Starting phenix.real_space_refine on Tue Mar 3 21:37:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wzg_21972/03_2026/6wzg_21972.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wzg_21972/03_2026/6wzg_21972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wzg_21972/03_2026/6wzg_21972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wzg_21972/03_2026/6wzg_21972.map" model { file = "/net/cci-nas-00/data/ceres_data/6wzg_21972/03_2026/6wzg_21972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wzg_21972/03_2026/6wzg_21972.cif" } resolution = 2.3 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= 0.004 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 57 5.16 5 C 5643 2.51 5 N 1592 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8939 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "R" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2781 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 11, 'TRANS': 367} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 311 Unresolved non-hydrogen angles: 404 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ARG:plan': 8, 'ASP:plan': 6, 'GLN:plan1': 7, 'TRP:plan': 4, 'GLU:plan': 9, 'ASN:plan1': 6, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 194 Chain: "A" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1960 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Time building chain proxies: 1.81, per 1000 atoms: 0.20 Number of scatterers: 8939 At special positions: 0 Unit cell: (94.62, 100.43, 161.02, 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 57 16.00 O 1647 8.00 N 1592 7.00 C 5643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 45 " - pdb=" SG CYS R 75 " distance=2.04 Simple disulfide: pdb=" SG CYS R 66 " - pdb=" SG CYS R 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 89 " - pdb=" SG CYS R 123 " distance=2.05 Simple disulfide: pdb=" SG CYS R 215 " - pdb=" SG CYS R 285 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 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: 0.68 Conformation dependent library (CDL) restraints added in 351.3 milliseconds 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2182 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 10 sheets defined 42.2% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'P' and resid 1 through 27 removed outlier: 3.518A pdb=" N LEU P 22 " --> pdb=" O ARG P 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 48 Processing helix chain 'R' and resid 90 through 95 removed outlier: 3.934A pdb=" N MET R 95 " --> pdb=" O ARG R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 167 removed outlier: 3.587A pdb=" N ILE R 163 " --> pdb=" O VAL R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 201 removed outlier: 3.601A pdb=" N SER R 201 " --> pdb=" O ALA R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 246 Processing helix chain 'R' and resid 254 through 280 Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 291 through 326 removed outlier: 3.750A pdb=" N ILE R 297 " --> pdb=" O SER R 293 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 332 through 352 Proline residue: R 349 - end of helix Processing helix chain 'R' and resid 354 through 359 removed outlier: 4.474A pdb=" N PHE R 358 " --> pdb=" O HIS R 354 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 364 No H-bonds generated for 'chain 'R' and resid 362 through 364' Processing helix chain 'R' and resid 365 through 375 Processing helix chain 'R' and resid 376 through 378 No H-bonds generated for 'chain 'R' and resid 376 through 378' Processing helix chain 'R' and resid 379 through 389 Processing helix chain 'R' and resid 392 through 408 Processing helix chain 'A' and resid 13 through 40 Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.611A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 293 through 304 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: 3.700A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.744A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 7.002A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 5.898A 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: 