Starting phenix.real_space_refine on Tue Mar 3 12:25:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n3a_9349/03_2026/6n3a_9349.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n3a_9349/03_2026/6n3a_9349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n3a_9349/03_2026/6n3a_9349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n3a_9349/03_2026/6n3a_9349.map" model { file = "/net/cci-nas-00/data/ceres_data/6n3a_9349/03_2026/6n3a_9349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n3a_9349/03_2026/6n3a_9349.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.008 sd= 0.873 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 2550 2.51 5 N 800 2.21 5 O 880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4310 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 359 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 72 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, L, M, N, O, P, Q, R, S, T Time building chain proxies: 0.45, per 1000 atoms: 0.10 Number of scatterers: 4310 At special positions: 0 Unit cell: (120.232, 67.032, 41.496, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 880 8.00 N 800 7.00 C 2550 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 163.9 milliseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1060 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 48.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'G' and resid 317 through 318 removed outlier: 6.431A pdb=" N SER D 317 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER A 317 " --> pdb=" O ILE D 318 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 321 through 323 removed outlier: 5.783A pdb=" N ALA D 321 " --> pdb=" O MET G 322 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ALA A 321 " --> pdb=" O MET D 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 328 through 335 removed outlier: 6.281A pdb=" N ALA D 329 " --> pdb=" O LEU G 330 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N SER G 332 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN D 331 " --> pdb=" O SER G 332 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N TRP G 334 " --> pdb=" O GLN D 331 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER D 333 " --> pdb=" O TRP G 334 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ALA A 329 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER D 332 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLN A 331 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N TRP D 334 " --> pdb=" O GLN A 331 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER A 333 " --> pdb=" O TRP D 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 338 through 346 removed outlier: 6.518A pdb=" N GLY D 338 " --> pdb=" O MET G 339 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ALA G 341 " --> pdb=" O GLY D 338 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU D 340 " --> pdb=" O ALA G 341 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLN G 343 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER D 342 " --> pdb=" O GLN G 343 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ASN G 345 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLN D 344 " --> pdb=" O ASN G 345 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLY A 338 " --> pdb=" O MET D 339 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ALA D 341 " --> pdb=" O GLY A 338 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 340 " --> pdb=" O ALA D 341 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN D 343 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER A 342 " --> pdb=" O GLN D 343 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N ASN D 345 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLN A 344 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 352 through 359 removed outlier: 6.904A pdb=" N ASN D 353 " --> pdb=" O GLN G 354 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N GLN G 356 " --> pdb=" O ASN D 353 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASN D 355 " --> pdb=" O GLN G 356 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ASN G 358 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLY D 357 " --> pdb=" O ASN G 358 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN A 353 " --> pdb=" O GLN D 354 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N GLN D 356 " --> pdb=" O ASN A 353 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASN A 355 " --> pdb=" O GLN D 356 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ASN D 358 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY A 357 " --> pdb=" O ASN D 358 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN F 353 " --> pdb=" O ASN A 352 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN I 353 " --> pdb=" O ASN F 352 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 317 through 318 removed outlier: 6.438A pdb=" N SER C 317 " --> pdb=" O ILE H 318 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER B 317 " --> pdb=" O ILE C 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 321 through 323 removed outlier: 5.790A pdb=" N ALA C 321 " --> pdb=" O MET H 322 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA B 321 " --> pdb=" O MET C 322 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 328 through 335 removed outlier: 6.288A pdb=" N ALA C 329 " --> pdb=" O LEU H 330 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N SER H 332 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLN C 331 " --> pdb=" O SER H 332 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N TRP H 334 " --> pdb=" O GLN C 331 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER