Starting phenix.real_space_refine on Thu Jul 2 11:57:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zla_14778/07_2026/7zla_14778.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zla_14778/07_2026/7zla_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zla_14778/07_2026/7zla_14778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zla_14778/07_2026/7zla_14778.map" model { file = "/net/cci-nas-00/data/ceres_data/7zla_14778/07_2026/7zla_14778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zla_14778/07_2026/7zla_14778.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7zla_14778/07_2026/7zla_14778.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zla_14778/07_2026/7zla_14778.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 1.25, per 1000 atoms: 0.14 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: 0.69 Conformation dependent library (CDL) restraints added in 319.7 milliseconds 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: 0.88 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: 1.18 Time building geometry restraints manager: 0.90 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: 12038 2.10 - 4.20: 522 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=" O4' DA D 42 " pdb=" C4' DA D 42 " pdb=" C3' DA D 42 " ideal model delta sigma weight residual 106.00 102.92 3.08 6.00e-01 2.78e+00 2.64e+01 angle pdb=" O4' DA C 34 " pdb=" C4' DA C 34 " pdb=" C3' DA C 34 " ideal model delta sigma weight residual 106.00 103.09 2.91 6.00e-01 2.78e+00 2.35e+01 angle pdb=" N3 DT D 28 " pdb=" C4 DT D 28 " pdb=" O4 DT D 28 " ideal model delta sigma weight residual 119.90 122.78 -2.88 6.00e-01 2.78e+00 2.31e+01 angle pdb=" O4 DT D 28 " pdb=" C4 DT D 28 " pdb=" C5 DT D 28 " ideal model delta sigma weight residual 124.90 121.65 3.25 7.00e-01 2.04e+00 2.15e+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: 883 0.045 - 0.090: 372 0.090 - 0.136: 115 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.810 Find NCS groups from input model: 0.040 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 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 : 0.008 0.179 9018 Z= 0.497 Angle : 0.921 10.499 12613 Z= 0.645 Chirality : 0.052 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 are 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/Z covalent geometry : bond 0.00777 / 0.50 ( 9018) covalent geometry : angle 0.92082 / 0.65 (12613) hydrogen bonds : bond 0.17597 / 11.20 ( 302) hydrogen bonds : angle 7.08822 / 4.84 ( 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 : 0.253 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.6771 (mmm) cc_final: 0.6560 (mmt) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0703 time to fit residues: 9.2853 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 : 0.207 ------------------------------------------------------------------------------- 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... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 HIS B 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.132877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.108130 restraints weight = 23586.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.110435 restraints weight = 13816.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.112046 restraints weight = 9294.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.113222 restraints weight = 6886.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.114011 restraints weight = 5507.559| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.1117 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= 0.151 Angle : 0.691 9.228 12613 Z= 0.385 Chirality : 0.047 0.178 1383 Planarity : 0.005 0.052 1288 Dihedral : 24.645 150.903 1965 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.82 % Allowed : 7.83 % Favored : 91.35 % 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 are not related in a simple way. whole: -1.35 (0.28), residues: 812 helix: -0.53 (0.29), residues: 314 sheet: -0.26 (0.51), residues: 99 loop : -1.31 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 258 TYR 0.018 0.001 TYR B 17 PHE 0.015 0.002 PHE B 109 TRP 0.015 0.001 TRP A 264 HIS 0.007 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 ( 9018) covalent geometry : angle 0.69109 / 0.38 (12613) hydrogen bonds : bond 0.05684 / 3.51 ( 302) hydrogen bonds : angle 4.86738 / 3.41 ( 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 77 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 123 GLN cc_start: 0.6569 (tp-100) cc_final: 0.5956 (pt0) REVERT: A 278 TYR cc_start: 0.6621 (t80) cc_final: 0.6237 (t80) REVERT: B 110 HIS cc_start: 0.8577 (t70) cc_final: 0.8360 (t70) REVERT: B 308 SER cc_start: 0.7297 (t) cc_final: 0.7000 (p) outliers start: 6 outliers final: 5 residues processed: 75 average time/residue: 0.0851 time to fit residues: 9.2130 Evaluate side-chains 64 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain B residue 11 ASP 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: 40.0000 chunk 4 optimal weight: 0.0570 chunk 26 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 HIS ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN ** B 110 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 = 0.4254 r_free = 0.4254 target = 0.131998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.107907 restraints weight = 23489.