Starting phenix.real_space_refine on Fri Aug 22 23:43:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zla_14778/08_2025/7zla_14778.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zla_14778/08_2025/7zla_14778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zla_14778/08_2025/7zla_14778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zla_14778/08_2025/7zla_14778.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zla_14778/08_2025/7zla_14778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zla_14778/08_2025/7zla_14778.map" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 94 5.49 5 S 18 5.16 5 C 5227 2.51 5 N 1497 2.21 5 O 1788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8624 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2995 Classifications: {'peptide': 364} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 347} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3743 Classifications: {'peptide': 458} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 435} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 935 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "D" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 951 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Time building chain proxies: 2.27, per 1000 atoms: 0.26 Number of scatterers: 8624 At special positions: 0 Unit cell: (83.566, 112.014, 131.572, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 94 15.00 O 1788 8.00 N 1497 7.00 C 5227 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 268.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1556 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 5 sheets defined 43.6% alpha, 8.9% beta 32 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.734A pdb=" N TRP A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 removed outlier: 3.574A pdb=" N LEU A 140 " --> pdb=" O HIS A 137 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 141 " --> pdb=" O ARG A 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 137 through 141' Processing helix chain 'A' and resid 148 through 164 removed outlier: 3.818A pdb=" N ILE A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 178 through 190 removed outlier: 4.408A pdb=" N GLN A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.696A pdb=" N VAL A 232 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 268 removed outlier: 3.900A pdb=" N ARG A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N HIS A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.999A pdb=" N VAL A 315 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 316' Processing helix chain 'A' and resid 323 through 334 removed outlier: 3.895A pdb=" N HIS A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 removed outlier: 3.871A pdb=" N GLN A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 348 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 382 removed outlier: 4.008A pdb=" N ARG A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 418 removed outlier: 3.880A pdb=" N ALA A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 450 through 463 removed outlier: 3.820A pdb=" N ALA A 456 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 30 removed outlier: 4.026A pdb=" N ALA B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS B 25 " --> pdb=" O TYR B 21 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 27 " --> pdb=" O HIS B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 52 through 62 removed outlier: 3.677A pdb=" N VAL B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA B 58 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 130 removed outlier: 3.760A pdb=" N GLN B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 163 removed outlier: 3.642A pdb=" N HIS B 161 " --> pdb=" O TYR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 178 through 190 removed outlier: 4.080A pdb=" N GLN B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.680A pdb=" N LEU B 209 " --> pdb=" O MET B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 254 through 268 removed outlier: 4.139A pdb=" N HIS B 268 " --> pdb=" O TRP B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 295 Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'B' and resid 342 through 355 removed outlier: 4.145A pdb=" N ALA B 351 " --> pdb=" O GLN B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 382 removed outlier: 3.699A pdb=" N LYS B 360 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG B 382 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 418 removed outlier: 4.146A pdb=" N LEU B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 449 No H-bonds generated