Starting phenix.real_space_refine on Fri Sep 11 08:14:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zla_14778/09_2026/7zla_14778.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zla_14778/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7zla_14778/09_2026/7zla_14778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zla_14778/09_2026/7zla_14778.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zla_14778/09_2026/7zla_14778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zla_14778/09_2026/7zla_14778.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zla_14778/09_2026/7zla_14778.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zla_14778/09_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-2.2.1-6174/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: 1.99, per 1000 atoms: 0.23 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: 1.10 Conformation dependent library (CDL) restraints added in 257.6 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: 1.20 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: 1.54 Time building geometry restraints manager: 1.37 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: 12036 2.10 - 4.20: 524 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.050 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.270 ------------------------------------------------------------------------------- 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 : 0.923 10.499 12613 Z= 0.648 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 0.92295 / 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 : 0.281 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: 0.0855 time to fit residues: 11.1924 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 : 0.323 ------------------------------------------------------------------------------- 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 = 0.4272 r_free = 0.4272 target = 0.133246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.108387 restraints weight = 23580.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.110764 restraints weight = 13705.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.112413 restraints weight = 9138.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.113624 restraints weight = 6755.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.114273 restraints weight = 5381.809| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9018 Z= 0.153 Angle : 0.695 9.207 12613 Z= 0.385 Chirality : 0.047 0.177 1383 Planarity : 0.005 0.052 1288 Dihedral : 24.604 150.261 1965 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.96 % Allowed : 7.83 % Favored : 91.21 % 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: -1.34 (0.28), residues: 812 helix: -0.52 (0.29), residues: 314 sheet: -0.24 (0.51), residues: 99 loop : -1.31 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 316 TYR 0.020 0.001 TYR B 17 PHE 0.015 0.002 PHE B 109 TRP 0.016 0.002 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 0.69508 / 0.39 (12613) hydrogen bonds : bond 0.05563 / 3.44 ( 302) hydrogen bonds : angle 4.80406 / 3.37 ( 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 78 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.289 Fit side-chains REVERT: A 123 GLN cc_start: 0.6547 (tp-100) cc_final: 0.5925 (pt0) REVERT: A 278 TYR cc_start: 0.6595 (t80) cc_final: 0.6298 (t80) REVERT: B 110 HIS cc_start: 0.8611 (t70) cc_final: 0.8360 (t70) REVERT: B 308 SER cc_start: 0.7279 (t) cc_final: 0.7000 (p) outliers start: 7 outliers final: 5 residues processed: 76 average time/residue: 0.0823 time to fit residues: 9.2198 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 : 0.291 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 80 optimal weight: 0.0970 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.132045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.107947 restraints weight = 23545.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.110141 restraints weight = 14109.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.111745 restraints weight = 9601.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.112900 restraints weight = 7141.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.113513 restraints weight = 5704.454| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.1438 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= 0.145 Angle : 0.637 8.913 12613 Z= 0.356 Chirality : 0.045 0.168 1383 Planarity : 0.005 0.051 1288 Dihedral : 24.541 150.155 1965 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.65 % Allowed : 11.26 % Favored : 87.09 % 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: -1.05 (0.29), residues: 812 helix: -0.24 (0.30), residues: 307 sheet: 0.02 (0.52), residues: 99 loop : -1.20 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 163 TYR 0.014 0.001 TYR A 278 PHE 0.015 0.002 PHE A 352 TRP 0.009 0.001 TRP A 264 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 ( 9018) covalent geometry : angle 0.63733 / 0.36 (12613) hydrogen bonds : bond 0.05272 / 3.24 ( 302) hydrogen bonds : angle 4.56504 / 3.18 ( 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 74 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.301 Fit side-chains REVERT: A 320 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6884 (ttp) REVERT: A 403 LYS cc_start: 0.8184 (pttt) cc_final: 0.7930 (pttm) REVERT: B 110 HIS cc_start: 0.8524 (t70) cc_final: 0.8115 (t70) REVERT: B 308 SER cc_start: 0.7418 (t) cc_final: 0.7085 (p) REVERT: B 320 MET cc_start: 0.5875 (tmm) cc_final: 0.5598 (tmm) outliers start: 12 outliers final: 5 residues processed: 70 average time/residue: 0.0743 time to fit residues: 7.9951 Evaluate side-chains 61 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 79 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 HIS B 110 HIS B 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.129774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.105512 restraints weight = 24387.