Starting phenix.real_space_refine on Fri Jun 6 08:02:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r5h_14320/06_2025/7r5h_14320.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r5h_14320/06_2025/7r5h_14320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r5h_14320/06_2025/7r5h_14320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r5h_14320/06_2025/7r5h_14320.map" model { file = "/net/cci-nas-00/data/ceres_data/7r5h_14320/06_2025/7r5h_14320.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r5h_14320/06_2025/7r5h_14320.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 S 6 5.16 5 C 2283 2.51 5 N 678 2.21 5 O 687 1.98 5 H 3786 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 7440 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1308 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "B" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1308 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "C" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1308 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "D" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 4.28, per 1000 atoms: 0.58 Number of scatterers: 7440 At special positions: 0 Unit cell: (121.952, 114.536, 40.376, 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 6 16.00 O 687 8.00 N 678 7.00 C 2283 6.00 H 3786 1.00 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: 1.54 Conformation dependent library (CDL) restraints added in 592.5 milliseconds 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 846 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 19 sheets defined 0.0% alpha, 52.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.506A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.758A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 325 removed outlier: 6.944A pdb=" N VAL B 318 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR A 319 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N SER B 320 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS A 321 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N CYS B 322 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY A 323 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N SER C 324 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A 325 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.250A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 341 removed outlier: 6.438A pdb=" N VAL A 337 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LYS B 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL A 339 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.526A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 351 through 356 removed outlier: 6.625A pdb=" N SER A 356 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER C 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N GLY A 355 " --> pdb=" O SER C 356 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.441A pdb=" N ASN A 359 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N HIS B 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N THR A 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 369 through 378 removed outlier: 6.583A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 381 through 386 removed outlier: 6.411A pdb=" N ASN A 381 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ALA B 384 " --> pdb=" O ASN A 381 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS A 383 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR B 386 " --> pdb=" O LYS A 383 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS A 385 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 306 through 310 Processing sheet with id=AB3, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.793A pdb=" N VAL D 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 317 through 325 removed outlier: 6.455A pdb=" N LYS D 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N SER F 320 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR D 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N CYS F 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS D 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N SER F 324 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY D 323 " --> pdb=" O SER F 324 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 328 through 330 Processing sheet with id=AB6, first strand: chain 'E' and resid 337 through 340 removed outlier: 6.508A pdb=" N VAL D 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LYS E 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL D 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU D 338 " --> pdb=" O VAL F 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 343 through 346 removed outlier: 6.061A pdb=" N LYS D 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N PHE F 346 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP D 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 350 through 354 removed outlier: 6.461A pdb=" N GLN D 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE F 354 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS D 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 357 through 362 removed outlier: 6.462A pdb=" N ASP D 358 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N THR F 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE D 360 " --> pdb=" O THR F 361 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 368 through 378 removed outlier: 6.307A pdb=" N LYS D 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLU F 372 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE D 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N HIS F 374 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR D 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU F 376 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS D 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE F 378 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR D 377 " --> pdb=" O PHE F 378 " (cutoff:3.500A) 85 hydrogen bonds defined for protein. 