for 'chain 'B' and resid 447 through 449' Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.762A pdb=" N TRP B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 175 removed outlier: 6.559A pdb=" N ILE A 273 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU A 304 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLU A 275 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA A 306 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL A 239 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ASP A 276 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR A 241 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR A 195 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 390 removed outlier: 4.074A pdb=" N VAL A 399 " --> pdb=" O ILE A 390 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 72 removed outlier: 4.223A pdb=" N ILE B 72 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLY B 76 " --> pdb=" O ILE B 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 173 through 175 removed outlier: 3.558A pdb=" N GLY B 305 " --> pdb=" O TYR B 319 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR B 303 " --> pdb=" O VAL B 321 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE B 273 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU B 304 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU B 275 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N ALA B 306 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL B 239 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ASP B 276 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR B 241 " --> pdb=" O ASP B 276 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL B 194 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N TYR B 240 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY B 196 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 387 through 390 removed outlier: 3.583A pdb=" N LEU B 388 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE B 390 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL B 399 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR B 423 " --> pdb=" O VAL B 440 " (cutoff:3.500A) 225 hydrogen bonds defined for protein. 636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1965 1.33 - 1.45: 2321 1.45 - 1.57: 4516 1.57 - 1.69: 184 1.69 - 1.81: 32 Bond restraints: 9018 Sorted by residual: bond pdb=" OP4 LLP A 309 " pdb=" P LLP A 309 " ideal model delta sigma weight residual 1.726 1.547 0.179 2.00e-02 2.50e+03 7.99e+01 bond pdb=" OP4 LLP B 309 " pdb=" P LLP B 309 " ideal model delta sigma weight residual 1.726 1.548 0.178 2.00e-02 2.50e+03 7.89e+01 bond pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " ideal model delta sigma weight residual 1.273 1.437 -0.164 2.00e-02 2.50e+03 6.75e+01 bond pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " ideal model delta sigma weight residual 1.273 1.434 -0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" C4 LLP B 309 " pdb=" C4' LLP B 309 " ideal model delta sigma weight residual 1.464 1.617 -0.153 2.00e-02 2.50e+03 5.87e+01 ... (remaining 9013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 12155 2.10 - 4.20: 405 4.20 - 6.30: 40 6.30 - 8.40: 8 8.40 - 10.50: 5 Bond angle restraints: 12613 Sorted by residual: angle pdb=" N LYS A 367 " pdb=" CA LYS A 367 " pdb=" C LYS A 367 " ideal model delta sigma weight residual 111.14 104.92 6.22 1.08e+00 8.57e-01 3.32e+01 angle pdb=" C TYR A 278 " pdb=" CA TYR A 278 " pdb=" CB TYR A 278 " ideal model delta sigma weight residual 117.23 111.22 6.01 1.36e+00 5.41e-01 1.95e+01 angle pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " pdb=" C4 LLP B 309 " ideal model delta sigma weight residual 120.09 109.59 10.50 3.00e+00 1.11e-01 1.22e+01 angle pdb=" N LYS A 367 " pdb=" CA LYS A 367 " pdb=" CB LYS A 367 " ideal model delta sigma weight residual 110.07 105.23 4.84 1.45e+00 4.76e-01 1.11e+01 angle pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " pdb=" C4 LLP A 309 " ideal model delta sigma weight residual 120.09 110.13 9.96 3.00e+00 1.11e-01 1.10e+01 ... (remaining 12608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.58: 4581 29.58 - 59.16: 551 59.16 - 88.73: 33 88.73 - 118.31: 1 118.31 - 147.89: 4 Dihedral angle restraints: 5170 sinusoidal: 2742 harmonic: 2428 Sorted by residual: dihedral pdb=" CA HIS B 137 " pdb=" C HIS B 137 " pdb=" N ARG B 138 " pdb=" CA ARG B 138 " ideal model delta harmonic sigma weight residual -180.00 -153.80 -26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA HIS B 298 " pdb=" C HIS B 298 " pdb=" N ASN B 299 " pdb=" CA ASN B 299 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA ASP A 199 " pdb=" C ASP A 199 " pdb=" N PRO A 200 " pdb=" CA PRO A 200 " ideal model delta harmonic sigma weight residual 180.00 156.89 23.11 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 5167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 963 0.045 - 0.090: 316 0.090 - 0.136: 91 0.136 - 0.181: 10 0.181 - 0.226: 3 Chirality restraints: 1383 Sorted by residual: chirality pdb=" CB ILE A 231 " pdb=" CA ILE A 231 " pdb=" CG1 ILE A 231 " pdb=" CG2 ILE A 231 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA LYS A 367 " pdb=" N LYS A 367 " pdb=" C LYS A 367 " pdb=" CB LYS A 367 " 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 ARG B 382 " pdb=" N ARG B 382 " pdb=" C ARG B 382 " pdb=" CB ARG B 382 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1380 not shown) Planarity restraints: 1288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP A 309 " 0.166 2.00e-02 2.50e+03 2.96e-01 8.75e+02 pdb=" NZ LLP A 309 " -0.409 2.00e-02 2.50e+03 pdb=" C4 LLP A 309 " -0.128 2.00e-02 2.50e+03 pdb=" C4' LLP A 309 " 0.372 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 378 " -0.015 2.00e-02 2.50e+03 2.87e-02 8.23e+00 pdb=" C SER B 378 " 0.050 2.00e-02 2.50e+03 pdb=" O SER B 378 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU B 379 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 370 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C ARG B 370 " 0.045 2.00e-02 2.50e+03 pdb=" O ARG B 370 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG B 371 " -0.015 2.00e-02 2.50e+03 ... (remaining 1285 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 894 2.74 - 3.28: 8477 3.28 - 3.82: 14524 3.82 - 4.36: 16726 4.36 - 4.90: 26038 Nonbonded interactions: 66659 Sorted by model distance: nonbonded pdb=" O MET A 132 " pdb=" NH2 ARG B 125 " model vdw 2.198 3.120 nonbonded pdb=" OE1 GLU B 148 " pdb=" NE2 GLN B 347 " model vdw 2.203 3.120 nonbonded pdb=" OH TYR B 127 " pdb=" OE1 GLN B 355 " model vdw 2.205 3.040 nonbonded pdb=" O LYS A 386 " pdb=" NZ LYS A 403 " model vdw 2.213 3.120 nonbonded pdb=" OD2 ASP A 115 " pdb=" NZ LYS A 372 " model vdw 2.216 3.120 ... (remaining 66654 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.520 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 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 : 0.007 0.179 9018 Z= 0.353 Angle : 0.860 10.499 12613 Z= 0.483 Chirality : 0.048 0.226 1383 Planarity : 0.010 0.296 1288 Dihedral : 21.723 147.890 3614 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.28), residues: 812 helix: -1.06 (0.29), residues: 306 sheet: -0.84 (0.50), residues: 85 loop : -1.51 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 382 TYR 0.025 0.002 TYR A 212 PHE 0.020 0.003 PHE B 247 TRP 0.036 0.003 TRP A 264 HIS 0.008 0.002 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00725 ( 9018) covalent geometry : angle 0.86007 (12613) hydrogen bonds : bond 0.17597 ( 302) hydrogen bonds : angle 7.08822 ( 790) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.6770 (mmm) cc_final: 0.6560 (mmt) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0839 time to fit residues: 10.9998 Evaluate side-chains 57 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.0070 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.0030 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.5610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 HIS ** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.135202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.110168 restraints weight = 23297.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.112594 restraints weight = 13562.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.114316 restraints weight = 9058.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.115566 restraints weight = 6674.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.116350 restraints weight = 5318.688| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9018 Z= 0.131 Angle : 0.602 8.965 12613 Z= 0.329 Chirality : 0.041 0.155 1383 Planarity : 0.005 0.053 1288 Dihedral : 24.273 149.720 1965 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.24 % Allowed : 7.28 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.29), residues: 812 helix: -0.36 (0.30), residues: 313 sheet: -0.13 (0.51), residues: 99 loop : -1.20 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 382 TYR 0.017 0.001 TYR B 17 PHE 0.013 0.001 PHE B 128 TRP 0.018 0.002 TRP A 264 HIS 0.005 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9018) covalent geometry : angle 0.60238 (12613) hydrogen bonds : bond 0.04097 ( 302) hydrogen bonds : angle 4.36072 ( 790) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.280 Fit side-chains REVERT: A 278 TYR cc_start: 0.6574 (t80) cc_final: 0.6298 (t80) REVERT: A 367 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8083 (mttp) REVERT: B 110 HIS cc_start: 0.8505 (t70) cc_final: 0.8074 (t70) REVERT: B 380 LEU cc_start: 0.8318 (tp) cc_final: 0.8110 (pp) outliers start: 9 outliers final: 6 residues processed: 80 average time/residue: 0.0897 time to fit residues: 10.4380 Evaluate side-chains 64 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 234 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 84 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 80 optimal weight: 0.1980 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN A 183 GLN B 110 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.132196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.107870 restraints weight = 23709.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.110064 restraints weight = 14268.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.111665 restraints weight = 9743.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.112828 restraints weight = 7268.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.113357 restraints weight = 5817.307| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9018 Z= 0.152 Angle : 0.607 9.181 12613 Z= 0.331 Chirality : 0.042 0.155 1383 Planarity : 0.005 0.054 1288 Dihedral : 24.287 149.243 1965 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.34 % Allowed : 11.95 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.29), residues: 812 helix: -0.16 (0.30), residues: 313 sheet: 0.34 (0.49), residues: 105 loop : -1.19 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 163 TYR 0.017 0.001 TYR B 17 PHE 0.017 0.002 PHE A 352 TRP 0.010 0.001 TRP A 264 HIS 0.005 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9018) covalent geometry : angle 0.60663 (12613) hydrogen bonds : bond 0.04373 ( 302) hydrogen bonds : angle 4.25190 ( 790) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.306 Fit side-chains REVERT: A 132 MET cc_start: 0.5696 (ppp) cc_final: 0.5410 (ppp) REVERT: A 183 GLN cc_start: 0.6429 (OUTLIER) cc_final: 0.5866 (mt0) REVERT: B 110 HIS cc_start: 0.8631 (t-90) cc_final: 0.7857 (t70) REVERT: B 320 MET cc_start: 0.5993 (tmm) cc_final: 0.5721 (tmm) outliers start: 17 outliers final: 7 residues processed: 79 average time/residue: 0.0924 time to fit residues: 10.4702 Evaluate side-chains 64 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 400 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 37 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 74 optimal weight: 0.0040 chunk 6 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN A 263 HIS B 145 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.131897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.107831 restraints weight = 24099.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.109911 restraints weight = 14890.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.111422 restraints weight = 10328.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.112531 restraints weight = 7794.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.113130 restraints weight = 6279.654| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9018 Z= 0.148 Angle : 0.594 9.318 12613 Z= 0.325 Chirality : 0.042 0.153 1383 Planarity : 0.005 0.061 1288 Dihedral : 24.279 148.732 1965 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.47 % Allowed : 14.42 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.29), residues: 812 helix: -0.12 (0.30), residues: 315 sheet: 0.36 (0.50), residues: 106 loop : -1.22 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 364 TYR 0.013 0.001 TYR B 17 PHE 0.016 0.002 PHE A 352 TRP 0.011 0.002 TRP B 124 HIS 0.005 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9018) covalent geometry : angle 0.59443 (12613) hydrogen bonds : bond 0.04185 ( 302) hydrogen bonds : angle 4.15242 ( 790) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.312 Fit side-chains REVERT: A 132 MET cc_start: 0.5711 (ppp) cc_final: 0.5495 (ppp) REVERT: A 183 GLN cc_start: 0.6311 (OUTLIER) cc_final: 0.5778 (mt0) REVERT: A 271 ARG cc_start: 0.6367 (mtm-85) cc_final: 0.6164 (mtm-85) REVERT: A 403 LYS cc_start: 0.8009 (pttt) cc_final: 0.7745 (pttm) REVERT: B 110 HIS cc_start: 0.8741 (t-90) cc_final: 0.8313 (t-90) outliers start: 18 outliers final: 9 residues processed: 74 average time/residue: 0.0899 time to fit residues: 9.6769 Evaluate side-chains 69 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 400 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 73 optimal weight: 0.1980 chunk 59 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN B 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.130319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.106219 restraints weight = 24500.