Starting phenix.real_space_refine on Tue Feb 11 05:03:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n3a_9349/02_2025/6n3a_9349.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n3a_9349/02_2025/6n3a_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_9349/02_2025/6n3a_9349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n3a_9349/02_2025/6n3a_9349.map" model { file = "/net/cci-nas-00/data/ceres_data/6n3a_9349/02_2025/6n3a_9349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n3a_9349/02_2025/6n3a_9349.cif" } resolution = 3.3 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 ------------------------------------------------------------------------------- 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: M, L, O, N, Q, P, S, R, T, C, B, E, D, G, F, I, H, J Time building chain proxies: 1.30, per 1000 atoms: 0.30 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: 0.93 Conformation dependent library (CDL) restraints added in 498.4 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: 0.64 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: 1.10 Time building geometry restraints manager: 1.09 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: 0.04 Found NCS groups: ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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: 0.080 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.710 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.560 ------------------------------------------------------------------------------- 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= 0.514 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 (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: -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 TRP 0.008 0.003 TRP E 334 PHE 0.018 0.008 PHE J 316 *********************** 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 : 0.455 Fit side-chains REVERT: C 323 MET cc_start: 0.7662 (tpp) cc_final: 0.7331 (tpp) REVERT: C 350 SER cc_start: 0.9403 (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: 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: 0.7245 (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: 0.8191 (ttt) REVERT: I 354 GLN cc_start: 0.8354 (mt0) cc_final: 0.8112 (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: 0.8119 (mt0) REVERT: K 347 SER cc_start: 0.8051 (t) cc_final: 0.7778 (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: 0.8063 (m) REVERT: R 347 SER cc_start: 0.8237 (t) cc_final: 0.7993 (m) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1117 time to fit residues: 32.0687 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 : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 54 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** ** A 353 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 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN F 356 GLN ** G 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4972 r_free = 0.4972 target = 0.191139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.159629 restraints weight = 5148.610| |-----------------------------------------------------------------------------| r_work (start): 0.4781 rms_B_bonded: 2.63 r_work: 0.4711 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4609 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.4609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 4350 Z= 0.320 Angle : 0.730 7.823 5810 Z= 0.364 Chirality : 0.042 0.137 570 Planarity : 0.004 0.036 830 Dihedral : 8.154 45.418 590 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 3.18 % Allowed : 19.32 % Favored : 77.50 % 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: -5.22 (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 TRP 0.016 0.003 TRP J 334 PHE 0.011 0.003 PHE A 316 *********************** 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 192 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.473 Fit side-chains REVERT: A 317 SER cc_start: 0.8726 (m) cc_final: 0.8518 (t) REVERT: A 336 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8157 (tmm) REVERT: B 317 SER cc_start: 0.8737 (m) cc_final: 0.8535 (t) REVERT: B 336 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8238 (tmm) REVERT: C 323 MET cc_start: 0.8159 (tpp) cc_final: 0.7508 (tpp) REVERT: C 337 MET cc_start: 0.8803 (ttt) cc_final: 0.8578 (ttt) REVERT: D 317 SER cc_start: 0.9066 (m) cc_final: 0.8864 (t) REVERT: D 323 MET cc_start: 0.8228 (tpp) cc_final: 0.7589 (tpp) REVERT: D 337 MET cc_start: 0.8782 (ttt) cc_final: 0.8532 (ttt) REVERT: E 336 MET cc_start: 0.8985 (tmm) cc_final: 0.8652 (tmm) REVERT: F 323 MET cc_start: 0.8128 (tpp) cc_final: 0.7709 (tpp) REVERT: G 345 ASN cc_start: 0.8210 (m-40) cc_final: 0.7790 (m-40) REVERT: H 345 ASN cc_start: 0.8174 (m-40) cc_final: 