C 333 " --> pdb=" O TRP H 334 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA B 329 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N SER C 332 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN B 331 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N TRP C 334 " --> pdb=" O GLN B 331 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER B 333 " --> pdb=" O TRP C 334 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 338 through 346 removed outlier: 6.520A pdb=" N GLY C 338 " --> pdb=" O MET H 339 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ALA H 341 " --> pdb=" O GLY C 338 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU C 340 " --> pdb=" O ALA H 341 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN H 343 " --> pdb=" O LEU C 340 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER C 342 " --> pdb=" O GLN H 343 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ASN H 345 " --> pdb=" O SER C 342 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLN C 344 " --> pdb=" O ASN H 345 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY B 338 " --> pdb=" O MET C 339 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ALA C 341 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU B 340 " --> pdb=" O ALA C 341 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLN C 343 " --> pdb=" O LEU B 340 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER B 342 " --> pdb=" O GLN C 343 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N ASN C 345 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLN B 344 " --> pdb=" O ASN C 345 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 352 through 359 removed outlier: 6.903A pdb=" N ASN C 353 " --> pdb=" O GLN H 354 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N GLN H 356 " --> pdb=" O ASN C 353 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ASN C 355 " --> pdb=" O GLN H 356 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ASN H 358 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY C 357 " --> pdb=" O ASN H 358 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASN B 353 " --> pdb=" O GLN C 354 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N GLN C 356 " --> pdb=" O ASN B 353 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASN B 355 " --> pdb=" O GLN C 356 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ASN C 358 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLY B 357 " --> pdb=" O ASN C 358 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN E 353 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN J 353 " --> pdb=" O ASN E 352 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 340 through 344 removed outlier: 7.182A pdb=" N ALA K 341 " --> pdb=" O SER P 342 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLN P 344 " --> pdb=" O ALA K 341 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLN K 343 " --> pdb=" O GLN P 344 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA P 341 " --> pdb=" O SER S 342 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N GLN S 344 " --> pdb=" O ALA P 341 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN P 343 " --> pdb=" O GLN S 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 340 through 344 removed outlier: 7.190A pdb=" N ALA L 341 " --> pdb=" O SER O 342 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N GLN O 344 " --> pdb=" O ALA L 341 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN L 343 " --> pdb=" O GLN O 344 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ALA O 341 " --> pdb=" O SER T 342 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N GLN T 344 " --> pdb=" O ALA O 341 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLN O 343 " --> pdb=" O GLN T 344 " (cutoff:3.500A) 112 hydrogen bonds defined for protein. 336 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: 0.59 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1570 1.34 - 1.45: 572 1.45 - 1.57: 2048 1.57 - 1.69: 0 1.69 - 1.81: 160 Bond restraints: 4350 Sorted by residual: bond pdb=" CG MET G 336 " pdb=" SD MET G 336 " ideal model delta sigma weight residual 1.803 1.774 0.029 2.50e-02 1.60e+03 1.39e+00 bond pdb=" CG MET D 336 " pdb=" SD MET D 336 " ideal model delta sigma weight residual 1.803 1.774 0.029 2.50e-02 1.60e+03 1.33e+00 bond pdb=" CB MET D 337 " pdb=" CG MET D 337 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CB MET G 337 " pdb=" CG MET G 337 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CG MET A 336 " pdb=" SD MET A 336 " ideal model delta sigma weight residual 1.803 1.774 0.029 2.50e-02 1.60e+03 1.32e+00 ... (remaining 4345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 5376 1.94 - 3.88: 324 3.88 - 5.82: 89 5.82 - 7.76: 11 7.76 - 9.70: 10 Bond angle restraints: 5810 Sorted by residual: angle pdb=" CB MET J 323 " pdb=" CG MET J 323 " pdb=" SD MET J 323 " ideal model delta sigma weight residual 112.70 122.40 -9.70 3.00e+00 1.11e-01 1.05e+01 angle pdb=" CB MET C 323 " pdb=" CG MET C 323 " pdb=" SD MET C 323 " ideal model delta sigma weight residual 112.70 122.39 -9.69 3.00e+00 1.11e-01 1.04e+01 angle pdb=" CB MET E 323 " pdb=" CG MET E 323 " pdb=" SD MET E 323 " ideal model delta sigma weight residual 112.70 122.38 -9.68 3.00e+00 1.11e-01 1.04e+01 angle pdb=" CB MET D 323 " pdb=" CG MET D 323 " pdb=" SD MET D 323 " ideal model delta sigma weight residual 112.70 122.38 -9.68 3.00e+00 1.11e-01 1.04e+01 angle pdb=" CB MET B 323 " pdb=" CG MET B 323 " pdb=" SD MET B 323 " ideal model delta sigma weight residual 112.70 122.38 -9.68 3.00e+00 1.11e-01 1.04e+01 ... (remaining 5805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.28: 2340 15.28 - 30.57: 240 30.57 - 45.85: 50 45.85 - 61.13: 20 61.13 - 76.42: 10 Dihedral angle restraints: 2660 sinusoidal: 1020 harmonic: 1640 Sorted by residual: dihedral pdb=" CA ALA C 325 " pdb=" C ALA C 325 " pdb=" N ALA C 326 " pdb=" CA ALA C 326 " ideal model delta harmonic sigma weight residual 180.00 161.39 18.61 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ALA I 325 " pdb=" C ALA I 325 " pdb=" N ALA I 326 " pdb=" CA ALA I 326 " ideal model delta harmonic sigma weight residual 180.00 161.40 18.60 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ALA E 325 " pdb=" C ALA E 325 " pdb=" N ALA E 326 " pdb=" CA ALA E 326 " ideal model delta harmonic sigma weight residual 180.00 161.40 18.60 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 2657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 206 0.023 - 0.046: 161 0.046 - 0.069: 150 0.069 - 0.091: 13 0.091 - 0.114: 40 Chirality restraints: 570 Sorted by residual: chirality pdb=" CG LEU H 340 " pdb=" CB LEU H 340 " pdb=" CD1 LEU H 340 " pdb=" CD2 LEU H 340 " both_signs ideal model delta sigma weight residual False -2.59 -2.70 0.11 2.00e-01 2.50e+01 3.26e-01 chirality pdb=" CG LEU G 340 " pdb=" CB LEU G 340 " pdb=" CD1 LEU G 340 " pdb=" CD2 LEU G 340 " both_signs ideal model delta sigma weight residual False -2.59 -2.70 0.11 2.00e-01 2.50e+01 3.20e-01 chirality pdb=" CG LEU I 340 " pdb=" CB LEU I 340 " pdb=" CD1 LEU I 340 " pdb=" CD2 LEU I 340 " both_signs ideal model delta sigma weight residual False -2.59 -2.70 0.11 2.00e-01 2.50e+01 3.18e-01 ... (remaining 567 not shown) Planarity restraints: 830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN S 344 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" CD GLN S 344 " -0.040 2.00e-02 2.50e+03 pdb=" OE1 GLN S 344 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN S 344 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN Q 344 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" CD GLN Q 344 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN Q 344 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN Q 344 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN L 344 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" CD GLN L 344 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN L 344 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN L 344 " -0.013 2.00e-02 2.50e+03 ... (remaining 827 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 1959 2.96 - 3.44: 4192 3.44 - 3.93: 7199 3.93 - 4.41: 8529 4.41 - 4.90: 16319 Nonbonded interactions: 38198 Sorted by model distance: nonbonded pdb=" O SER C 332 " pdb=" NE2 GLN M 344 " model vdw 2.469 3.120 nonbonded pdb=" O SER E 332 " pdb=" NE2 GLN O 344 " model vdw 2.469 3.120 nonbonded pdb=" O SER G 332 " pdb=" NE2 GLN Q 344 " model vdw 2.469 3.120 nonbonded pdb=" O SER I 332 " pdb=" NE2 GLN S 344 " model vdw 2.470 3.120 nonbonded pdb=" O SER J 332 " pdb=" NE2 GLN T 344 " model vdw 2.470 3.120 ... (remaining 38193 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 0.090 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.360 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 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 0.049 4350 Z= 0.333 Angle : 1.143 9.699 5810 Z= 0.553 Chirality : 0.047 0.114 570 Planarity : 0.007 0.055 830 Dihedral : 14.532 76.417 1600 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.23 (0.15), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.11), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.008 PHE J 316 TRP 0.008 0.003 TRP E 334 Details of bonding type rmsd covalent geometry : bond 0.00785 ( 4350) covalent geometry : angle 1.14299 ( 5810) hydrogen bonds : bond 0.18176 ( 112) hydrogen bonds : angle 8.49767 ( 336) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.164 Fit side-chains REVERT: C 323 MET cc_start: 0.7662 (tpp) cc_final: 0.7332 (tpp) REVERT: C 350 SER cc_start: 0.9404 (m) cc_final: 0.9035 (p) REVERT: D 323 MET cc_start: 0.7687 (tpp) cc_final: 0.7361 (tpp) REVERT: D 350 SER cc_start: 0.9403 (m) cc_final: 0.9033 (p) REVERT: E 323 MET cc_start: 0.7735 (tpp) cc_final: 0.7028 (tpp) REVERT: F 323 MET cc_start: 0.7750 (tpp) cc_final: 0.7059 (tpp) REVERT: F 359 MET cc_start: 0.8245 (ttt) cc_final: 0.8033 (ttp) REVERT: G 345 ASN cc_start: 0.7589 (m-40) cc_final: 0.7241 (m-40) REVERT: H 345 ASN cc_start: 0.7591 (m-40) cc_final: 0.7246 (m-40) REVERT: I 334 TRP cc_start: 0.8649 (m-90) cc_final: 0.7876 (m-90) REVERT: I 337 MET cc_start: 0.8572 (ttt) cc_final: 0.8192 (ttt) REVERT: I 354 GLN cc_start: 0.8354 (mt0) cc_final: 0.8111 (mt0) REVERT: J 334 TRP cc_start: 0.8633 (m-90) cc_final: 0.7645 (m-90) REVERT: J 337 MET cc_start: 0.8583 (ttt) cc_final: 0.8219 (ttt) REVERT: J 354 GLN cc_start: 0.8358 (mt0) cc_final: 0.8118 (mt0) REVERT: K 347 SER cc_start: 0.8051 (t) cc_final: 0.7777 (m) REVERT: L 347 SER cc_start: 0.8079 (t) cc_final: 0.7857 (m) REVERT: Q 347 SER cc_start: 0.8303 (t) cc_final: 0.8064 (m) REVERT: R 347 SER cc_start: 0.8237 (t) cc_final: 0.7994 (m) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.0431 time to fit residues: 12.9365 Evaluate side-chains 170 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 30.0000 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.0870 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 58 optimal weight: 0.0040 overall best weight: 3.