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.108392 restraints weight = 14679.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.109942 restraints weight = 10019.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.111107 restraints weight = 7490.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.111850 restraints weight = 5997.782| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9018 Z= 0.171 Angle : 0.628 9.613 12613 Z= 0.342 Chirality : 0.043 0.168 1383 Planarity : 0.005 0.059 1288 Dihedral : 24.381 148.224 1965 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.61 % Allowed : 16.21 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.30), residues: 812 helix: -0.06 (0.31), residues: 311 sheet: 0.29 (0.50), residues: 106 loop : -1.23 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 364 TYR 0.014 0.001 TYR B 17 PHE 0.018 0.002 PHE A 352 TRP 0.009 0.002 TRP A 264 HIS 0.006 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 9018) covalent geometry : angle 0.62784 (12613) hydrogen bonds : bond 0.04460 ( 302) hydrogen bonds : angle 4.23241 ( 790) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.5504 (ppp) cc_final: 0.5209 (ppp) REVERT: A 157 TYR cc_start: 0.6677 (OUTLIER) cc_final: 0.6403 (t80) REVERT: A 403 LYS cc_start: 0.8055 (pttt) cc_final: 0.7793 (pttm) REVERT: B 110 HIS cc_start: 0.8790 (t-90) cc_final: 0.8394 (t-90) REVERT: B 308 SER cc_start: 0.7481 (t) cc_final: 0.7120 (p) REVERT: B 320 MET cc_start: 0.6148 (tmm) cc_final: 0.5883 (tmm) REVERT: B 393 ARG cc_start: 0.5911 (pmt170) cc_final: 0.5532 (ptt-90) outliers start: 19 outliers final: 13 residues processed: 83 average time/residue: 0.0939 time to fit residues: 11.0459 Evaluate side-chains 76 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 400 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 52 optimal weight: 0.4980 chunk 66 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.131519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.107973 restraints weight = 24187.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.110030 restraints weight = 14816.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.111500 restraints weight = 10293.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.112621 restraints weight = 7773.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.113234 restraints weight = 6219.955| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9018 Z= 0.144 Angle : 0.598 9.795 12613 Z= 0.328 Chirality : 0.042 0.175 1383 Planarity : 0.005 0.059 1288 Dihedral : 24.316 148.346 1965 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.61 % Allowed : 17.17 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.30), residues: 812 helix: 0.06 (0.31), residues: 310 sheet: 0.38 (0.50), residues: 106 loop : -1.22 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 271 TYR 0.010 0.001 TYR B 17 PHE 0.034 0.002 PHE A 219 TRP 0.011 0.002 TRP A 264 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9018) covalent geometry : angle 0.59809 (12613) hydrogen bonds : bond 0.04078 ( 302) hydrogen bonds : angle 4.05826 ( 790) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.5714 (ppp) cc_final: 0.5460 (ppp) REVERT: A 157 TYR cc_start: 0.6548 (OUTLIER) cc_final: 0.6241 (t80) REVERT: A 403 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7610 (pttm) REVERT: B 110 HIS cc_start: 0.8758 (t-90) cc_final: 0.8338 (t-90) REVERT: B 202 TYR cc_start: 0.5850 (OUTLIER) cc_final: 0.4555 (t80) REVERT: B 320 MET cc_start: 0.6149 (tmm) cc_final: 0.5870 (tmm) REVERT: B 393 ARG cc_start: 0.5922 (pmt170) cc_final: 0.5589 (ptt-90) outliers start: 19 outliers final: 13 residues processed: 80 average time/residue: 0.0953 time to fit residues: 10.6844 Evaluate side-chains 77 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 400 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 66 optimal weight: 0.0970 chunk 60 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.130967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.106957 restraints weight = 24259.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.109168 restraints weight = 14596.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.110739 restraints weight = 9951.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.111712 restraints weight = 7405.