255 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.15 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3780 1.12 - 1.29: 614 1.29 - 1.47: 1190 1.47 - 1.64: 1907 1.64 - 1.81: 6 Bond restraints: 7497 Sorted by residual: bond pdb=" CE2 PHE F 346 " pdb=" HE2 PHE F 346 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N SER D 356 " pdb=" H SER D 356 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N LEU B 344 " pdb=" H LEU B 344 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" NE2 HIS E 329 " pdb=" HE2 HIS E 329 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ARG D 349 " pdb=" H ARG D 349 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 7492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 11574 2.64 - 5.28: 1640 5.28 - 7.91: 430 7.91 - 10.55: 6 10.55 - 13.19: 6 Bond angle restraints: 13656 Sorted by residual: angle pdb=" CA PHE D 346 " pdb=" CB PHE D 346 " pdb=" CG PHE D 346 " ideal model delta sigma weight residual 113.80 119.27 -5.47 1.00e+00 1.00e+00 2.99e+01 angle pdb=" CA PHE A 346 " pdb=" CB PHE A 346 " pdb=" CG PHE A 346 " ideal model delta sigma weight residual 113.80 119.20 -5.40 1.00e+00 1.00e+00 2.92e+01 angle pdb=" CA PHE C 346 " pdb=" CB PHE C 346 " pdb=" CG PHE C 346 " ideal model delta sigma weight residual 113.80 119.09 -5.29 1.00e+00 1.00e+00 2.80e+01 angle pdb=" CB HIS B 388 " pdb=" CG HIS B 388 " pdb=" CD2 HIS B 388 " ideal model delta sigma weight residual 131.20 124.59 6.61 1.30e+00 5.92e-01 2.59e+01 angle pdb=" CB HIS C 362 " pdb=" CG HIS C 362 " pdb=" CD2 HIS C 362 " ideal model delta sigma weight residual 131.20 124.61 6.59 1.30e+00 5.92e-01 2.57e+01 ... (remaining 13651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 3079 16.74 - 33.48: 209 33.48 - 50.22: 57 50.22 - 66.97: 100 66.97 - 83.71: 11 Dihedral angle restraints: 3456 sinusoidal: 1968 harmonic: 1488 Sorted by residual: dihedral pdb=" C GLU A 342 " pdb=" N GLU A 342 " pdb=" CA GLU A 342 " pdb=" CB GLU A 342 " ideal model delta harmonic sigma weight residual -122.60 -141.21 18.61 0 2.50e+00 1.60e-01 5.54e+01 dihedral pdb=" N GLU A 342 " pdb=" C GLU A 342 " pdb=" CA GLU A 342 " pdb=" CB GLU A 342 " ideal model delta harmonic sigma weight residual 122.80 139.67 -16.87 0 2.50e+00 1.60e-01 4.56e+01 dihedral pdb=" CA GLN C 336 " pdb=" C GLN C 336 " pdb=" N VAL C 337 " pdb=" CA VAL C 337 " ideal model delta harmonic sigma weight residual 180.00 151.79 28.21 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 3453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 468 0.144 - 0.288: 80 0.288 - 0.431: 8 0.431 - 0.575: 1 0.575 - 0.719: 1 Chirality restraints: 558 Sorted by residual: chirality pdb=" CA GLU A 342 " pdb=" N GLU A 342 " pdb=" C GLU A 342 " pdb=" CB GLU A 342 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CA GLU C 342 " pdb=" N GLU C 342 " pdb=" C GLU C 342 " pdb=" CB GLU C 342 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.05e+00 chirality pdb=" CA LYS A 375 " pdb=" N LYS A 375 " pdb=" C LYS A 375 " pdb=" CB LYS A 375 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 555 not shown) Planarity restraints: 1086 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 341 " 0.035 2.00e-02 2.50e+03 6.53e-02 4.27e+01 pdb=" N GLU D 342 " -0.113 2.00e-02 2.50e+03 pdb=" CA GLU D 342 " 0.032 2.00e-02 2.50e+03 pdb=" H GLU D 342 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 368 " -0.013 2.00e-02 2.50e+03 4.39e-02 2.90e+01 pdb=" CG ASN A 368 " -0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN A 368 " 0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN A 368 " -0.079 2.00e-02 2.50e+03 pdb="HD21 ASN A 368 " 0.063 2.00e-02 2.50e+03 pdb="HD22 ASN A 368 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 349 " 0.234 9.50e-02 1.11e+02 8.41e-02 2.89e+01 pdb=" NE ARG C 349 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG C 349 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 349 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 349 " -0.004 2.00e-02 2.50e+03 pdb="HH11 ARG C 349 " -0.060 2.00e-02 2.50e+03 pdb="HH12 ARG C 349 " 0.066 2.00e-02 2.50e+03 pdb="HH21 ARG C 349 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG C 349 " -0.029 2.00e-02 2.50e+03 ... (remaining 1083 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 555 2.17 - 2.78: 12683 2.78 - 3.39: 19262 3.39 - 3.99: 26383 3.99 - 4.60: 36293 Nonbonded interactions: 95176 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.564 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.572 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.573 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.585 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.608 2.450 ... (remaining 95171 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 305 through 379) selection = (chain 'B' and resid 305 through 379) selection = (chain 'C' and resid 305 through 379) selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.690 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: 0.110 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.770 Find NCS groups from input model: 0.220 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:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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 : 0.011 0.040 3711 Z= 0.691 Angle : 1.849 7.917 4965 Z= 1.219 Chirality : 0.113 0.719 558 Planarity : 0.010 0.082 633 Dihedral : 11.921 83.708 1425 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.31), residues: 465 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.24), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.003 HIS C 330 PHE 0.033 0.009 PHE D 346 TYR 0.055 0.011 TYR D 310 ARG 0.004 0.001 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.06741 ( 85) hydrogen bonds : angle 7.50027 ( 255) covalent geometry : bond 0.01091 ( 3711) covalent geometry : angle 1.84858 ( 4965) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 2.5061 time to fit residues: 394.2870 Evaluate side-chains 88 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 327 ASN A 351 GLN A 368 ASN B 307 GLN B 327 ASN B 368 ASN C 307 GLN C 327 ASN C 368 ASN D 351 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.134416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.121300 restraints weight = 14569.714| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.63 r_work: 0.3884 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3805 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3711 Z= 0.141 Angle : 0.649 4.913 4965 Z= 0.343 Chirality : 0.054 0.156 558 Planarity : 0.003 0.026 633 Dihedral : 6.668 20.416 489 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.56 % Allowed : 16.55 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.32), residues: 465 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 329 PHE 0.004 0.001 PHE A 346 TYR 0.008 0.001 TYR D 310 ARG 0.002 0.001 ARG C 349 Details of bonding type rmsd hydrogen bonds : bond 0.02592 ( 85) hydrogen bonds : angle 5.40085 ( 255) covalent geometry : bond 0.00317 ( 3711) covalent geometry : angle 0.64858 ( 4965) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.557 Fit side-chains REVERT: B 356 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.8184 (t) REVERT: B 385 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8495 (tmtm) REVERT: C 379 ARG cc_start: 0.8746 (mtp85) cc_final: 0.8541 (mtp85) REVERT: E 340 LYS cc_start: 0.8491 (tmtt) cc_final: 0.8198 (tttm) REVERT: F 370 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8295 (tmtt) outliers start: 19 outliers final: 4 residues processed: 98 average time/residue: 2.3757 time to fit residues: 240.0273 Evaluate side-chains 83 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 370 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 9 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.127408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.114450 restraints weight = 14640.345| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.60 r_work: 0.3782 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3711 Z= 0.162 Angle : 0.601 5.002 4965 Z= 0.320 Chirality : 0.054 0.168 558 Planarity : 0.003 0.031 633 Dihedral : 5.875 18.648 489 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.84 % Allowed : 18.23 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.33), residues: 465 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 329 PHE 0.004 0.001 PHE A 346 TYR 0.012 0.002 TYR D 310 ARG 0.002 0.000 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.02411 ( 85) hydrogen bonds : angle 4.97663 ( 255) covalent geometry : bond 0.00371 ( 3711) covalent geometry : angle 0.60085 ( 4965) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.566 Fit side-chains REVERT: A 356 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8803 (t) REVERT: B 385 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8508 (tmtm) REVERT: C 381 ASN cc_start: 0.8505 (t0) cc_final: 0.8232 (t0) REVERT: E 336 GLN cc_start: 0.8658 (mp10) cc_final: 0.8303 (mt0) REVERT: F 370 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8252 (tmtt) outliers start: 16 outliers final: 5 residues processed: 91 average time/residue: 2.5161 time to fit residues: 235.6379 Evaluate side-chains 83 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 379 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 3 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.126856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.114229 restraints weight = 14826.527| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.60 r_work: 0.3763 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3711 Z= 0.172 Angle : 0.568 4.585 4965 Z= 0.301 Chirality : 0.053 0.154 558 Planarity : 0.003 0.032 633 Dihedral : 5.567 18.033 489 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.28 % Allowed : 16.55 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.33), residues: 465 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.004 0.001 PHE E 378 TYR 0.011 0.002 TYR D 310 ARG 0.001 0.000 ARG C 379 Details of bonding type rmsd hydrogen bonds : bond 0.02224 ( 85) hydrogen bonds : angle 4.79101 ( 255) covalent geometry : bond 0.00391 ( 3711) covalent geometry : angle 0.56808 ( 4965) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: B 356 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8587 (t) REVERT: B 385 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8483 (tmtm) REVERT: E 336 GLN cc_start: 0.8621 (mp10) cc_final: 0.8306 (mt0) REVERT: F 338 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: F 340 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8388 (mtpm) outliers start: 22 outliers final: 11 residues processed: 89 average time/residue: 2.5442 time to fit residues: 233.2870 Evaluate side-chains 89 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 340 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 34 optimal weight: 