6.972A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.729A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.967A 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: 6.874A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.600A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.972A 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: 6.611A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.117A 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: 6.120A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.653A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.573A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1347 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: 1.53 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1473 1.29 - 1.43: 2428 1.43 - 1.56: 5133 1.56 - 1.69: 0 1.69 - 1.82: 78 Bond restraints: 9112 Sorted by residual: bond pdb=" C HIS R 178 " pdb=" O HIS R 178 " ideal model delta sigma weight residual 1.237 1.164 0.072 1.17e-02 7.31e+03 3.82e+01 bond pdb=" N ILE B 93 " pdb=" CA ILE B 93 " ideal model delta sigma weight residual 1.460 1.495 -0.035 7.60e-03 1.73e+04 2.09e+01 bond pdb=" C ILE R 297 " pdb=" O ILE R 297 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.23e-02 6.61e+03 2.07e+01 bond pdb=" C ARG R 174 " pdb=" O ARG R 174 " ideal model delta sigma weight residual 1.237 1.188 0.049 1.19e-02 7.06e+03 1.67e+01 bond pdb=" C ILE R 298 " pdb=" O ILE R 298 " ideal model delta sigma weight residual 1.231 1.187 0.044 1.07e-02 8.73e+03 1.66e+01 ... (remaining 9107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 10072 2.10 - 4.21: 2115 4.21 - 6.31: 125 6.31 - 8.41: 23 8.41 - 10.52: 4 Bond angle restraints: 12339 Sorted by residual: angle pdb=" N SER R 74 " pdb=" CA SER R 74 " pdb=" C SER R 74 " ideal model delta sigma weight residual 111.07 102.97 8.10 1.07e+00 8.73e-01 5.73e+01 angle pdb=" N ASP R 209 " pdb=" CA ASP R 209 " pdb=" C ASP R 209 " ideal model delta sigma weight residual 114.39 103.87 10.52 1.45e+00 4.76e-01 5.26e+01 angle pdb=" C THR R 326 " pdb=" CA THR R 326 " pdb=" CB THR R 326 " ideal model delta sigma weight residual 111.74 101.83 9.91 1.37e+00 5.33e-01 5.23e+01 angle pdb=" N ASP B 333 " pdb=" CA ASP B 333 " pdb=" C ASP B 333 " ideal model delta sigma weight residual 113.02 105.22 7.80 1.20e+00 6.94e-01 4.23e+01 angle pdb=" N ASP B 163 " pdb=" CA ASP B 163 " pdb=" C ASP B 163 " ideal model delta sigma weight residual 113.02 105.42 7.60 1.20e+00 6.94e-01 4.01e+01 ... (remaining 12334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4919 17.92 - 35.84: 406 35.84 - 53.76: 70 53.76 - 71.67: 22 71.67 - 89.59: 7 Dihedral angle restraints: 5424 sinusoidal: 2048 harmonic: 3376 Sorted by residual: dihedral pdb=" CB CYS R 89 " pdb=" SG CYS R 89 " pdb=" SG CYS R 123 " pdb=" CB CYS R 123 " ideal model delta sinusoidal sigma weight residual 93.00 169.26 -76.26 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" C TYR R 146 " pdb=" N TYR R 146 " pdb=" CA TYR R 146 " pdb=" CB TYR R 146 " ideal model delta harmonic sigma weight residual -122.60 -138.79 16.19 0 2.50e+00 1.60e-01 4.19e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 40.19 52.81 1 1.00e+01 1.00e-02 3.80e+01 ... (remaining 5421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 870 0.108 - 0.216: 435 0.216 - 0.324: 65 0.324 - 0.432: 13 0.432 - 0.540: 4 Chirality restraints: 1387 Sorted by residual: chirality pdb=" CA TYR R 146 " pdb=" N TYR R 146 " pdb=" C TYR R 146 " pdb=" CB TYR R 146 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.28e+00 chirality pdb=" CA ASN R 175 " pdb=" N ASN R 175 " pdb=" C ASN R 175 " pdb=" CB ASN R 175 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.79e+00 chirality pdb=" CA TRP A 234 " pdb=" N TRP A 234 " pdb=" C TRP A 234 " pdb=" CB TRP A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.15e+00 ... (remaining 1384 not shown) Planarity restraints: 1589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 205 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C SER A 205 " -0.059 2.00e-02 2.50e+03 pdb=" O SER A 205 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY A 206 