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.112638 restraints weight = 5959.327| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9018 Z= 0.155 Angle : 0.614 9.911 12613 Z= 0.334 Chirality : 0.042 0.182 1383 Planarity : 0.005 0.059 1288 Dihedral : 24.307 148.295 1965 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.02 % Allowed : 17.03 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.30), residues: 812 helix: 0.02 (0.31), residues: 312 sheet: 0.37 (0.52), residues: 100 loop : -1.22 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 271 TYR 0.011 0.001 TYR B 17 PHE 0.022 0.002 PHE A 219 TRP 0.026 0.002 TRP A 264 HIS 0.004 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9018) covalent geometry : angle 0.61402 (12613) hydrogen bonds : bond 0.04160 ( 302) hydrogen bonds : angle 4.08161 ( 790) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.5438 (ppp) cc_final: 0.5183 (ppp) REVERT: A 157 TYR cc_start: 0.6579 (OUTLIER) cc_final: 0.6188 (t80) REVERT: A 271 ARG cc_start: 0.6239 (mtm-85) cc_final: 0.5975 (mtm-85) REVERT: A 403 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7664 (pttm) REVERT: B 110 HIS cc_start: 0.8811 (t-90) cc_final: 0.8438 (t-90) REVERT: B 202 TYR cc_start: 0.5946 (OUTLIER) cc_final: 0.4611 (t80) REVERT: B 308 SER cc_start: 0.7469 (t) cc_final: 0.7102 (p) REVERT: B 320 MET cc_start: 0.6070 (tmm) cc_final: 0.5748 (tmm) REVERT: B 393 ARG cc_start: 0.5886 (pmt170) cc_final: 0.5558 (ptt-90) outliers start: 22 outliers final: 14 residues processed: 83 average time/residue: 0.0948 time to fit residues: 11.2864 Evaluate side-chains 82 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 400 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN A 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.128356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.104855 restraints weight = 24447.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.106892 restraints weight = 14852.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.108423 restraints weight = 10274.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.109171 restraints weight = 7677.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.110251 restraints weight = 6343.185| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9018 Z= 0.201 Angle : 0.688 10.314 12613 Z= 0.373 Chirality : 0.045 0.198 1383 Planarity : 0.005 0.058 1288 Dihedral : 24.498 147.686 1965 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.30 % Allowed : 16.90 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.29), residues: 812 helix: -0.34 (0.30), residues: 312 sheet: 0.14 (0.52), residues: 100 loop : -1.36 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 271 TYR 0.016 0.002 TYR B 17 PHE 0.021 0.003 PHE B 352 TRP 0.025 0.002 TRP A 264 HIS 0.007 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 9018) covalent geometry : angle 0.68825 (12613) hydrogen bonds : bond 0.04915 ( 302) hydrogen bonds : angle 4.40991 ( 790) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.322 Fit side-chains REVERT: A 132 MET cc_start: 0.5651 (ppp) cc_final: 0.5387 (ppp) REVERT: A 157 TYR cc_start: 0.6543 (OUTLIER) cc_final: 0.6237 (t80) REVERT: A 271 ARG cc_start: 0.6304 (mtm-85) cc_final: 0.5871 (mtm-85) REVERT: B 110 HIS cc_start: 0.8835 (t-90) cc_final: 0.8533 (t-90) REVERT: B 202 TYR cc_start: 0.6128 (OUTLIER) cc_final: 0.4838 (t80) REVERT: B 393 ARG cc_start: 0.5929 (pmt170) cc_final: 0.5563 (ptt-90) outliers start: 24 outliers final: 18 residues processed: 78 average time/residue: 0.0906 time to fit residues: 10.2120 Evaluate side-chains 78 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 422 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 71 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 73 optimal weight: 0.0980 chunk 67 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.128786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.105311 restraints weight = 24480.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.107130 restraints weight = 15447.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.108499 restraints weight = 10876.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.109236 restraints weight = 8357.