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.110070 restraints weight = 14089.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.111534 restraints weight = 9622.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.112746 restraints weight = 7252.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.113477 restraints weight = 5784.960| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9018 Z= 0.143 Angle : 0.634 8.812 12613 Z= 0.354 Chirality : 0.045 0.168 1383 Planarity : 0.005 0.051 1288 Dihedral : 24.571 150.795 1965 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.92 % Allowed : 10.85 % Favored : 87.23 % 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 are not related in a simple way. whole: -1.04 (0.29), residues: 812 helix: -0.19 (0.31), residues: 307 sheet: -0.02 (0.51), residues: 99 loop : -1.22 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 163 TYR 0.013 0.001 TYR B 17 PHE 0.014 0.002 PHE A 247 TRP 0.009 0.001 TRP A 264 HIS 0.005 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 ( 9018) covalent geometry : angle 0.63364 / 0.35 (12613) hydrogen bonds : bond 0.05230 / 3.22 ( 302) hydrogen bonds : angle 4.53765 / 3.16 ( 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 76 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 320 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.7017 (ttp) REVERT: B 110 HIS cc_start: 0.8523 (t70) cc_final: 0.8112 (t70) REVERT: B 308 SER cc_start: 0.7447 (t) cc_final: 0.7122 (p) REVERT: B 320 MET cc_start: 0.5866 (tmm) cc_final: 0.5514 (tmm) outliers start: 14 outliers final: 6 residues processed: 72 average time/residue: 0.0630 time to fit residues: 6.9215 Evaluate side-chains 63 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 MET 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 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: 9.9990 chunk 74 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN A 263 HIS A 328 HIS B 110 HIS B 214 ASN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.130283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.106004 restraints weight = 24253.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.108185 restraints weight = 14589.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.109717 restraints weight = 9952.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.110878 restraints weight = 7463.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.111594 restraints weight = 5973.469| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9018 Z= 0.172 Angle : 0.657 9.095 12613 Z= 0.367 Chirality : 0.046 0.166 1383 Planarity : 0.005 0.051 1288 Dihedral : 24.638 150.768 1965 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.02 % Allowed : 12.23 % Favored : 84.75 % 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 are not related in a simple way. whole: -1.02 (0.29), residues: 812 helix: -0.26 (0.30), residues: 308 sheet: 0.25 (0.52), residues: 99 loop : -1.20 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 271 TYR 0.012 0.001 TYR B 17 PHE 0.020 0.002 PHE A 352 TRP 0.011 0.002 TRP B 124 HIS 0.007 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 ( 9018) covalent geometry : angle 0.65695 / 0.37 (12613) hydrogen bonds : bond 0.05259 / 3.20 ( 302) hydrogen bonds : angle 4.53393 / 3.16 ( 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 86 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 320 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6954 (ttp) REVERT: B 110 HIS cc_start: 0.8693 (t-90) cc_final: 0.8004 (t-90) REVERT: B 320 MET cc_start: 0.5971 (tmm) cc_final: 0.5635 (tmm) outliers start: 22 outliers final: 9 residues processed: 83 average time/residue: 0.0654 time to fit residues: 7.9938 Evaluate side-chains 68 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 320 MET 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 173 VAL 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: 6.9990 chunk 83 optimal weight: 30.0000 chunk 73 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.130567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.106709 restraints weight = 24341.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.108878 restraints weight = 14607.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.110301 restraints weight = 9940.