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 277 " -0.016 2.00e-02 2.50e+03 3.16e-02 9.98e+00 pdb=" C TRP A 277 " 0.055 2.00e-02 2.50e+03 pdb=" O TRP A 277 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN A 278 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 332 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.60e+00 pdb=" C TRP B 332 " 0.051 2.00e-02 2.50e+03 pdb=" O TRP B 332 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP B 333 " -0.017 2.00e-02 2.50e+03 ... (remaining 1586 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1630 2.80 - 3.32: 9004 3.32 - 3.85: 14916 3.85 - 4.37: 19498 4.37 - 4.90: 30896 Nonbonded interactions: 75944 Sorted by model distance: nonbonded pdb=" OG SER A 205 " pdb=" O ILE A 207 " model vdw 2.270 3.040 nonbonded pdb=" N GLU R 251 " pdb=" OE1 GLU R 251 " model vdw 2.276 3.120 nonbonded pdb=" N VAL R 85 " pdb=" O LEU R 103 " model vdw 2.377 3.120 nonbonded pdb=" NE2 GLN B 220 " pdb=" OD1 ASP B 258 " model vdw 2.392 3.120 nonbonded pdb=" O GLU B 12 " pdb=" ND2 ASN B 16 " model vdw 2.394 3.120 ... (remaining 75939 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=0.00 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: 1.640 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.720 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: 0.000 Load rotamer database and sin/cos tables:9.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 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 : 0.012 0.072 9118 Z= 0.893 Angle : 1.563 10.517 12351 Z= 1.199 Chirality : 0.121 0.540 1387 Planarity : 0.007 0.034 1589 Dihedral : 14.021 89.594 3224 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.65 % Allowed : 9.35 % Favored : 89.00 % Cbeta Deviations : 1.65 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.24), residues: 1151 helix: 1.41 (0.24), residues: 453 sheet: 0.76 (0.34), residues: 208 loop : -0.32 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 228 TYR 0.018 0.002 TYR R 146 PHE 0.022 0.002 PHE G 61 TRP 0.022 0.003 TRP R 232 HIS 0.007 0.002 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.01172 ( 9112) covalent geometry : angle 1.56112 (12339) SS BOND : bond 0.00911 ( 6) SS BOND : angle 2.81721 ( 12) hydrogen bonds : bond 0.20309 ( 476) hydrogen bonds : angle 6.92264 ( 1347) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: R 321 MET cc_start: 0.6158 (tpt) cc_final: 0.5830 (mmm) REVERT: A 17 LYS cc_start: 0.6608 (pttp) cc_final: 0.6228 (tppt) REVERT: A 357 HIS cc_start: 0.8689 (OUTLIER) cc_final: 0.8263 (p90) REVERT: B 124 TYR cc_start: 0.8512 (m-80) cc_final: 0.8310 (m-80) outliers start: 15 outliers final: 3 residues processed: 178 average time/residue: 0.7150 time to fit residues: 133.5470 Evaluate side-chains 129 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 123 CYS Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 292 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 132 ASN R 178 HIS R 180 HIS R 229 ASN R 327 GLN R 354 HIS R 396 GLN R 404 GLN A 220 HIS A 362 HIS B 35 ASN B 91 HIS B 259 GLN B 340 ASN N 1 GLN N 3 GLN N 120 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.178547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.121551 restraints weight = 8271.473| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.43 r_work: 0.3207 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9118 Z= 0.143 Angle : 0.585 6.923 12351 Z= 0.326 Chirality : 0.043 0.142 1387 Planarity : 0.004 0.037 1589 Dihedral : 5.048 54.052 1273 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.31 % Allowed : 14.08 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.24), residues: 1151 helix: 2.32 (0.23), residues: 462 sheet: 0.78 (0.33), residues: 217 loop : -0.14 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 96 TYR 0.026 0.002 TYR R 146 PHE 0.020 0.002 PHE G 61 TRP 0.021 0.002 TRP B 82 HIS 0.005 0.001 HIS R 407 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9112) covalent geometry : angle 0.58327 (12339) SS BOND : bond 0.00310 ( 6) SS BOND : angle 1.51355 ( 12) hydrogen bonds : bond 0.05917 ( 476) hydrogen bonds : angle 4.82156 ( 1347) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: R 140 LEU cc_start: 0.7373 (mt) cc_final: 0.7108 (mm) REVERT: R 169 ARG cc_start: 0.6312 (ttt180) cc_final: 0.5955 (ttm-80) REVERT: R 297 ILE cc_start: 0.7608 (mt) cc_final: 0.7277 (mp) REVERT: A 24 LYS cc_start: 0.7266 (mmpt) cc_final: 0.7060 (pptt) REVERT: A 53 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7972 (pttp) REVERT: A 59 GLN cc_start: 0.7078 (mm-40) cc_final: 0.6756 (mm110) REVERT: A 240 ASP cc_start: 0.7743 (p0) cc_final: 0.7441 (p0) REVERT: B 9 GLN cc_start: 0.6328 (OUTLIER) cc_final: 0.6060 (tm-30) outliers start: 21 outliers final: 8 residues processed: 159 average time/residue: 0.6957 time to fit residues: 116.7528 Evaluate side-chains 137 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 CYS Chi-restraints excluded: chain R residue 123 CYS Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 75 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 0.1980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 259 GLN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.176491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.119271 restraints weight = 8202.029| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.41 r_work: 0.3176 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9118 Z= 0.138 Angle : 0.544 5.965 12351 Z= 0.306 Chirality : 0.042 0.143 1387 Planarity : 0.004 0.036 1589 Dihedral : 4.953 59.244 1267 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.64 % Allowed : 13.97 % Favored : 83.39 % 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 are not related in a simple way. whole: 1.68 (0.25), residues: 1151 helix: 2.64 (0.23), residues: 462 sheet: 0.52 (0.33), residues: 220 loop : -0.12 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.026 0.002 TYR R 146 PHE 0.018 0.002 PHE R 313 TRP 0.020 0.002 TRP A 234 HIS 0.004 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9112) covalent geometry : angle 0.54231 (12339) SS BOND : bond 0.00347 ( 6) SS BOND : angle 1.37207 ( 12) hydrogen bonds : bond 0.05652 ( 476) hydrogen bonds : angle 4.69078 ( 1347) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.352 Fit side-chains REVERT: R 135 ARG cc_start: 0.5837 (ttt90) cc_final: 0.5073 (ttm-80) REVERT: R 140 LEU cc_start: 0.7462 (mt) cc_final: 0.7195 (mm) REVERT: R 169 ARG cc_start: 0.6408 (ttt180) cc_final: 0.6044 (ttm-80) REVERT: R 297 ILE cc_start: 0.7642 (mt) cc_final: 0.7308 (mp) REVERT: R 366 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6745 (tmt) REVERT: A 24 LYS cc_start: 0.7336 (mmtt) cc_final: 0.7117 (pptt) REVERT: A 31 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7208 (tp40) REVERT: A 53 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7983 (pttp) REVERT: A 59 GLN cc_start: 0.7067 (mm-40) cc_final: 0.6748 (mm110) REVERT: A 240 ASP cc_start: 0.7785 (p0) cc_final: 0.7490 (p0) REVERT: B 9 GLN cc_start: 0.6319 (OUTLIER) cc_final: 0.6010 (tm-30) REVERT: B 261 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8526 (mp) outliers start: 24 outliers final: 7 residues processed: 148 average time/residue: 0.7458 time to fit residues: 116.0041 Evaluate side-chains 139 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 366 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 74 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 38 optimal weight: 0.0270 chunk 103 optimal weight: 0.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 136 HIS A 54 ASN A 387 HIS B 35 ASN B 268 ASN B 340 ASN N 120 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.176630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119507 restraints weight = 8349.258| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.42 r_work: 0.3185 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9118 Z= 0.123 Angle : 0.505 5.395 12351 Z= 0.285 Chirality : 0.041 0.144 1387 Planarity : 0.004 0.038 1589 Dihedral : 4.503 21.016 1266 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.75 % Allowed : 13.75 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.25), residues: 1151 helix: 2.82 (0.23), residues: 456 sheet: 0.49 (0.33), residues: 218 loop : -0.21 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 