0.7766 (m-40) REVERT: I 317 SER cc_start: 0.9004 (m) cc_final: 0.8632 (t) REVERT: J 317 SER cc_start: 0.9008 (m) cc_final: 0.8620 (t) REVERT: J 323 MET cc_start: 0.7871 (tpp) cc_final: 0.7613 (tpp) REVERT: K 347 SER cc_start: 0.8235 (t) cc_final: 0.7987 (m) REVERT: L 347 SER cc_start: 0.8462 (t) cc_final: 0.8211 (m) REVERT: R 347 SER cc_start: 0.8593 (t) cc_final: 0.8351 (m) outliers start: 14 outliers final: 6 residues processed: 178 average time/residue: 0.1152 time to fit residues: 27.8458 Evaluate side-chains 165 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 350 SER 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 H residue 311 MET Chi-restraints excluded: chain H residue 339 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 34 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 36 optimal weight: 30.0000 chunk 33 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 overall best weight: 3.6586 ------------------------------------------------------------------------------- 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** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5015 r_free = 0.5015 target = 0.228612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.173831 restraints weight = 5925.113| |-----------------------------------------------------------------------------| r_work (start): 0.4746 rms_B_bonded: 2.98 r_work: 0.4848 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4741 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.4741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 4350 Z= 0.214 Angle : 0.667 7.519 5810 Z= 0.326 Chirality : 0.040 0.132 570 Planarity : 0.003 0.027 830 Dihedral : 7.497 50.333 590 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.05 % Allowed : 22.05 % 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 (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: -5.13 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 334 PHE 0.007 0.002 PHE J 316 *********************** 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 177 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 168 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 ASN cc_start: 0.8395 (m-40) cc_final: 0.8150 (m-40) REVERT: B 317 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8524 (t) REVERT: B 336 MET cc_start: 0.8656 (tmm) cc_final: 0.7802 (tmm) REVERT: C 336 MET cc_start: 0.8350 (tmm) cc_final: 0.5993 (tmm) REVERT: D 323 MET cc_start: 0.7899 (tpp) cc_final: 0.7282 (tpp) REVERT: D 336 MET cc_start: 0.8298 (tmm) cc_final: 0.6022 (tmm) REVERT: E 311 MET cc_start: 0.8442 (ptp) cc_final: 0.8001 (mtm) REVERT: F 311 MET cc_start: 0.8427 (ptp) cc_final: 0.8020 (mtm) REVERT: G 345 ASN cc_start: 0.8160 (m-40) cc_final: 0.7652 (m110) REVERT: H 345 ASN cc_start: 0.8246 (m-40) cc_final: 0.7728 (m110) REVERT: I 317 SER cc_start: 0.8993 (m) cc_final: 0.8668 (t) REVERT: I 334 TRP cc_start: 0.8703 (m-90) cc_final: 0.7359 (m-90) REVERT: J 317 SER cc_start: 0.9010 (m) cc_final: 0.8669 (t) REVERT: J 323 MET cc_start: 0.7898 (tpp) cc_final: 0.7556 (tpp) REVERT: J 360 GLN cc_start: 0.8172 (tp-100) cc_final: 0.5691 (pt0) REVERT: K 347 SER cc_start: 0.8233 (t) cc_final: 0.7924 (m) REVERT: L 347 SER cc_start: 0.8226 (t) cc_final: 0.7959 (m) outliers start: 9 outliers final: 7 residues processed: 168 average time/residue: 0.1170 time to fit residues: 26.4185 Evaluate side-chains 158 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 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 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 36 optimal weight: 40.0000 chunk 45 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 58 optimal weight: 0.0570 chunk 3 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 overall best weight: 7.6108 ------------------------------------------------------------------------------- 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** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN E 319 ASN ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 ASN ** 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** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 344 GLN ** S 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 344 GLN ** T 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.218680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.168221 restraints weight = 6042.823| |-----------------------------------------------------------------------------| r_work (start): 0.4703 rms_B_bonded: 2.93 r_work: 0.4800 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4697 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.4697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 4350 Z= 0.353 Angle : 0.727 8.278 5810 Z= 0.350 Chirality : 0.039 0.125 570 Planarity : 0.003 0.026 830 Dihedral : 7.697 52.321 590 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 3.18 % Allowed : 21.82 % Favored : 75.00 % 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: -5.12 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 334 PHE 0.009 0.002 PHE A 316 *********************** 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 163 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 317 SER cc_start: 0.8979 (OUTLIER) cc_final: 0.8741 (t) REVERT: B 336 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7911 (tmm) REVERT: C 336 MET cc_start: 0.8467 (tmm) cc_final: 0.6424 (tmm) REVERT: F 336 MET cc_start: 0.8820 (tmm) cc_final: 0.7768 (tmm) REVERT: G 345 ASN cc_start: 0.8261 (m-40) cc_final: 0.7682 (m110) REVERT: H 345 ASN cc_start: 0.8281 (m-40) cc_final: 0.7738 (m110) REVERT: I 317 SER cc_start: 0.9067 (m) cc_final: 0.8660 (t) REVERT: I 359 MET cc_start: 0.8581 (ttp) cc_final: 0.8189 (ttp) REVERT: J 317 SER cc_start: 0.9090 (m) cc_final: 0.8682 (t) REVERT: J 323 MET cc_start: 0.7853 (tpp) cc_final: 0.7497 (tpp) REVERT: K 347 SER cc_start: 0.8302 (t) cc_final: 0.7949 (m) REVERT: L 347 SER cc_start: 0.8352 (t) cc_final: 0.8019 (m) outliers start: 14 outliers final: 10 residues processed: 149 average time/residue: 0.1138 time to fit residues: 22.8818 Evaluate side-chains 158 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 350 SER Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 350 SER Chi-restraints excluded: chain M residue 339 MET Chi-restraints excluded: chain N residue 339 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 30.0000 chunk 34 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 33 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 41 optimal weight: 40.0000 chunk 31 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- 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 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** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5014 r_free = 0.5014 target = 0.215348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.167615 restraints weight = 6031.200| |-----------------------------------------------------------------------------| r_work (start): 0.4704 rms_B_bonded: 2.96 r_work: 0.4794 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4684 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.4684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3858 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= 0.394 Angle : 0.747 10.984 5810 Z= 0.358 Chirality : 0.039 0.125 570 Planarity : 0.003 0.028 830 Dihedral : 7.735 50.447 590 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 4.55 % Allowed : 19.32 % Favored : 76.14 % 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: -5.13 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP F 334 PHE 0.010 0.002 PHE A 316 *********************** 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 159 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.9165 (tmm) cc_final: 0.7443 (tmm) REVERT: B 336 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7991 (tmm) REVERT: C 336 MET cc_start: 0.8644 (tmm) cc_final: 0.7102 (tmm) REVERT: G 345 ASN cc_start: 0.8293 (m-40) cc_final: 0.7675 (m110) REVERT: H 345 ASN cc_start: 0.8282 (m-40) cc_final: 0.7646 (m110) REVERT: I 317 SER cc_start: 0.9155 (m) cc_final: 0.8777 (t) REVERT: I 359 MET cc_start: 0.8552 (ttp) cc_final: 0.7762 (ttp) REVERT: J 317 SER cc_start: 0.9129 (m) cc_final: 0.8707 (t) REVERT: J 323 MET cc_start: 0.8137 (tpp) cc_final: 0.7697 (tpp) REVERT: J 359 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.6982 (ttm) REVERT: K 347 SER cc_start: 0.8334 (t) cc_final: 0.7998 (m) REVERT: L 347 SER cc_start: 0.8433 (t) cc_final: 0.8099 (m) outliers start: 20 outliers final: 18 residues processed: 141 average time/residue: 0.1102 time to fit residues: 21.1221 Evaluate side-chains 157 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 53 optimal weight: 40.0000 chunk 35 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 51 optimal weight: 50.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5054 r_free = 0.5054 target = 0.222312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.171645 restraints weight = 5973.628| |-----------------------------------------------------------------------------| r_work (start): 0.4765 rms_B_bonded: 2.91 r_work: 0.4843 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4739 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.4739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4350 Z= 0.283 Angle : 0.720 11.560 5810 Z= 0.335 Chirality : 0.039 0.126 570 Planarity : 0.003 0.025 830 Dihedral : 7.326 50.445 590 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 3.64 % Allowed : 21.14 % Favored : 75.23 % 