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.111471 restraints weight = 7485.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.112108 restraints weight = 5975.953| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.1727 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= 0.156 Angle : 0.635 9.504 12613 Z= 0.356 Chirality : 0.045 0.178 1383 Planarity : 0.005 0.051 1288 Dihedral : 24.621 150.600 1965 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.20 % Allowed : 15.38 % Favored : 82.42 % 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 are not related in a simple way. whole: -0.96 (0.29), residues: 812 helix: -0.15 (0.30), residues: 307 sheet: 0.25 (0.52), residues: 100 loop : -1.22 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 271 TYR 0.018 0.001 TYR A 278 PHE 0.016 0.002 PHE A 352 TRP 0.012 0.002 TRP B 124 HIS 0.005 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 ( 9018) covalent geometry : angle 0.63514 / 0.36 (12613) hydrogen bonds : bond 0.04994 / 3.04 ( 302) hydrogen bonds : angle 4.41765 / 3.09 ( 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 81 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: B 110 HIS cc_start: 0.8776 (t-90) cc_final: 0.8208 (t-90) REVERT: B 353 MET cc_start: 0.7015 (tpt) cc_final: 0.6682 (tpt) outliers start: 16 outliers final: 10 residues processed: 79 average time/residue: 0.0605 time to fit residues: 7.4125 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 : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 308 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 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: 7.9990 chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 73 optimal weight: 0.0040 chunk 7 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 84 optimal weight: 40.0000 chunk 52 optimal weight: 10.0000 chunk 66 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.132473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.108697 restraints weight = 23811.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.110771 restraints weight = 14676.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.112317 restraints weight = 10111.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.113367 restraints weight = 7614.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.114045 restraints weight = 6191.043| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9018 Z= 0.127 Angle : 0.592 9.495 12613 Z= 0.333 Chirality : 0.043 0.179 1383 Planarity : 0.005 0.051 1288 Dihedral : 24.535 150.395 1965 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.79 % Allowed : 17.17 % Favored : 81.04 % 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 are not related in a simple way. whole: -0.77 (0.30), residues: 812 helix: 0.09 (0.31), residues: 308 sheet: 0.42 (0.53), residues: 99 loop : -1.20 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 271 TYR 0.014 0.001 TYR B 17 PHE 0.016 0.001 PHE B 109 TRP 0.028 0.003 TRP A 124 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.13 ( 9018) covalent geometry : angle 0.59168 / 0.33 (12613) hydrogen bonds : bond 0.04575 / 2.77 ( 302) hydrogen bonds : angle 4.15600 / 2.90 ( 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 78 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: B 110 HIS cc_start: 0.8658 (t-90) cc_final: 0.7933 (t70) REVERT: B 202 TYR cc_start: 0.5734 (OUTLIER) cc_final: 0.4512 (t80) REVERT: B 308 SER cc_start: 0.7493 (t) cc_final: 0.7154 (p) REVERT: B 320 MET cc_start: 0.6096 (tmm) cc_final: 0.5839 (tmm) REVERT: B 353 MET cc_start: 0.6846 (tpt) cc_final: 0.6605 (tpt) outliers start: 13 outliers final: 9 residues processed: 73 average time/residue: 0.0641 time to fit residues: 6.9561 Evaluate side-chains 72 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 353 MET 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 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: 0.9990 chunk 60 optimal weight: 8.9990 chunk 85 optimal weight: 50.0000 chunk 14 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 83 optimal weight: 30.0000 chunk 43 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.132184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.107931 restraints weight = 23999.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.110141 restraints weight = 14523.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.111669 restraints weight = 9940.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.112691 restraints weight = 7460.