20 TYR 0.024 0.002 TYR R 146 PHE 0.017 0.002 PHE R 313 TRP 0.019 0.002 TRP A 234 HIS 0.003 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9112) covalent geometry : angle 0.50371 (12339) SS BOND : bond 0.00306 ( 6) SS BOND : angle 1.16106 ( 12) hydrogen bonds : bond 0.05076 ( 476) hydrogen bonds : angle 4.52889 ( 1347) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.259 Fit side-chains REVERT: R 135 ARG cc_start: 0.5786 (ttt90) cc_final: 0.4982 (ttm-80) REVERT: R 140 LEU cc_start: 0.7460 (mt) cc_final: 0.7213 (mm) REVERT: R 169 ARG cc_start: 0.6431 (ttt180) cc_final: 0.6054 (ttm-80) REVERT: R 221 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7312 (tp) REVERT: R 297 ILE cc_start: 0.7607 (mt) cc_final: 0.7267 (mp) REVERT: R 366 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6788 (tmt) REVERT: R 369 GLN cc_start: 0.7127 (tm-30) cc_final: 0.6586 (tm-30) REVERT: A 24 LYS cc_start: 0.7261 (mmtt) cc_final: 0.7018 (pptt) REVERT: A 31 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7261 (tp40) REVERT: A 53 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7986 (pttp) REVERT: A 240 ASP cc_start: 0.7764 (p0) cc_final: 0.7517 (p0) REVERT: B 9 GLN cc_start: 0.6314 (OUTLIER) cc_final: 0.6009 (tm-30) REVERT: B 214 ARG cc_start: 0.7600 (mmt180) cc_final: 0.7158 (mtt180) REVERT: B 261 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8564 (mp) REVERT: B 325 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8386 (mmt) outliers start: 25 outliers final: 7 residues processed: 147 average time/residue: 0.7570 time to fit residues: 116.7976 Evaluate side-chains 141 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 366 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 0.0470 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 50.0000 chunk 92 optimal weight: 0.7980 chunk 49 optimal weight: 20.0000 chunk 48 optimal weight: 0.0010 chunk 15 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 56 optimal weight: 0.0970 overall best weight: 0.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 340 ASN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.179097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.125648 restraints weight = 8356.627| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.67 r_work: 0.3209 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9118 Z= 0.099 Angle : 0.454 5.366 12351 Z= 0.256 Chirality : 0.040 0.137 1387 Planarity : 0.003 0.039 1589 Dihedral : 4.180 19.950 1266 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.21 % Allowed : 15.73 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.25), residues: 1151 helix: 3.19 (0.23), residues: 444 sheet: 0.40 (0.33), residues: 221 loop : -0.09 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.023 0.001 TYR R 146 PHE 0.014 0.001 PHE R 313 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 407 Details of bonding type rmsd covalent geometry : bond 0.00188 ( 9112) covalent geometry : angle 0.45326 (12339) SS BOND : bond 0.00234 ( 6) SS BOND : angle 1.00015 ( 12) hydrogen bonds : bond 0.04392 ( 476) hydrogen bonds : angle 4.28562 ( 1347) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.302 Fit side-chains REVERT: R 135 ARG cc_start: 0.5632 (ttt90) cc_final: 0.4806 (ttm-80) REVERT: R 169 ARG cc_start: 0.6410 (ttt180) cc_final: 0.5973 (ttm-80) REVERT: R 221 LEU cc_start: 0.7490 (tp) cc_final: 0.7284 (tp) REVERT: R 297 ILE cc_start: 0.7609 (mt) cc_final: 0.7278 (mp) REVERT: R 366 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6684 (tmt) REVERT: R 369 GLN cc_start: 0.7234 (tm-30) cc_final: 0.6551 (tm-30) REVERT: A 24 LYS cc_start: 0.7131 (mmtt) cc_final: 0.6877 (pptt) REVERT: A 28 LYS cc_start: 0.7874 (ttpp) cc_final: 0.7507 (tttp) REVERT: A 59 GLN cc_start: 0.7078 (mm-40) cc_final: 0.5794 (pt0) REVERT: A 240 ASP cc_start: 0.7816 (p0) cc_final: 0.7594 (p0) REVERT: A 307 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.7075 (mptt) outliers start: 11 outliers final: 6 residues processed: 145 average time/residue: 0.7778 time to fit residues: 118.2886 Evaluate side-chains 136 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 366 