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN F 356 GLN G 356 GLN H 356 GLN ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 356 GLN ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 356 GLN K 346 GLN L 346 GLN M 346 GLN N 346 GLN O 346 GLN P 346 GLN S 346 GLN T 346 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5099 r_free = 0.5099 target = 0.204614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.171140 restraints weight = 5146.042| |-----------------------------------------------------------------------------| r_work (start): 0.4799 rms_B_bonded: 2.71 r_work: 0.4695 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4350 Z= 0.148 Angle : 0.677 7.615 5810 Z= 0.337 Chirality : 0.042 0.137 570 Planarity : 0.004 0.037 830 Dihedral : 7.559 40.744 590 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.18 % Allowed : 17.27 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.23 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE A 316 TRP 0.015 0.003 TRP J 334 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 4350) covalent geometry : angle 0.67652 ( 5810) hydrogen bonds : bond 0.03281 ( 112) hydrogen bonds : angle 6.08164 ( 336) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 193 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 336 MET cc_start: 0.8478 (tmm) cc_final: 0.8127 (tmm) REVERT: B 336 MET cc_start: 0.8479 (tmm) cc_final: 0.8144 (tmm) REVERT: C 323 MET cc_start: 0.7834 (tpp) cc_final: 0.7264 (tpp) REVERT: D 323 MET cc_start: 0.7849 (tpp) cc_final: 0.7276 (tpp) REVERT: E 336 MET cc_start: 0.8774 (tmm) cc_final: 0.8499 (tmm) REVERT: E 356 GLN cc_start: 0.8660 (mt0) cc_final: 0.8458 (mt0) REVERT: F 336 MET cc_start: 0.8793 (tmm) cc_final: 0.8490 (tmm) REVERT: G 345 ASN cc_start: 0.8205 (m-40) cc_final: 0.7900 (m-40) REVERT: H 345 ASN cc_start: 0.8203 (m-40) cc_final: 0.7911 (m-40) REVERT: I 317 SER cc_start: 0.8913 (m) cc_final: 0.8576 (t) REVERT: I 323 MET cc_start: 0.7648 (tpp) cc_final: 0.7424 (tpp) REVERT: J 317 SER cc_start: 0.8925 (m) cc_final: 0.8585 (t) REVERT: J 323 MET cc_start: 0.7622 (tpp) cc_final: 0.7399 (tpp) REVERT: K 347 SER cc_start: 0.8165 (t) cc_final: 0.7913 (m) REVERT: Q 347 SER cc_start: 0.8591 (t) cc_final: 0.8380 (m) REVERT: R 347 SER cc_start: 0.8473 (t) cc_final: 0.8227 (m) outliers start: 14 outliers final: 8 residues processed: 193 average time/residue: 0.0380 time to fit residues: 10.4031 Evaluate side-chains 168 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 350 SER Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 350 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 2 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 21 optimal weight: 40.0000 chunk 14 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 34 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 51 optimal weight: 50.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 ASN ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 ASN ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 GLN ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.224184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.166025 restraints weight = 6232.368| |-----------------------------------------------------------------------------| r_work (start): 0.4626 rms_B_bonded: 2.94 r_work: 0.4737 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4633 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.4633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 4350 Z= 0.257 Angle : 0.748 7.785 5810 Z= 0.364 Chirality : 0.040 0.128 570 Planarity : 0.003 0.026 830 Dihedral : 7.948 51.691 590 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 4.09 % Allowed : 21.59 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.14 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE B 316 TRP 0.013 0.003 TRP B 334 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 4350) covalent geometry : angle 0.74768 ( 5810) hydrogen bonds : bond 0.02701 ( 112) hydrogen bonds : angle 5.54032 ( 336) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 336 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7631 (tmm) REVERT: A 345 ASN cc_start: 0.8418 (m-40) cc_final: 0.8146 (m-40) REVERT: B 336 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.7980 (tmm) REVERT: C 336 MET cc_start: 0.8473 (tmm) cc_final: 0.7511 (tmm) REVERT: C 337 MET cc_start: 0.8570 (ttt) cc_final: 0.8084 (ttt) REVERT: E 339 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8151 (ttp) REVERT: F 339 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8086 (ttp) REVERT: F 345 ASN cc_start: 0.8640 (m-40) cc_final: 0.8426 (m-40) REVERT: F 359 MET cc_start: 0.8639 (ttm) cc_final: 0.8419 (ttm) REVERT: G 345 ASN cc_start: 0.8223 (m-40) cc_final: 0.7602 (m110) REVERT: H 345 ASN cc_start: 0.8275 (m-40) cc_final: 0.7651 (m110) REVERT: I 317 SER cc_start: 0.9113 (m) cc_final: 0.8722 (t) REVERT: I 323 MET cc_start: 0.7936 (tpp) cc_final: 0.7544 (tpp) REVERT: J 317 SER cc_start: 0.9107 (m) cc_final: 0.8714 (t) REVERT: J 323 MET cc_start: 0.8041 (tpp) cc_final: 0.7661 (tpp) REVERT: K 347 SER cc_start: 0.8304 (t) cc_final: 0.7966 (m) REVERT: Q 347 SER cc_start: 0.8420 (t) cc_final: 0.8217 (m) REVERT: R 347 SER cc_start: 0.8354 (t) cc_final: 0.8126 (m) outliers start: 18 outliers final: 10 residues processed: 156 average time/residue: 0.0418 time to fit residues: 9.1347 Evaluate side-chains 162 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 346 GLN Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain I residue 332 SER Chi-restraints excluded: chain M residue 339 MET Chi-restraints excluded: chain O residue 347 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 2 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 16 optimal weight: 50.0000 chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 0.0870 chunk 40 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 59 optimal weight: 30.0000 chunk 45 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 overall best weight: 5.