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.113598 restraints weight = 6032.407| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9018 Z= 0.131 Angle : 0.599 9.667 12613 Z= 0.332 Chirality : 0.043 0.181 1383 Planarity : 0.005 0.051 1288 Dihedral : 24.508 150.236 1965 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.34 % Allowed : 17.17 % Favored : 80.49 % 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 are not related in a simple way. whole: -0.79 (0.30), residues: 812 helix: 0.01 (0.31), residues: 316 sheet: 0.48 (0.53), residues: 99 loop : -1.20 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 74 TYR 0.019 0.001 TYR A 278 PHE 0.021 0.002 PHE B 109 TRP 0.016 0.002 TRP B 124 HIS 0.004 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 ( 9018) covalent geometry : angle 0.59933 / 0.33 (12613) hydrogen bonds : bond 0.04430 / 2.69 ( 302) hydrogen bonds : angle 4.10045 / 2.86 ( 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 83 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: B 110 HIS cc_start: 0.8655 (t-90) cc_final: 0.7930 (t70) REVERT: B 202 TYR cc_start: 0.5742 (OUTLIER) cc_final: 0.4527 (t80) REVERT: B 308 SER cc_start: 0.7477 (t) cc_final: 0.7169 (p) REVERT: B 320 MET cc_start: 0.6067 (tmm) cc_final: 0.5804 (tmm) REVERT: B 353 MET cc_start: 0.6828 (tpt) cc_final: 0.6604 (tpt) outliers start: 17 outliers final: 12 residues processed: 79 average time/residue: 0.0594 time to fit residues: 7.1078 Evaluate side-chains 73 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 141 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 400 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 28 optimal weight: 7.9990 chunk 83 optimal weight: 30.0000 chunk 73 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 87 optimal weight: 30.0000 chunk 29 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.131972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.108010 restraints weight = 23869.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.110074 restraints weight = 14837.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.111576 restraints weight = 10339.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.112551 restraints weight = 7819.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.113442 restraints weight = 6354.022| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.2237 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= 0.137 Angle : 0.606 9.689 12613 Z= 0.334 Chirality : 0.044 0.179 1383 Planarity : 0.005 0.054 1288 Dihedral : 24.501 150.031 1965 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.61 % Allowed : 17.58 % 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 are not related in a simple way. whole: -0.85 (0.29), residues: 812 helix: -0.02 (0.31), residues: 318 sheet: 0.51 (0.52), residues: 100 loop : -1.29 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 271 TYR 0.016 0.001 TYR A 278 PHE 0.022 0.002 PHE B 109 TRP 0.018 0.002 TRP B 124 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 ( 9018) covalent geometry : angle 0.60577 / 0.33 (12613) hydrogen bonds : bond 0.04393 / 2.67 ( 302) hydrogen bonds : angle 4.05982 / 2.84 ( 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 82 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: B 110 HIS cc_start: 0.8678 (t-90) cc_final: 0.8213 (t-90) REVERT: B 202 TYR cc_start: 0.5799 (OUTLIER) cc_final: 0.4564 (t80) REVERT: B 308 SER cc_start: 0.7484 (t) cc_final: 0.7178 (p) REVERT: B 320 MET cc_start: 0.6113 (tmm) cc_final: 0.5860 (tmm) REVERT: B 393 ARG cc_start: 0.5895 (pmt170) cc_final: 0.5569 (ptt-90) outliers start: 19 outliers final: 11 residues processed: 78 average time/residue: 0.0748 time to fit residues: 8.5766 Evaluate side-chains 73 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE 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 308 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 141 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 400 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 71 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 chunk 88 optimal weight: 30.0000 chunk 49 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.131212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.107489 restraints weight = 23849.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.109640 restraints weight = 14362.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.111213 restraints weight = 9817.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.112361 restraints weight = 7303.