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.107646 restraints weight = 14724.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.109185 restraints weight = 10081.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.110188 restraints weight = 7553.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.111009 restraints weight = 6136.694| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9018 Z= 0.185 Angle : 0.674 8.847 12613 Z= 0.376 Chirality : 0.047 0.168 1383 Planarity : 0.005 0.051 1288 Dihedral : 24.654 150.043 1965 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.88 % Allowed : 12.09 % Favored : 85.03 % 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: -1.12 (0.29), residues: 812 helix: -0.38 (0.30), residues: 308 sheet: 0.23 (0.52), residues: 99 loop : -1.25 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 74 TYR 0.014 0.002 TYR B 240 PHE 0.021 0.003 PHE A 352 TRP 0.011 0.002 TRP B 124 HIS 0.006 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 ( 9018) covalent geometry : angle 0.67371 / 0.38 (12613) hydrogen bonds : bond 0.05486 / 3.34 ( 302) hydrogen bonds : angle 4.61288 / 3.21 ( 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 82 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.297 Fit side-chains REVERT: A 320 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6969 (ttp) REVERT: A 403 LYS cc_start: 0.8238 (pttt) cc_final: 0.7969 (pttm) REVERT: B 110 HIS cc_start: 0.8722 (t-90) cc_final: 0.8068 (t-90) REVERT: B 320 MET cc_start: 0.5972 (tmm) cc_final: 0.5655 (tmm) outliers start: 21 outliers final: 9 residues processed: 79 average time/residue: 0.0795 time to fit residues: 9.3925 Evaluate side-chains 65 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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: 3.9990 chunk 83 optimal weight: 30.0000 chunk 73 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 = 0.4248 r_free = 0.4248 target = 0.131405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.107041 restraints weight = 24140.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.109237 restraints weight = 14391.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.110848 restraints weight = 9801.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.111887 restraints weight = 7304.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.112789 restraints weight = 5886.574| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.1745 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= 0.140 Angle : 0.624 8.917 12613 Z= 0.351 Chirality : 0.045 0.180 1383 Planarity : 0.005 0.051 1288 Dihedral : 24.583 149.917 1965 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.92 % Allowed : 15.38 % Favored : 82.69 % 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: -0.88 (0.29), residues: 812 helix: -0.10 (0.31), residues: 307 sheet: 0.37 (0.52), residues: 100 loop : -1.18 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 163 TYR 0.015 0.001 TYR B 17 PHE 0.013 0.002 PHE B 109 TRP 0.008 0.001 TRP B 124 HIS 0.004 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 ( 9018) covalent geometry : angle 0.62434 / 0.35 (12613) hydrogen bonds : bond 0.04889 / 2.96 ( 302) hydrogen bonds : angle 4.34606 / 3.04 ( 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 77 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.285 Fit side-chains REVERT: A 403 LYS cc_start: 0.8134 (pttt) cc_final: 0.7884 (pttm) REVERT: B 110 HIS cc_start: 0.8716 (t-90) cc_final: 0.8156 (t-90) REVERT: B 308 SER cc_start: 0.7503 (t) cc_final: 0.7074 (p) REVERT: B 320 MET cc_start: 0.5957 (tmm) cc_final: 0.5611 (tmm) REVERT: B 353 MET cc_start: 0.6893 (tpt) cc_final: 0.6635 (tpt) outliers start: 14 outliers final: 9 residues processed: 74 average time/residue: 0.0764 time to fit residues: 8.6452 Evaluate side-chains 66 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 273 ILE 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: 5.9990 chunk 73 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 84 optimal weight: 40.0000 chunk 52 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS B 9 ASN ** B 293 GLN ** 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 = 0.4198 r_free = 0.4198 target = 0.128217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.104235 restraints weight = 24435.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.106271 restraints weight = 14795.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.107764 restraints weight = 10207.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.108832 restraints weight = 7681.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.109476 restraints weight = 6188.776| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9018 Z= 0.215 Angle : 0.711 8.948 12613 Z= 0.392 Chirality : 0.048 0.185 1383 Planarity : 0.005 0.051 1288 Dihedral : 24.723 149.607 1965 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.92 % Allowed : 16.48 % Favored : 81.59 % 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: -1.32 (0.29), residues: 812 helix: -0.43 (0.29), residues: 308 sheet: 0.16 (0.52), residues: 99 loop : -1.47 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 271 TYR 0.016 0.002 TYR A 212 PHE 0.027 0.003 PHE A 352 TRP 0.010 0.002 TRP A 124 HIS 0.007 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 ( 9018) covalent geometry : angle 0.71126 / 0.39 (12613) hydrogen bonds : bond 0.05710 / 3.47 ( 302) hydrogen bonds : angle 4.67421 / 3.25 ( 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 71 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.292 Fit side-chains REVERT: A 