MET Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 110 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 51 optimal weight: 0.0870 chunk 9 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 11 optimal weight: 40.0000 chunk 24 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 102 optimal weight: 0.0770 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 268 ASN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.177751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.122819 restraints weight = 8291.783| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.73 r_work: 0.3186 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9118 Z= 0.110 Angle : 0.473 5.376 12351 Z= 0.266 Chirality : 0.040 0.139 1387 Planarity : 0.003 0.040 1589 Dihedral : 4.262 19.502 1266 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.20 % Allowed : 15.84 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.25), residues: 1151 helix: 3.22 (0.23), residues: 444 sheet: 0.30 (0.33), residues: 222 loop : -0.11 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 20 TYR 0.023 0.001 TYR R 146 PHE 0.015 0.001 PHE R 313 TRP 0.015 0.002 TRP A 234 HIS 0.003 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 9112) covalent geometry : angle 0.47223 (12339) SS BOND : bond 0.00299 ( 6) SS BOND : angle 0.85751 ( 12) hydrogen bonds : bond 0.04629 ( 476) hydrogen bonds : angle 4.32908 ( 1347) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.377 Fit side-chains REVERT: R 169 ARG cc_start: 0.6439 (ttt180) cc_final: 0.6063 (ttm-80) REVERT: R 221 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7247 (tp) REVERT: R 297 ILE cc_start: 0.7608 (mt) cc_final: 0.7267 (mp) REVERT: R 325 ARG cc_start: 0.6371 (OUTLIER) cc_final: 0.5670 (mpt-90) REVERT: R 369 GLN cc_start: 0.7218 (tm-30) cc_final: 0.6496 (tm-30) REVERT: A 24 LYS cc_start: 0.7227 (mmtt) cc_final: 0.6945 (pptt) REVERT: A 59 GLN cc_start: 0.7101 (mm-40) cc_final: 0.5829 (pt0) REVERT: A 240 ASP cc_start: 0.7817 (p0) cc_final: 0.7605 (p0) REVERT: A 307 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.7089 (mptt) REVERT: B 9 GLN cc_start: 0.6317 (OUTLIER) cc_final: 0.6018 (tm-30) REVERT: B 261 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8559 (mp) REVERT: B 325 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7793 (tpp) REVERT: B 339 TRP cc_start: 0.9145 (OUTLIER) cc_final: 0.8348 (m100) REVERT: N 43 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7307 (mmmm) outliers start: 20 outliers final: 9 residues processed: 136 average time/residue: 0.7188 time to fit residues: 102.7874 Evaluate side-chains 140 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain R residue 45 CYS Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 325 ARG Chi-restraints excluded: chain R residue 366 MET Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 48 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 5 optimal weight: 30.0000 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 327 GLN B 35 ASN B 340 ASN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.172440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.122199 restraints weight = 8192.727| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.66 r_work: 0.3112 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 9118 Z= 0.234 Angle : 0.642 7.085 12351 Z= 0.361 Chirality : 0.047 0.165 1387 Planarity : 0.005 0.051 1589 Dihedral : 5.011 25.614 1266 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.31 % Allowed : 15.29 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.24), residues: 1151 helix: 2.40 (0.23), residues: 450 sheet: 0.27 (0.33), residues: 214 loop : -0.33 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 251 TYR 0.027 0.003 TYR A 339 PHE 0.020 0.003 PHE R 313 TRP 0.018 0.003 TRP B 169 HIS 0.007 0.002 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 9112) covalent geometry : angle 0.64211 (12339) SS BOND : bond 0.00739 ( 6) SS BOND : angle 0.95751 ( 12) hydrogen bonds : bond 0.06471 ( 476) hydrogen bonds : angle 4.87861 ( 1347) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.345 Fit side-chains REVERT: R 169 ARG cc_start: 