Dihedral : 4.467 58.605 1205 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.77 % Allowed : 19.42 % Favored : 77.80 % 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: 1.22 (0.26), residues: 1091 helix: 1.96 (0.26), residues: 397 sheet: 0.19 (0.31), residues: 275 loop : 0.26 (0.31), residues: 419 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 0.012 0.001 TYR A 318 ARG 0.007 0.000 ARG G 27 *********************** 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 126 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7108 (mt-10) REVERT: A 213 GLN cc_start: 0.7559 (tt0) cc_final: 0.6860 (mt0) REVERT: A 232 ARG cc_start: 0.8019 (ttp-170) cc_final: 0.7769 (ttp-170) REVERT: A 299 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7469 (pm20) REVERT: A 310 ASP cc_start: 0.6753 (OUTLIER) cc_final: 0.6273 (t0) REVERT: A 391 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.6458 (m-80) REVERT: B 153 ASP cc_start: 0.6907 (m-30) cc_final: 0.6674 (t70) REVERT: B 251 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7845 (mmt-90) REVERT: B 260 GLU cc_start: 0.7939 (tt0) cc_final: 0.7506 (tt0) REVERT: E 34 MET cc_start: 0.4546 (mmm) cc_final: 0.3888 (mmm) REVERT: E 230 MET cc_start: 0.2401 (ttp) cc_final: 0.1879 (mpt) REVERT: R 141 MET cc_start: 0.7106 (ptp) cc_final: 0.6429 (tmt) REVERT: R 334 LYS cc_start: 0.6864 (tttp) cc_final: 0.6649 (tttp) outliers start: 26 outliers final: 14 residues processed: 118 average time/residue: 1.1088 time to fit residues: 140.9132 Evaluate side-chains 114 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP 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 190 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 226 GLU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 27 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 60 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 392 ASN B 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.218539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.144410 restraints weight = 9493.814| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.87 r_work: 0.3471 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2373 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= 0.159 Angle : 0.546 16.446 12033 Z= 0.277 Chirality : 0.041 0.144 1374 Planarity : 0.004 0.037 1529 Dihedral : 4.433 59.050 1205 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.92 % Allowed : 20.49 % Favored : 77.59 % 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: 2.01 (0.26), residues: 397 sheet: 0.20 (0.31), residues: 274 loop : 0.21 (0.32), residues: 420 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 0.010 0.001 TYR B 289 ARG 0.009 0.000 ARG G 27 *********************** 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 119 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7362 (mt-10) REVERT: A 213 GLN cc_start: 0.7522 (tt0) cc_final: 0.6834 (mt0) REVERT: A 299 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7420 (pm20) REVERT: A 391 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.6488 (m-80) REVERT: B 153 ASP cc_start: 0.7026 (m-30) cc_final: 0.6763 (t70) REVERT: B 251 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7906 (mmt-90) REVERT: B 260 GLU cc_start: 0.8086 (tt0) cc_final: 0.7616 (tt0) REVERT: E 34 MET cc_start: 0.4492 (mmm) cc_final: 0.3805 (mmm) REVERT: E 230 MET cc_start: 0.2335 (ttp) cc_final: 0.1843 (mpt) REVERT: R 141 MET cc_start: 0.7377 (ptp) cc_final: 0.6633 (tmt) outliers start: 18 outliers final: 12 residues processed: 114 average time/residue: 1.1864 time to fit residues: 145.5409 Evaluate side-chains 112 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP 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 391 TYR 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 185 SER Chi-restraints excluded: chain R residue 247 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.6114 > 50: distance: 76 - 95: 19.097 distance: 92 - 95: 15.541 distance: 95 - 96: 7.812 distance: 96 - 97: 3.625 distance: 96 - 99: 13.539 distance: 97 - 98: 17.582 distance: 97 - 106: 4.951 distance: 99 - 100: 20.789 distance: 100 - 101: 9.754 distance: 101 - 102: 14.110 distance: 103 - 104: 9.526 distance: 103 - 105: 3.709 distance: 106 - 107: 12.484 distance: 107 - 108: 11.272 distance: 107 - 110: 11.423 distance: 108 - 111: 5.218 distance: 111 - 112: 19.771 distance: 112 - 113: 3.337 distance: 112 - 115: 20.296 distance: 113 - 114: 20.898 distance: 113 - 119: 14.596 distance: 115 - 116: 7.996 distance: 116 - 117: 15.223 distance: 117 - 118: 20.448 distance: 120 - 121: 12.323 distance: 120 - 123: 7.110 distance: 121 - 122: 30.633 distance: 121 - 130: 22.879 distance: 123 - 124: 15.865 distance: 124 - 125: 16.314 distance: 125 - 126: 5.457 distance: 126 - 127: 4.940 distance: 127 - 128: 8.193 distance: 127 - 129: 33.389 distance: 130 - 131: 16.096 distance: 131 - 132: 16.118 distance: 131 - 134: 20.094 distance: 132 - 133: 35.450 distance: 132 - 136: 28.717 distance: 134 - 135: 36.056 distance: 136 - 137: 26.446 distance: 137 - 138: 14.947 distance: 137 - 140: 36.337 distance: 138 - 139: 22.513 distance: 138 - 142: 8.640 distance: 140 - 141: 18.876 distance: 142 - 143: 8.114 distance: 143 - 144: 5.489 distance: 143 - 146: 27.086 distance: 144 - 145: 12.882 distance: 144 - 150: 6.652 distance: 147 - 148: 34.127 distance: 147 - 149: 22.869 distance: 151 - 154: 7.881 distance: 152 - 153: 9.963 distance: 152 - 161: 3.142 distance: 154 - 155: 11.362 distance: 155 - 156: 15.658 distance: 155 - 157: 12.464 distance: 156 - 158: 16.378 distance: 157 - 159: 17.444 distance: 158 - 160: 11.811 distance: 159 - 160: 14.509 distance: 161 - 162: 17.322 distance: 162 - 163: 16.140 distance: 162 - 165: 15.255 distance: 163 - 164: 10.046 distance: 163 - 172: 18.443 distance: 165 - 166: 13.477 distance: 166 - 167: 17.683 distance: 167 - 168: 6.693 distance: 168 - 169: 11.355 distance: 169 - 170: 5.667 distance: 169 - 171: 7.125 distance: 172 - 173: 4.034 distance: 173 - 174: 13.896 distance: 173 - 176: 5.800 distance: 174 - 175: 9.478 distance: 174 - 179: 10.417 distance: 175 - 200: 17.216 distance: 176 - 177: 14.449 distance: 176 - 178: 18.433