403 LYS cc_start: 0.8208 (pttt) cc_final: 0.7956 (pttm) REVERT: B 110 HIS cc_start: 0.8786 (t-90) cc_final: 0.8320 (t-90) REVERT: B 320 MET cc_start: 0.6001 (tmm) cc_final: 0.5792 (tmm) REVERT: B 353 MET cc_start: 0.6980 (tpt) cc_final: 0.6740 (tpt) outliers start: 14 outliers final: 11 residues processed: 69 average time/residue: 0.0735 time to fit residues: 7.8587 Evaluate side-chains 64 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 273 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 308 SER 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 341 VAL 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: 5.9990 chunk 60 optimal weight: 10.0000 chunk 85 optimal weight: 50.0000 chunk 14 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 chunk 43 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 overall best weight: 2.4584 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.129848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.105679 restraints weight = 24419.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.107804 restraints weight = 14687.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.109364 restraints weight = 10056.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.110418 restraints weight = 7530.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.111071 restraints weight = 6082.499| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.2004 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= 0.159 Angle : 0.647 9.310 12613 Z= 0.361 Chirality : 0.046 0.196 1383 Planarity : 0.005 0.052 1288 Dihedral : 24.682 149.434 1965 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.47 % Allowed : 17.31 % 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 are not related in a simple way. whole: -1.14 (0.29), residues: 812 helix: -0.22 (0.31), residues: 309 sheet: 0.20 (0.52), residues: 100 loop : -1.42 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 74 TYR 0.017 0.001 TYR B 17 PHE 0.037 0.003 PHE A 219 TRP 0.011 0.002 TRP A 124 HIS 0.005 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 ( 9018) covalent geometry : angle 0.64728 / 0.36 (12613) hydrogen bonds : bond 0.05004 / 3.03 ( 302) hydrogen bonds : angle 4.40404 / 3.07 ( 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 78 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.292 Fit side-chains REVERT: A 403 LYS cc_start: 0.8124 (pttt) cc_final: 0.7864 (pttm) REVERT: B 202 TYR cc_start: 0.5934 (OUTLIER) cc_final: 0.4687 (t80) REVERT: B 320 MET cc_start: 0.6095 (tmm) cc_final: 0.5856 (tmm) outliers start: 18 outliers final: 11 residues processed: 76 average time/residue: 0.0742 time to fit residues: 8.7102 Evaluate side-chains 67 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 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 197 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 28 optimal weight: 0.6980 chunk 83 optimal weight: 30.0000 chunk 73 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 87 optimal weight: 30.0000 chunk 29 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** 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 = 0.4237 r_free = 0.4237 target = 0.130939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.106962 restraints weight = 23964.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.109118 restraints weight = 14367.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.110665 restraints weight = 9826.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.111715 restraints weight = 7339.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.112487 restraints weight = 5919.393| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.2166 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= 0.140 Angle : 0.631 9.491 12613 Z= 0.349 Chirality : 0.044 0.195 1383 Planarity : 0.005 0.052 1288 Dihedral : 24.611 149.199 1965 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.34 % Allowed : 17.86 % 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: -1.01 (0.30), residues: 812 helix: -0.12 (0.31), residues: 312 sheet: 0.38 (0.53), residues: 99 loop : -1.38 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 74 TYR 0.015 0.001 TYR B 17 PHE 0.026 0.002 PHE A 219 TRP 0.013 0.002 TRP A 124 HIS 0.004 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 9018) covalent geometry : angle 0.63052 / 0.35 (12613) hydrogen bonds : bond 0.04691 / 2.83 ( 302) hydrogen bonds : angle 4.23293 / 2.95 ( 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 78 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.219 Fit side-chains REVERT: A 403 LYS cc_start: 0.8060 (pttt) cc_final: 0.7806 (pttm) REVERT: B 110 HIS cc_start: 0.8776 (t-90) cc_final: 0.8089 (t-90) REVERT: B 202 TYR cc_start: 0.5897 (OUTLIER) cc_final: 0.4665 (t80) REVERT: B 308 SER cc_start: 0.7526 (t) cc_final: 0.7160 (p) REVERT: B 320 MET cc_start: 0.6027 (tmm) cc_final: 0.5777 (tmm) REVERT: B 393 ARG cc_start: 0.5858 (pmt170) cc_final: 0.5479 (ptt-90) outliers start: 17 outliers final: 11 residues processed: 76 average time/residue: 0.0788 time to fit residues: 8.9113 Evaluate side-chains 71 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 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 273 ILE Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 11 ASP 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: 0.9980 chunk 44 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 88 optimal weight: 30.0000 chunk 49 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 67 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4272 r_free = 0.4272 target = 0.133183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.108884 restraints weight = 23573.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.111121 restraints weight = 14156.