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 344 GLN T 344 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4994 r_free = 0.4994 target = 0.222142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.169385 restraints weight = 5936.089| |-----------------------------------------------------------------------------| r_work (start): 0.4704 rms_B_bonded: 2.93 r_work: 0.4804 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4709 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.4709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4350 Z= 0.177 Angle : 0.663 8.246 5810 Z= 0.321 Chirality : 0.039 0.127 570 Planarity : 0.003 0.024 830 Dihedral : 7.525 49.885 590 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 2.73 % Allowed : 20.91 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.10 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE A 316 TRP 0.013 0.002 TRP E 334 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 4350) covalent geometry : angle 0.66292 ( 5810) hydrogen bonds : bond 0.02223 ( 112) hydrogen bonds : angle 5.24215 ( 336) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 336 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8084 (tmm) REVERT: B 336 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8093 (tmm) REVERT: C 336 MET cc_start: 0.8683 (tmm) cc_final: 0.6692 (tmm) REVERT: D 336 MET cc_start: 0.8411 (tmm) cc_final: 0.7256 (tmm) REVERT: E 322 MET cc_start: 0.8989 (mtp) cc_final: 0.8556 (mtt) REVERT: E 339 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.7327 (ttp) REVERT: F 339 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.7939 (ttp) REVERT: G 345 ASN cc_start: 0.8233 (m-40) cc_final: 0.7655 (m110) REVERT: H 345 ASN cc_start: 0.8218 (m-40) cc_final: 0.7667 (m110) REVERT: I 317 SER cc_start: 0.9077 (m) cc_final: 0.8717 (t) REVERT: I 323 MET cc_start: 0.7859 (tpp) cc_final: 0.7466 (tpp) REVERT: I 339 MET cc_start: 0.8601 (tpt) cc_final: 0.7621 (tpt) REVERT: J 317 SER cc_start: 0.9057 (m) cc_final: 0.8674 (t) REVERT: J 323 MET cc_start: 0.8002 (tpp) cc_final: 0.7636 (tpp) REVERT: J 339 MET cc_start: 0.8656 (tpt) cc_final: 0.7430 (tpt) REVERT: K 347 SER cc_start: 0.8191 (t) cc_final: 0.7848 (m) REVERT: Q 347 SER cc_start: 0.8468 (t) cc_final: 0.8260 (m) REVERT: R 347 SER cc_start: 0.8277 (t) cc_final: 0.8022 (m) outliers start: 12 outliers final: 8 residues processed: 154 average time/residue: 0.0419 time to fit residues: 9.1216 Evaluate side-chains 151 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 346 GLN Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 346 GLN Chi-restraints excluded: chain O residue 347 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 37 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 22 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5015 r_free = 0.5015 target = 0.221603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.170360 restraints weight = 6054.666| |-----------------------------------------------------------------------------| r_work (start): 0.4722 rms_B_bonded: 2.97 r_work: 0.4816 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4718 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.4718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4350 Z= 0.178 Angle : 0.664 9.115 5810 Z= 0.317 Chirality : 0.038 0.124 570 Planarity : 0.003 0.024 830 Dihedral : 7.414 49.665 590 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 3.41 % Allowed : 21.14 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.07 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE A 316 TRP 0.013 0.002 TRP E 334 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 4350) covalent geometry : angle 0.66418 ( 5810) hydrogen bonds : bond 0.02064 ( 112) hydrogen bonds : angle 5.06223 ( 336) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.150 Fit side-chains REVERT: A 336 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8043 (tmm) REVERT: B 336 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7980 (tmm) REVERT: C 336 MET cc_start: 0.8586 (tmm) cc_final: 0.6841 (tmm) REVERT: D 336 MET cc_start: 0.8608 (tmm) cc_final: 0.6876 (tmm) REVERT: E 339 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.7773 (ttp) REVERT: F 339 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.7618 (ttp) REVERT: G 345 ASN cc_start: 0.8215 (m-40) cc_final: 0.7838 (m-40) REVERT: H 336 MET cc_start: 0.8006 (tpt) cc_final: 0.7726 (tpt) REVERT: H 345 ASN cc_start: 0.8244 (m-40) cc_final: 0.7891 (m-40) REVERT: I 317 SER cc_start: 0.9061 (m) cc_final: 0.8688 (t) REVERT: I 323 MET cc_start: 0.7779 (tpp) cc_final: 0.7381 (tpp) REVERT: I 339 MET cc_start: 0.8668 (tpt) cc_final: 0.7519 (tpt) REVERT: I 360 GLN cc_start: 0.7857 (mm-40) cc_final: 0.5004 (pm20) REVERT: J 317 SER cc_start: 0.9079 (m) cc_final: 0.8719 (t) REVERT: J 323 MET cc_start: 0.7788 (tpp) cc_final: 0.7384 (tpp) REVERT: J 339 MET cc_start: 0.8746 (tpt) cc_final: 0.7691 (tpt) REVERT: K 347 SER cc_start: 0.8242 (t) cc_final: 0.7949 (m) REVERT: Q 347 SER cc_start: 0.8384 (t) cc_final: 0.8127 (m) REVERT: R 347 SER cc_start: 0.8360 (t) cc_final: 0.8095 (m) outliers start: 15 outliers final: 11 residues processed: 145 average time/residue: 0.0437 time to fit residues: 8.9498 Evaluate side-chains 154 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 346 GLN Chi-restraints excluded: chain H residue 347 SER Chi-restraints excluded: chain M residue 339 MET Chi-restraints excluded: chain O residue 347 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 31 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 54 optimal weight: 40.0000 chunk 45 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 59 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 3 optimal weight: 7.