0.6561 (ttt180) cc_final: 0.6145 (ttm-80) REVERT: R 369 GLN cc_start: 0.7251 (tm-30) cc_final: 0.6500 (tm-30) REVERT: A 24 LYS cc_start: 0.7324 (mmtt) cc_final: 0.7081 (pptt) REVERT: A 31 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7240 (tp40) REVERT: A 314 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: B 9 GLN cc_start: 0.6470 (OUTLIER) cc_final: 0.6099 (tm-30) REVERT: B 261 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8544 (mp) REVERT: B 325 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8008 (tpp) outliers start: 21 outliers final: 10 residues processed: 134 average time/residue: 0.7816 time to fit residues: 109.7389 Evaluate side-chains 133 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain R residue 45 CYS Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 111 optimal weight: 0.2980 chunk 110 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 327 GLN B 35 ASN B 340 ASN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.175566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.118342 restraints weight = 8214.313| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.44 r_work: 0.3172 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9118 Z= 0.120 Angle : 0.499 5.503 12351 Z= 0.283 Chirality : 0.041 0.144 1387 Planarity : 0.003 0.040 1589 Dihedral : 4.595 21.910 1266 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.09 % Allowed : 15.62 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.24), residues: 1151 helix: 2.79 (0.23), residues: 450 sheet: 0.23 (0.33), residues: 222 loop : -0.25 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.024 0.002 TYR R 146 PHE 0.017 0.002 PHE R 313 TRP 0.020 0.002 TRP A 234 HIS 0.004 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9112) covalent geometry : angle 0.49806 (12339) SS BOND : bond 0.00305 ( 6) SS BOND : angle 0.84023 ( 12) hydrogen bonds : bond 0.05164 ( 476) hydrogen bonds : angle 4.53774 ( 1347) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.378 Fit side-chains REVERT: R 169 ARG cc_start: 0.6515 (ttt180) cc_final: 0.6139 (ttm-80) REVERT: R 221 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7345 (tp) REVERT: R 325 ARG cc_start: 0.6267 (OUTLIER) cc_final: 0.5713 (mpt-90) REVERT: R 369 GLN cc_start: 0.7300 (tm-30) cc_final: 0.6617 (tm-30) REVERT: A 24 LYS cc_start: 0.7258 (mmtt) cc_final: 0.7011 (pptt) REVERT: A 31 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7261 (tp40) REVERT: A 59 GLN cc_start: 0.7130 (mm-40) cc_final: 0.5848 (pt0) REVERT: B 9 GLN cc_start: 0.6452 (OUTLIER) cc_final: 0.6094 (tm-30) REVERT: B 261 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8511 (mp) outliers start: 19 outliers final: 8 residues processed: 135 average time/residue: 0.7736 time to fit residues: 109.5028 Evaluate side-chains 132 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 325 ARG Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 0.0980 chunk 19 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 50.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 340 ASN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.174535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.117152 restraints weight = 8168.915| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.42 r_work: 0.3153 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9118 Z= 0.141 Angle : 0.533 5.482 12351 Z= 0.301 Chirality : 0.042 0.141 1387 Planarity : 0.004 0.041 1589 Dihedral : 4.670 23.247 1266 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.65 % Allowed : 15.84 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.24), residues: 1151 helix: 2.73 (0.23), residues: 450 sheet: 0.15 (0.33), residues: 214 loop : -0.31 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 20 TYR 0.023 0.002 TYR R 146 PHE 0.018 0.002 PHE R 313 TRP 0.018 0.002 TRP A 234 HIS 0.005 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9112) covalent geometry : angle 0.52991 (12339) SS BOND : bond 0.00399 ( 6) SS BOND : angle 1.76847 ( 12) hydrogen bonds : bond 0.05397 ( 476) hydrogen bonds : angle 4.59955 ( 1347) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.395 Fit