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.112754 restraints weight = 9641.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.113826 restraints weight = 7163.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.114781 restraints weight = 5743.473| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9018 Z= 0.124 Angle : 0.624 13.778 12613 Z= 0.337 Chirality : 0.043 0.171 1383 Planarity : 0.005 0.051 1288 Dihedral : 24.507 149.148 1965 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.20 % Allowed : 18.54 % Favored : 79.26 % 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: 0.15 (0.31), residues: 313 sheet: 0.54 (0.51), residues: 100 loop : -1.42 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 271 TYR 0.013 0.001 TYR B 17 PHE 0.024 0.002 PHE A 219 TRP 0.016 0.002 TRP A 124 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 ( 9018) covalent geometry : angle 0.62444 / 0.34 (12613) hydrogen bonds : bond 0.04221 / 2.53 ( 302) hydrogen bonds : angle 4.01622 / 2.80 ( 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 87 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.178 Fit side-chains REVERT: A 403 LYS cc_start: 0.7958 (pttt) cc_final: 0.7690 (pttm) REVERT: B 110 HIS cc_start: 0.8725 (t-90) cc_final: 0.8132 (t-90) REVERT: B 202 TYR cc_start: 0.5736 (OUTLIER) cc_final: 0.4553 (t80) REVERT: B 308 SER cc_start: 0.7488 (t) cc_final: 0.7147 (p) REVERT: B 320 MET cc_start: 0.5988 (tmm) cc_final: 0.5555 (tmm) REVERT: B 353 MET cc_start: 0.6372 (tpt) cc_final: 0.5988 (tpp) REVERT: B 393 ARG cc_start: 0.5993 (pmt170) cc_final: 0.5673 (ptt-90) REVERT: B 411 LEU cc_start: 0.8461 (mt) cc_final: 0.7661 (pp) outliers start: 16 outliers final: 12 residues processed: 83 average time/residue: 0.0805 time to fit residues: 9.8371 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 : 0.280 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 84 optimal weight: 40.0000 chunk 39 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 25 optimal weight: 0.0980 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.131152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.107377 restraints weight = 23864.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.109530 restraints weight = 14511.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.111114 restraints weight = 9948.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.112175 restraints weight = 7417.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.113135 restraints weight = 5947.324| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9018 Z= 0.165 Angle : 0.657 12.940 12613 Z= 0.356 Chirality : 0.045 0.171 1383 Planarity : 0.005 0.050 1288 Dihedral : 24.556 149.059 1965 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.79 % Allowed : 18.96 % Favored : 79.26 % 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: -0.99 (0.29), residues: 812 helix: -0.04 (0.31), residues: 313 sheet: 0.29 (0.50), residues: 105 loop : -1.43 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 271 TYR 0.011 0.001 TYR B 21 PHE 0.023 0.003 PHE B 109 TRP 0.024 0.003 TRP B 124 HIS 0.006 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 9018) covalent geometry : angle 0.65695 / 0.36 (12613) hydrogen bonds : bond 0.04621 / 2.78 ( 302) hydrogen bonds : angle 4.17629 / 2.89 ( 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 75 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.226 Fit side-chains REVERT: A 271 ARG cc_start: 0.6612 (mpp-170) cc_final: 0.6112 (mtm-85) REVERT: A 403 LYS cc_start: 0.7997 (pttt) cc_final: 0.7753 (pttm) REVERT: B 110 HIS cc_start: 0.8777 (t-90) cc_final: 0.8218 (t-90) REVERT: B 202 TYR cc_start: 0.5846 (OUTLIER) cc_final: 0.4610 (t80) REVERT: B 308 SER cc_start: 0.7515 (t) cc_final: 0.7148 (p) REVERT: B 320 MET cc_start: 0.6006 (tmm) cc_final: 0.5735 (tmm) REVERT: B 393 ARG cc_start: 0.5863 (pmt170) cc_final: 0.5487 (ptt-90) outliers start: 13 outliers final: 11 residues processed: 73 average time/residue: 0.0853 time to fit residues: 9.0775 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 : 0.285 ------------------------------------------------------------------------------- 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 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 78 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** 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 = 0.4202 r_free = 0.4202 target = 0.128751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.105214 restraints weight = 24240.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.107242 restraints weight = 14777.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.108803 restraints weight = 10150.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.109852 restraints weight = 7616.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.110715 restraints weight = 6141.307| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9018 Z= 0.192 Angle : 0.718 12.542 12613 Z= 0.388 Chirality : 0.047 0.185 1383 Planarity : 0.005 0.050 1288 Dihedral : 24.722 148.995 1965 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 1.92 % Allowed : 18.82 % Favored : 79.26 % 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: -1.34 (0.29), residues: 812 helix: -0.40 (0.30), residues: 313 sheet: 0.11 (0.54), residues: 99 loop : -1.54 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 271 TYR 0.018 0.002 TYR B 17 PHE 0.021 0.003 PHE B 109 TRP 0.018 0.002 TRP B 124 HIS 0.007 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 ( 9018) covalent geometry : angle 0.71849 / 0.39 (12613) hydrogen bonds : bond 0.05274 / 3.18 ( 302) hydrogen bonds : angle 4.48682 / 3.11 ( 790) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1505.92 seconds wall clock time: 26 minutes 43.68 seconds (1603.68 seconds total)