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** 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 = 0.4970 r_free = 0.4970 target = 0.211326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.164924 restraints weight = 6137.159| |-----------------------------------------------------------------------------| r_work (start): 0.4679 rms_B_bonded: 2.86 r_work: 0.4765 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4657 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.4657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 4350 Z= 0.254 Angle : 0.743 9.884 5810 Z= 0.352 Chirality : 0.039 0.122 570 Planarity : 0.003 0.025 830 Dihedral : 7.641 47.956 590 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 5.00 % Allowed : 19.55 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.11 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE B 316 TRP 0.014 0.002 TRP F 334 Details of bonding type rmsd covalent geometry : bond 0.00578 ( 4350) covalent geometry : angle 0.74321 ( 5810) hydrogen bonds : bond 0.02226 ( 112) hydrogen bonds : angle 4.98141 ( 336) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.191 Fit side-chains REVERT: A 336 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8055 (tmm) REVERT: B 336 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8023 (tmm) REVERT: C 336 MET cc_start: 0.8674 (tmm) cc_final: 0.6899 (tmm) REVERT: D 336 MET cc_start: 0.8617 (tmm) cc_final: 0.7055 (tmm) REVERT: E 339 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.7700 (ttp) REVERT: F 339 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.7957 (ttp) REVERT: G 345 ASN cc_start: 0.8290 (m-40) cc_final: 0.7828 (m-40) REVERT: H 345 ASN cc_start: 0.8308 (m-40) cc_final: 0.7917 (m-40) REVERT: I 317 SER cc_start: 0.9141 (m) cc_final: 0.8755 (t) REVERT: I 323 MET cc_start: 0.7873 (tpp) cc_final: 0.7371 (tpp) REVERT: I 339 MET cc_start: 0.8787 (tpt) cc_final: 0.7795 (tpt) REVERT: J 317 SER cc_start: 0.9153 (m) cc_final: 0.8794 (t) REVERT: J 323 MET cc_start: 0.7955 (tpp) cc_final: 0.7463 (tpp) REVERT: J 334 TRP cc_start: 0.8739 (m-90) cc_final: 0.7414 (m-90) REVERT: J 339 MET cc_start: 0.8757 (tpt) cc_final: 0.7738 (tpt) REVERT: J 359 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.6894 (ttm) REVERT: K 347 SER cc_start: 0.8288 (t) cc_final: 0.7967 (m) REVERT: Q 347 SER cc_start: 0.8586 (t) cc_final: 0.8382 (m) REVERT: R 347 SER cc_start: 0.8405 (t) cc_final: 0.8157 (m) outliers start: 22 outliers final: 17 residues processed: 143 average time/residue: 0.0401 time to fit residues: 8.1440 Evaluate side-chains 160 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 346 GLN Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain G residue 350 SER Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 346 GLN Chi-restraints excluded: chain H residue 347 SER Chi-restraints excluded: chain H residue 350 SER Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain M residue 339 MET Chi-restraints excluded: chain N residue 339 MET Chi-restraints excluded: chain O residue 347 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 51 optimal weight: 50.0000 chunk 15 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** 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 = 0.5008 r_free = 0.5008 target = 0.214336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.167259 restraints weight = 6105.647| |-----------------------------------------------------------------------------| r_work (start): 0.4711 rms_B_bonded: 2.91 r_work: 0.4803 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4701 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.4701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4350 Z= 0.212 Angle : 0.720 11.480 5810 Z= 0.337 Chirality : 0.039 0.124 570 Planarity : 0.003 0.025 830 Dihedral : 7.429 46.978 590 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 5.23 % Allowed : 19.09 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.10 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE A 316 TRP 0.013 0.002 TRP E 334 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 4350) covalent geometry : angle 0.72023 ( 5810) hydrogen bonds : bond 0.02131 ( 112) hydrogen bonds : angle 4.92101 ( 336) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 336 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8077 (tmm) REVERT: B 336 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8007 (tmm) REVERT: B 339 MET cc_start: 0.8849 (tmm) cc_final: 0.8034 (ttp) REVERT: C 336 MET cc_start: 0.8553 (tmm) cc_final: 0.6915 (tmm) REVERT: D 336 MET cc_start: 0.8539 (tmm) cc_final: 0.6886 (tmm) REVERT: E 323 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7788 (tpt) REVERT: E 339 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.7966 (ttp) REVERT: F 339 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8096 (ttp) REVERT: G 345 ASN cc_start: 0.8291 (m-40) cc_final: 0.7664 (m110) REVERT: H 345 ASN cc_start: 0.8290 (m-40) cc_final: 0.7685 (m110) REVERT: I 317 SER cc_start: 0.9118 (m) cc_final: 0.8755 (t) REVERT: I 323 MET cc_start: 0.7786 (tpp) cc_final: 0.7272 (tpp) REVERT: J 317 SER cc_start: 0.9127 (m) cc_final: 0.8767 (t) REVERT: J 323 MET cc_start: 0.7923 (tpp) cc_final: 0.7328 (tpp) REVERT: J 334 TRP cc_start: 0.8704 (m-90) cc_final: 0.7410 (m-90) REVERT: J 339 MET cc_start: 0.8815 (tpt) cc_final: 0.8132 (tpt) REVERT: J 359 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.6944 (ttm) REVERT: K 347 SER cc_start: 0.8345 (t) cc_final: 0.8018 (m) REVERT: Q 347 SER cc_start: 0.8620 (t) cc_final: 0.8409 (m) REVERT: R 347 SER cc_start: 0.8568 (t) cc_final: 0.8342 (m) outliers start: 23 outliers final: 16 residues processed: 145 average time/residue: 0.0448 time to fit residues: 9.0917 Evaluate side-chains 160 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 346 GLN Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain G residue 350 SER Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 346 GLN Chi-restraints excluded: chain H residue 347 SER Chi-restraints excluded: chain H residue 350 SER Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain M residue 339 MET Chi-restraints excluded: chain O residue 347 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 5.9990 chunk 26 optimal weight: 0.0970 chunk 17 optimal weight: 9.9990 chunk 55 optimal weight: 40.0000 chunk 49 optimal weight: 20.0000 chunk 30 optimal weight: 0.0870 chunk 22 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 overall best weight: 3.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** 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 = 0.5066 r_free = 0.5066 target = 0.219934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.172581 restraints weight = 5984.689| |-----------------------------------------------------------------------------| r_work (start): 0.4803 rms_B_bonded: 2.98 r_work: 0.4876 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4770 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.4770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4350 Z= 0.149 Angle : 0.731 13.957 5810 Z= 0.330 Chirality : 0.038 0.125 570 Planarity : 0.003 0.024 830 Dihedral : 7.033 47.224 590 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 3.86 % Allowed : 20.23 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.11 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE D 316 TRP 0.013 0.002 TRP E 334 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 4350) covalent geometry : angle 0.73141 ( 5810) hydrogen bonds : bond 0.02026 ( 112) hydrogen bonds : angle 4.84476 ( 336) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: C 336 MET cc_start: 0.8542 (tmm) cc_final: 0.6805 (tmm) REVERT: C 337 MET cc_start: 0.8311 (ttt) cc_final: 0.7862 (ttt) REVERT: D 336 MET cc_start: 0.8463 (tmm) cc_final: 0.6694 (tmm) REVERT: E 339 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.7663 (ttp) REVERT: F 339 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8065 (ttp) REVERT: G 345 ASN cc_start: 0.8323 (m-40) cc_final: 0.7788 (m110) REVERT: H 345 ASN cc_start: 0.8262 (m-40) cc_final: 0.7696 (m110) REVERT: I 317 SER cc_start: 0.9038 (m) cc_final: 0.8690 (t) REVERT: I 322 MET cc_start: 0.8004 (mmm) cc_final: 0.7548 (mmt) REVERT: I 323 MET cc_start: 0.7719 (tpp) cc_final: 0.7188 (tpp) REVERT: I 334 TRP cc_start: 0.8657 (m-90) cc_final: 0.7410 (m-90) REVERT: J 317 SER cc_start: 0.9006 (m) cc_final: 0.8658 (t) REVERT: J 323 MET cc_start: 0.7773 (tpp) cc_final: 0.7232 (tpp) REVERT: J 334 TRP cc_start: 0.8658 (m-90) cc_final: 0.7442 (m-90) REVERT: J 339 MET cc_start: 0.8758 (tpt) cc_final: 0.8116 (tpt) REVERT: K 347 SER cc_start: 0.8268 (t) cc_final: 0.7950 (m) REVERT: Q 347 SER cc_start: 0.8553 (t) cc_final: 0.8352 (m) REVERT: R 347 SER cc_start: 0.8438 (t) cc_final: 0.8178 (m) outliers start: 17 outliers final: 13 residues processed: 145 average time/residue: 0.0436 time to fit residues: 8.8271 Evaluate side-chains 155 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 360 GLN Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 346 GLN Chi-restraints excluded: chain G residue 350 SER Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 346 GLN Chi-restraints excluded: chain H residue 350 SER Chi-restraints excluded: chain O residue 347 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 12 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** 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 = 0.5077 r_free = 0.5077 target = 0.242209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.171673 restraints weight = 6353.937| |-----------------------------------------------------------------------------| r_work (start): 0.4759 rms_B_bonded: 3.25 r_work: 0.4837 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.4721 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4350 Z= 0.206 Angle : 0.829 17.524 5810 Z= 0.368 Chirality : 0.039 0.122 570 Planarity : 0.003 0.026 830 Dihedral : 7.089 43.251 590 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 4.09 % Allowed : 20.45 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.10 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE D 316 TRP 0.012 0.002 TRP E 334 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 4350) covalent geometry : angle 0.82872 ( 5810) hydrogen bonds : bond 0.02250 ( 112) hydrogen bonds : angle 4.88601 ( 336) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 336 MET cc_start: 0.9022 (tmm) cc_final: 0.8055 (tmm) REVERT: E 323 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7760 (tpt) REVERT: E 339 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.7594 (ttp) REVERT: F 339 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8096 (ttp) REVERT: G 345 ASN cc_start: 0.8312 (m-40) cc_final: 0.7652 (m110) REVERT: H 345 ASN cc_start: 0.8338 (m-40) cc_final: 0.7737 (m110) REVERT: I 317 SER cc_start: 0.9042 (m) cc_final: 0.8660 (t) REVERT: I 323 MET cc_start: 0.7785 (tpp) cc_final: 0.7203 (tpp) REVERT: I 334 