6.9990 chunk 14 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN A 381 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.129954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.117188 restraints weight = 14369.922| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.57 r_work: 0.3813 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3711 Z= 0.098 Angle : 0.504 4.373 4965 Z= 0.263 Chirality : 0.051 0.135 558 Planarity : 0.003 0.029 633 Dihedral : 5.115 15.341 489 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.36 % Allowed : 17.99 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.34), residues: 465 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 374 PHE 0.002 0.001 PHE F 346 TYR 0.008 0.001 TYR D 310 ARG 0.002 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.01809 ( 85) hydrogen bonds : angle 4.46378 ( 255) covalent geometry : bond 0.00220 ( 3711) covalent geometry : angle 0.50383 ( 4965) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 379 ARG cc_start: 0.8784 (mtp85) cc_final: 0.8397 (mtp85) REVERT: B 356 SER cc_start: 0.8849 (OUTLIER) cc_final: 0.8619 (t) REVERT: B 385 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8436 (tmtm) REVERT: B 387 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8112 (m-30) REVERT: C 381 ASN cc_start: 0.8546 (t0) cc_final: 0.8281 (t0) REVERT: C 387 ASP cc_start: 0.8197 (t0) cc_final: 0.7988 (m-30) REVERT: E 336 GLN cc_start: 0.8596 (mp10) cc_final: 0.8324 (mt0) REVERT: F 336 GLN cc_start: 0.8371 (mp10) cc_final: 0.7623 (mp10) REVERT: F 338 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: F 340 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8185 (mtpm) outliers start: 14 outliers final: 7 residues processed: 94 average time/residue: 2.4566 time to fit residues: 238.0183 Evaluate side-chains 91 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 340 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN A 381 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.126420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.113616 restraints weight = 14841.145| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.62 r_work: 0.3757 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3711 Z= 0.172 Angle : 0.539 4.411 4965 Z= 0.285 Chirality : 0.052 0.138 558 Planarity : 0.003 0.030 633 Dihedral : 5.153 15.871 489 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.84 % Allowed : 18.47 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.33), residues: 465 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.004 0.001 PHE F 346 TYR 0.011 0.002 TYR D 310 ARG 0.001 0.000 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.02029 ( 85) hydrogen bonds : angle 4.55556 ( 255) covalent geometry : bond 0.00384 ( 3711) covalent geometry : angle 0.53880 ( 4965) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 ARG cc_start: 0.8817 (mtp85) cc_final: 0.8430 (mtp85) REVERT: B 356 SER cc_start: 0.8907 (OUTLIER) cc_final: 0.8671 (t) REVERT: B 385 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8430 (tmtm) REVERT: B 387 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8126 (m-30) REVERT: C 381 ASN cc_start: 0.8588 (t0) cc_final: 0.8306 (t0) REVERT: E 336 GLN cc_start: 0.8600 (mp10) cc_final: 0.8372 (mt0) outliers start: 16 outliers final: 6 residues processed: 84 average time/residue: 2.5061 time to fit residues: 216.7020 Evaluate side-chains 83 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 340 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 30 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN A 381 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.129554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.116860 restraints weight = 14550.866| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 1.61 r_work: 0.3803 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.5866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3711 Z= 0.103 Angle : 0.491 4.371 4965 Z= 0.256 Chirality : 0.051 0.133 558 Planarity : 0.003 0.028 633 Dihedral : 4.860 14.719 489 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.60 % Allowed : 18.23 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.34), residues: 465 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.002 0.001 PHE A 378 TYR 0.008 0.001 TYR D 310 ARG 0.001 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.01693 ( 85) hydrogen bonds : angle 4.34817 ( 255) covalent geometry : bond 0.00234 ( 3711) covalent geometry : angle 0.49092 ( 4965) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 ARG cc_start: 0.8807 (mtp85) cc_final: 0.8433 (mtp85) REVERT: A 387 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8247 (m-30) REVERT: B 356 SER cc_start: 0.8918 (OUTLIER) cc_final: 0.8711 (t) REVERT: B 385 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8474 (tmtm) REVERT: C 381 ASN cc_start: 0.8561 (t0) cc_final: 0.8280 (t0) REVERT: C 387 ASP cc_start: 0.8196 (t0) cc_final: 0.7988 (m-30) REVERT: F 317 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8707 (ptpp) outliers start: 15 outliers final: 8 residues processed: 89 average time/residue: 2.4929 time to fit residues: 228.6228 Evaluate side-chains 88 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 340 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN A 381 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.124186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.111261 restraints weight = 14717.204| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.60 r_work: 0.3728 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3711 Z= 0.212 Angle : 0.560 4.837 4965 Z= 0.299 Chirality : 0.053 0.142 558 Planarity : 0.003 0.031 633 Dihedral : 5.152 16.982 489 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.28 % Allowed : 17.75 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.33), residues: 465 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.007 0.001 PHE F 346 TYR 0.013 0.002 TYR D 310 ARG 0.001 0.000 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.02130 ( 85) hydrogen bonds : angle 4.65376 ( 255) covalent geometry : bond 0.00473 ( 3711) covalent geometry : angle 0.56038 ( 4965) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8174 (m-30) REVERT: B 356 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8738 (t) REVERT: B 385 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8507 (tmtm) REVERT: C 387 ASP cc_start: 0.8298 (t0) cc_final: 0.8056 (m-30) outliers start: 22 outliers final: 11 residues processed: 87 average time/residue: 2.6434 time to fit residues: 236.4287 Evaluate side-chains 86 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 340 LYS Chi-restraints excluded: chain F residue 344 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 38 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN A 381 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.125935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.113219 restraints weight = 14633.904| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.59 r_work: 0.3758 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.5979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3711 Z= 0.149 Angle : 0.523 4.368 4965 Z= 0.275 Chirality : 0.052 0.136 558 Planarity : 0.003 0.031 633 Dihedral : 5.027 15.251 489 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.36 % Allowed : 19.90 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.33), residues: 465 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.003 0.001 PHE C 346 TYR 0.010 0.002 TYR D 310 ARG 0.001 0.000 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.01913 ( 85) hydrogen bonds : angle 4.55003 ( 255) covalent geometry : bond 0.00332 ( 3711) covalent geometry : angle 0.52305 ( 4965) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 ARG cc_start: 0.8796 (mtp85) cc_final: 0.8420 (mtp85) REVERT: A 387 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8172 (m-30) REVERT: B 385 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8455 (tmtm) REVERT: B 387 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8126 (m-30) REVERT: C 387 ASP cc_start: 0.8324 (t0) cc_final: 0.8077 (m-30) outliers start: 14 outliers final: 8 residues processed: 81 average time/residue: 2.5743 time to fit residues: 214.4101 Evaluate side-chains 83 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 340 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 11 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 44 optimal weight: 0.0570 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN A 381 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.128464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.115782 restraints weight = 14566.897| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.60 r_work: 0.3796 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.6064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3711 Z= 0.100 Angle : 0.487 4.251 4965 Z= 0.253 Chirality : 0.051 0.131 558 Planarity : 0.003 0.028 633 Dihedral : 4.791 14.563 489 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.88 % Allowed : 20.38 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.34), residues: 465 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.002 0.001 PHE D 346 TYR 0.008 0.002 TYR D 310 ARG 0.001 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.01704 ( 85) hydrogen bonds : angle 4.34142 ( 255) covalent geometry : bond 0.00225 ( 3711) covalent geometry : angle 0.48688 ( 4965) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 ARG cc_start: 0.8795 (mtp85) cc_final: 0.8430 (mtp85) REVERT: A 387 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8237 (m-30) REVERT: B 385 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8453 (tmtm) REVERT: B 387 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8092 (m-30) REVERT: C 381 ASN cc_start: 0.8582 (t0) cc_final: 0.8301 (t0) REVERT: C 387 ASP cc_start: 0.8270 (t0) cc_final: 0.8060 (m-30) outliers start: 12 outliers final: 8 residues processed: 86 average time/residue: 2.5575 time to fit residues: 226.3419 Evaluate side-chains 87 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 340 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 1 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.130096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.117519 restraints weight = 14367.237| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.60 r_work: 0.3823 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.6157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3711 Z= 0.083 Angle : 0.468 4.206 4965 Z= 0.242 Chirality : 0.051 0.131 558 Planarity : 0.003 0.026 633 Dihedral : 4.563 13.444 489 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.64 % Allowed : 20.38 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.34), residues: 465 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS C 330 PHE 0.003 0.000 PHE D 378 TYR 0.007 0.001 TYR D 310 ARG 0.001 0.000 ARG A 379 Details of bonding type rmsd hydrogen bonds : bond 0.01590 ( 85) hydrogen bonds : angle 4.18486 ( 255) covalent geometry : bond 0.00192 ( 3711) covalent geometry : angle 0.46846 ( 4965) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7276.65 seconds wall clock time: 123 minutes 46.63 seconds (7426.63 seconds total)