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.113102 restraints weight = 5825.383| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9018 Z= 0.152 Angle : 0.638 13.626 12613 Z= 0.346 Chirality : 0.044 0.182 1383 Planarity : 0.005 0.055 1288 Dihedral : 24.534 149.825 1965 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.92 % Allowed : 18.27 % 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 are not related in a simple way. whole: -0.83 (0.30), residues: 812 helix: 0.06 (0.31), residues: 309 sheet: 0.46 (0.53), residues: 100 loop : -1.29 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 271 TYR 0.016 0.001 TYR A 278 PHE 0.022 0.002 PHE B 109 TRP 0.017 0.002 TRP B 124 HIS 0.004 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 9018) covalent geometry : angle 0.63768 / 0.35 (12613) hydrogen bonds : bond 0.04574 / 2.77 ( 302) hydrogen bonds : angle 4.11776 / 2.88 ( 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 76 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: B 110 HIS cc_start: 0.8785 (t-90) cc_final: 0.8351 (t-90) REVERT: B 132 MET cc_start: 0.5298 (ttp) cc_final: 0.4879 (ttt) REVERT: B 202 TYR cc_start: 0.5854 (OUTLIER) cc_final: 0.4584 (t80) REVERT: B 308 SER cc_start: 0.7436 (t) cc_final: 0.7091 (p) REVERT: B 320 MET cc_start: 0.6130 (tmm) cc_final: 0.5864 (tmm) REVERT: B 393 ARG cc_start: 0.5886 (pmt170) cc_final: 0.5518 (ptt-90) outliers start: 14 outliers final: 11 residues processed: 72 average time/residue: 0.0756 time to fit residues: 8.1188 Evaluate side-chains 72 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE 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 308 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 141 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 400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 84 optimal weight: 40.0000 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 63 optimal weight: 0.0470 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.133759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.109496 restraints weight = 23498.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.111790 restraints weight = 14127.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.113362 restraints weight = 9590.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.114476 restraints weight = 7196.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.115462 restraints weight = 5748.328| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9018 Z= 0.119 Angle : 0.596 12.614 12613 Z= 0.326 Chirality : 0.043 0.180 1383 Planarity : 0.005 0.057 1288 Dihedral : 24.442 149.401 1965 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.37 % Allowed : 19.09 % Favored : 79.53 % 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 are not related in a simple way. whole: -0.72 (0.30), residues: 812 helix: 0.21 (0.31), residues: 313 sheet: 0.50 (0.53), residues: 101 loop : -1.29 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 271 TYR 0.015 0.001 TYR A 278 PHE 0.038 0.002 PHE A 219 TRP 0.021 0.002 TRP B 124 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.12 ( 9018) covalent geometry : angle 0.59649 / 0.33 (12613) hydrogen bonds : bond 0.04005 / 2.42 ( 302) hydrogen bonds : angle 3.88346 / 2.74 ( 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 79 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 271 ARG cc_start: 0.6231 (mpp-170) cc_final: 0.5808 (mpp-170) REVERT: B 110 HIS cc_start: 0.8714 (t-90) cc_final: 0.8330 (t-90) REVERT: B 202 TYR cc_start: 0.5758 (OUTLIER) cc_final: 0.4599 (t80) REVERT: B 320 MET cc_start: 0.6156 (tmm) cc_final: 0.5882 (tmm) REVERT: B 393 ARG cc_start: 0.5859 (pmt170) cc_final: 0.5577 (ptt-90) REVERT: B 411 LEU cc_start: 0.8442 (mt) cc_final: 0.7613 (pp) outliers start: 10 outliers final: 9 residues processed: 76 average time/residue: 0.0890 time to fit residues: 9.7202 Evaluate side-chains 70 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 273 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 78 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.130078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.106249 restraints weight = 24163.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.108331 restraints weight = 14699.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.109905 restraints weight = 10106.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.111053 restraints weight = 7577.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.111739 restraints weight = 6045.599| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9018 Z= 0.191 Angle : 0.691 11.850 12613 Z= 0.375 Chirality : 0.046 0.181 1383 Planarity : 0.005 0.057 1288 Dihedral : 24.556 149.519 1965 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.79 % Allowed : 19.09 % 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 are not related in a simple way. whole: -1.08 (0.29), residues: 812 helix: -0.23 (0.30), residues: 319 sheet: 0.49 (0.53), residues: 99 loop : -1.44 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 271 TYR 0.025 0.002 TYR A 278 PHE 0.023 0.003 PHE A 219 TRP 0.016 0.002 TRP A 264 HIS 0.006 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 ( 9018) covalent geometry : angle 0.69127 / 0.37 (12613) hydrogen bonds : bond 0.04877 / 2.94 ( 302) hydrogen bonds : angle 4.26640 / 2.99 ( 790) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1316.88 seconds wall clock time: 23 minutes 29.33 seconds (1409.33 seconds total)