side-chains REVERT: R 169 ARG cc_start: 0.6506 (ttt180) cc_final: 0.6130 (ttm-80) REVERT: R 221 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7316 (tp) REVERT: R 369 GLN cc_start: 0.7316 (tm-30) cc_final: 0.6622 (tm-30) REVERT: A 24 LYS cc_start: 0.7301 (mmtt) cc_final: 0.7081 (pptt) REVERT: A 31 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7239 (tp40) REVERT: A 59 GLN cc_start: 0.7103 (mm-40) cc_final: 0.5858 (pt0) REVERT: B 9 GLN cc_start: 0.6463 (OUTLIER) cc_final: 0.6097 (tm-30) REVERT: B 261 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8522 (mp) REVERT: B 325 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7940 (tpp) outliers start: 15 outliers final: 7 residues processed: 133 average time/residue: 0.7857 time to fit residues: 109.5207 Evaluate side-chains 135 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 340 ASN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.174197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.116800 restraints weight = 8175.764| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.43 r_work: 0.3151 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9118 Z= 0.149 Angle : 0.542 5.496 12351 Z= 0.306 Chirality : 0.043 0.143 1387 Planarity : 0.004 0.042 1589 Dihedral : 4.717 23.713 1266 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.54 % Allowed : 16.06 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.24), residues: 1151 helix: 2.68 (0.23), residues: 450 sheet: 0.25 (0.33), residues: 213 loop : -0.32 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 356 TYR 0.023 0.002 TYR R 146 PHE 0.018 0.002 PHE R 313 TRP 0.018 0.002 TRP A 234 HIS 0.005 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9112) covalent geometry : angle 0.53967 (12339) SS BOND : bond 0.00417 ( 6) SS BOND : angle 1.62875 ( 12) hydrogen bonds : bond 0.05509 ( 476) hydrogen bonds : angle 4.64758 ( 1347) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.363 Fit side-chains REVERT: R 169 ARG cc_start: 0.6493 (ttt180) cc_final: 0.6121 (ttm-80) REVERT: R 221 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7324 (tp) REVERT: R 325 ARG cc_start: 0.6255 (OUTLIER) cc_final: 0.5621 (mpt-90) REVERT: R 369 GLN cc_start: 0.7326 (tm-30) cc_final: 0.6623 (tm-30) REVERT: A 31 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7244 (tp40) REVERT: A 59 GLN cc_start: 0.7092 (mm-40) cc_final: 0.6754 (mm110) REVERT: B 9 GLN cc_start: 0.6488 (OUTLIER) cc_final: 0.6119 (tm-30) REVERT: B 261 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8527 (mp) REVERT: B 325 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.7947 (tpp) REVERT: N 105 ARG cc_start: 0.7620 (mtm110) cc_final: 0.7408 (mtm110) outliers start: 14 outliers final: 7 residues processed: 133 average time/residue: 0.7999 time to fit residues: 111.2996 Evaluate side-chains 137 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 325 ARG Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 76 optimal weight: 0.0470 chunk 93 optimal weight: 2.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.175293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120347 restraints weight = 8128.001| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.68 r_work: 0.3153 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9118 Z= 0.124 Angle : 0.509 5.493 12351 Z= 0.288 Chirality : 0.041 0.144 1387 Planarity : 0.003 0.041 1589 Dihedral : 4.542 22.037 1266 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.65 % Allowed : 15.84 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.24), residues: 1151 helix: 2.81 (0.24), residues: 450 sheet: 0.17 (0.33), residues: 212 loop : -0.30 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.023 0.002 TYR R 146 PHE 0.017 0.002 PHE R 313 TRP 0.019 0.002 TRP A 234 HIS 0.004 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9112) covalent geometry : angle 0.50738 (12339) SS BOND : bond 0.00314 ( 6) SS BOND : angle 1.45011 ( 12) hydrogen bonds : bond 0.05089 ( 476) hydrogen bonds : angle 4.51278 ( 1347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5082.02 seconds wall clock time: 86 minutes 41.98 seconds (5201.98 seconds total)