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.110117 restraints weight = 6976.964| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9018 Z= 0.236 Angle : 0.747 10.334 12613 Z= 0.405 Chirality : 0.047 0.188 1383 Planarity : 0.006 0.059 1288 Dihedral : 24.784 146.833 1965 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 3.02 % Allowed : 17.86 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.29), residues: 812 helix: -0.67 (0.29), residues: 310 sheet: -0.15 (0.54), residues: 93 loop : -1.45 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 257 TYR 0.020 0.002 TYR B 17 PHE 0.024 0.003 PHE B 352 TRP 0.023 0.002 TRP A 264 HIS 0.012 0.002 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00542 ( 9018) covalent geometry : angle 0.74703 (12613) hydrogen bonds : bond 0.05515 ( 302) hydrogen bonds : angle 4.69029 ( 790) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.313 Fit side-chains REVERT: A 132 MET cc_start: 0.5871 (ppp) cc_final: 0.5618 (ppp) REVERT: A 157 TYR cc_start: 0.6548 (OUTLIER) cc_final: 0.6289 (t80) REVERT: A 271 ARG cc_start: 0.6396 (mtm-85) cc_final: 0.5923 (mtm-85) REVERT: A 403 LYS cc_start: 0.8207 (pttt) cc_final: 0.7951 (pttm) REVERT: B 110 HIS cc_start: 0.8742 (t-90) cc_final: 0.8534 (t-90) REVERT: B 202 TYR cc_start: 0.6099 (OUTLIER) cc_final: 0.4923 (t80) REVERT: B 393 ARG cc_start: 0.6011 (pmt170) cc_final: 0.5619 (ptt-90) outliers start: 22 outliers final: 16 residues processed: 80 average time/residue: 0.0921 time to fit residues: 10.6221 Evaluate side-chains 77 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 422 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 24 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 19 optimal weight: 0.0770 chunk 84 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN B 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.130702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.106763 restraints weight = 24261.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.108952 restraints weight = 14598.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.110532 restraints weight = 9980.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.111485 restraints weight = 7482.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.112440 restraints weight = 6060.298| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9018 Z= 0.148 Angle : 0.628 10.515 12613 Z= 0.342 Chirality : 0.042 0.196 1383 Planarity : 0.005 0.057 1288 Dihedral : 24.545 148.034 1965 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.34 % Allowed : 18.68 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.30), residues: 812 helix: -0.23 (0.30), residues: 313 sheet: 0.05 (0.55), residues: 93 loop : -1.39 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 271 TYR 0.013 0.001 TYR B 21 PHE 0.018 0.002 PHE B 109 TRP 0.026 0.002 TRP A 264 HIS 0.008 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9018) covalent geometry : angle 0.62781 (12613) hydrogen bonds : bond 0.04217 ( 302) hydrogen bonds : angle 4.21371 ( 790) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.319 Fit side-chains REVERT: A 271 ARG cc_start: 0.6280 (mtm-85) cc_final: 0.6062 (mtm-85) REVERT: A 403 LYS cc_start: 0.8016 (pttt) cc_final: 0.7712 (pttm) REVERT: B 110 HIS cc_start: 0.8788 (t-90) cc_final: 0.8564 (t-90) REVERT: B 202 TYR cc_start: 0.6097 (OUTLIER) cc_final: 0.4924 (t80) REVERT: B 393 ARG cc_start: 0.5875 (pmt170) cc_final: 0.5582 (ptt-90) outliers start: 17 outliers final: 14 residues processed: 78 average time/residue: 0.0778 time to fit residues: 8.7726 Evaluate side-chains 78 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 78 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 74 optimal weight: 0.3980 chunk 82 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN A 328 HIS ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.128471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.104876 restraints weight = 24371.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.106950 restraints weight = 14728.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.108474 restraints weight = 10140.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.109176 restraints weight = 7625.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.110302 restraints weight = 6373.242| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9018 Z= 0.198 Angle : 0.695 11.899 12613 Z= 0.374 Chirality : 0.045 0.193 1383 Planarity : 0.005 0.060 1288 Dihedral : 24.625 147.957 1965 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.20 % Allowed : 19.23 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.29), residues: 812 helix: -0.36 (0.30), residues: 311 sheet: -0.07 (0.54), residues: 93 loop : -1.45 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 271 TYR 0.012 0.002 TYR B 202 PHE 0.020 0.003 PHE B 352 TRP 0.026 0.003 TRP A 264 HIS 0.006 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 9018) covalent geometry : angle 0.69479 (12613) hydrogen bonds : bond 0.04821 ( 302) hydrogen bonds : angle 4.40866 ( 790) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1580.56 seconds wall clock time: 28 minutes 3.37 seconds (1683.37 seconds total)