TRP cc_start: 0.8724 (m-90) cc_final: 0.7537 (m-90) REVERT: J 317 SER cc_start: 0.9053 (m) cc_final: 0.8671 (t) REVERT: J 323 MET cc_start: 0.7775 (tpp) cc_final: 0.7181 (tpp) REVERT: J 334 TRP cc_start: 0.8704 (m-90) cc_final: 0.7471 (m-90) REVERT: J 336 MET cc_start: 0.7779 (tmm) cc_final: 0.6289 (tpt) REVERT: J 339 MET cc_start: 0.8764 (tpt) cc_final: 0.8121 (tpt) REVERT: K 347 SER cc_start: 0.8236 (t) cc_final: 0.7905 (m) REVERT: Q 347 SER cc_start: 0.8554 (t) cc_final: 0.8342 (m) REVERT: R 347 SER cc_start: 0.8598 (t) cc_final: 0.8372 (m) outliers start: 18 outliers final: 13 residues processed: 140 average time/residue: 0.0451 time to fit residues: 8.8570 Evaluate side-chains 153 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 346 GLN Chi-restraints excluded: chain G residue 350 SER Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 346 GLN Chi-restraints excluded: chain H residue 350 SER Chi-restraints excluded: chain O residue 347 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 59 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 30 optimal weight: 0.0000 chunk 58 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** 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 = 0.5159 r_free = 0.5159 target = 0.226814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.180064 restraints weight = 5916.597| |-----------------------------------------------------------------------------| r_work (start): 0.4873 rms_B_bonded: 3.04 r_work: 0.4958 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4842 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.4842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4350 Z= 0.131 Angle : 0.826 17.469 5810 Z= 0.361 Chirality : 0.038 0.126 570 Planarity : 0.003 0.025 830 Dihedral : 6.404 43.033 590 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.41 % Allowed : 21.82 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.07 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE D 316 TRP 0.010 0.002 TRP F 334 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 4350) covalent geometry : angle 0.82644 ( 5810) hydrogen bonds : bond 0.02425 ( 112) hydrogen bonds : angle 4.92551 ( 336) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.096 Fit side-chains REVERT: A 339 MET cc_start: 0.8711 (tmm) cc_final: 0.7943 (ttp) REVERT: B 339 MET cc_start: 0.8710 (tmm) cc_final: 0.7624 (ttp) REVERT: E 323 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7665 (tpt) REVERT: E 339 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.7638 (ttp) REVERT: F 339 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.7630 (ttp) REVERT: G 345 ASN cc_start: 0.8295 (m-40) cc_final: 0.7751 (m110) REVERT: H 334 TRP cc_start: 0.8536 (m-90) cc_final: 0.7417 (m100) REVERT: H 336 MET cc_start: 0.7359 (tpt) cc_final: 0.7096 (tpt) REVERT: H 345 ASN cc_start: 0.8300 (m-40) cc_final: 0.7817 (m110) REVERT: I 317 SER cc_start: 0.8890 (m) cc_final: 0.8579 (t) REVERT: I 322 MET cc_start: 0.7817 (mmm) cc_final: 0.7605 (mmt) REVERT: I 323 MET cc_start: 0.7496 (tpp) cc_final: 0.7006 (tpp) REVERT: I 334 TRP cc_start: 0.8589 (m-90) cc_final: 0.7675 (m-90) REVERT: I 336 MET cc_start: 0.7040 (tmm) cc_final: 0.6165 (tpp) REVERT: I 339 MET cc_start: 0.8563 (tpt) cc_final: 0.7922 (tpt) REVERT: J 317 SER cc_start: 0.8912 (m) cc_final: 0.8634 (t) REVERT: J 323 MET cc_start: 0.7456 (tpp) cc_final: 0.6890 (tpp) REVERT: J 334 TRP cc_start: 0.8617 (m-90) cc_final: 0.7496 (m-90) REVERT: J 336 MET cc_start: 0.7061 (tmm) cc_final: 0.6012 (tpp) REVERT: J 339 MET cc_start: 0.8546 (tpt) cc_final: 0.7927 (tpt) REVERT: K 347 SER cc_start: 0.8195 (t) cc_final: 0.7886 (m) REVERT: Q 347 SER cc_start: 0.8547 (t) cc_final: 0.8281 (m) REVERT: R 347 SER cc_start: 0.8518 (t) cc_final: 0.8235 (m) outliers start: 15 outliers final: 9 residues processed: 152 average time/residue: 0.0455 time to fit residues: 9.7067 Evaluate side-chains 150 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 350 SER Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 350 SER Chi-restraints excluded: chain O residue 347 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 38 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 59 optimal weight: 30.0000 chunk 25 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 GLN ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** 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 = 0.5077 r_free = 0.5077 target = 0.217934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.169962 restraints weight = 5984.849| |-----------------------------------------------------------------------------| r_work (start): 0.4768 rms_B_bonded: 3.01 r_work: 0.4853 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4741 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.4741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4350 Z= 0.233 Angle : 0.919 20.193 5810 Z= 0.404 Chirality : 0.039 0.122 570 Planarity : 0.003 0.026 830 Dihedral : 6.788 41.409 590 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 4.55 % Allowed : 22.50 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.05 (0.17), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.13), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE B 316 TRP 0.011 0.002 TRP E 334 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 4350) covalent geometry : angle 0.91903 ( 5810) hydrogen bonds : bond 0.02724 ( 112) hydrogen bonds : angle 5.00348 ( 336) =============================================================================== Job complete usr+sys time: 1219.53 seconds wall clock time: 21 minutes 34.59 seconds (1294.59 seconds total)