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: -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 TRP 0.013 0.002 TRP E 334 PHE 0.008 0.002 PHE A 316 *********************** 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 161 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.9247 (tmm) cc_final: 0.8751 (tmm) REVERT: B 336 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8078 (tmm) REVERT: C 336 MET cc_start: 0.8600 (tmm) cc_final: 0.6959 (tmm) REVERT: C 337 MET cc_start: 0.8474 (ttt) cc_final: 0.8144 (ttt) REVERT: F 311 MET cc_start: 0.8497 (ptp) cc_final: 0.8270 (mtm) REVERT: F 336 MET cc_start: 0.8843 (tmm) cc_final: 0.8132 (tmm) REVERT: G 345 ASN cc_start: 0.8191 (m-40) cc_final: 0.7788 (m-40) REVERT: H 345 ASN cc_start: 0.8189 (m-40) cc_final: 0.7814 (m-40) REVERT: I 317 SER cc_start: 0.9104 (m) cc_final: 0.8741 (t) REVERT: I 334 TRP cc_start: 0.8674 (m-90) cc_final: 0.7647 (m-90) REVERT: J 317 SER cc_start: 0.9070 (m) cc_final: 0.8660 (t) REVERT: J 323 MET cc_start: 0.7891 (tpp) cc_final: 0.7448 (tpp) REVERT: J 334 TRP cc_start: 0.8600 (m-90) cc_final: 0.7415 (m-90) REVERT: J 359 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7207 (ttm) REVERT: K 347 SER cc_start: 0.8324 (t) cc_final: 0.7986 (m) REVERT: L 347 SER cc_start: 0.8318 (t) cc_final: 0.8018 (m) outliers start: 16 outliers final: 13 residues processed: 145 average time/residue: 0.1157 time to fit residues: 22.5611 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 : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain E residue 350 SER 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 J residue 359 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 51 optimal weight: 50.0000 chunk 52 optimal weight: 5.9990 chunk 6 optimal weight: 50.0000 chunk 25 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 19 optimal weight: 20.0000 chunk 59 optimal weight: 40.0000 chunk 35 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5047 r_free = 0.5047 target = 0.223686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.170936 restraints weight = 6009.525| |-----------------------------------------------------------------------------| r_work (start): 0.4759 rms_B_bonded: 2.92 r_work: 0.4842 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4734 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.4734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4350 Z= 0.287 Angle : 0.742 13.413 5810 Z= 0.339 Chirality : 0.038 0.124 570 Planarity : 0.003 0.025 830 Dihedral : 7.185 50.223 590 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 4.32 % Allowed : 21.14 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.09 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 334 PHE 0.008 0.002 PHE C 316 *********************** 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 160 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.9247 (tmm) cc_final: 0.7559 (tmm) REVERT: B 317 SER cc_start: 0.8980 (m) cc_final: 0.8678 (t) REVERT: B 336 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8012 (tmm) REVERT: B 339 MET cc_start: 0.8951 (ttp) cc_final: 0.7942 (ttp) REVERT: C 336 MET cc_start: 0.8554 (tmm) cc_final: 0.6732 (tmm) REVERT: E 336 MET cc_start: 0.9027 (tmm) cc_final: 0.8684 (tmm) REVERT: F 311 MET cc_start: 0.8489 (ptp) cc_final: 0.8265 (mtm) REVERT: G 345 ASN cc_start: 0.8245 (m-40) cc_final: 0.7852 (m-40) REVERT: H 345 ASN cc_start: 0.8238 (m-40) cc_final: 0.7834 (m-40) REVERT: I 317 SER cc_start: 0.9023 (m) cc_final: 0.8628 (t) REVERT: I 334 TRP cc_start: 0.8634 (m-90) cc_final: 0.7565 (m-90) REVERT: I 336 MET cc_start: 0.7565 (tmm) cc_final: 0.6406 (tpt) REVERT: I 359 MET cc_start: 0.8561 (ttp) cc_final: 0.8036 (ttp) REVERT: J 317 SER cc_start: 0.8991 (m) cc_final: 0.8565 (t) REVERT: J 323 MET cc_start: 0.7835 (tpp) cc_final: 0.7361 (tpp) REVERT: J 334 TRP cc_start: 0.8675 (m-90) cc_final: 0.7398 (m-90) REVERT: J 359 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7075 (ttm) REVERT: K 347 SER cc_start: 0.8276 (t) cc_final: 0.7945 (m) REVERT: L 347 SER cc_start: 0.8378 (t) cc_final: 0.8074 (m) outliers start: 19 outliers final: 16 residues processed: 143 average time/residue: 0.1189 time to fit residues: 23.0712 Evaluate side-chains 159 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 350 SER 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 N 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 18 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 53 optimal weight: 30.0000 chunk 42 optimal weight: 20.0000 chunk 31 optimal weight: 0.2980 chunk 16 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- 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 360 GLN ** 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** ** M 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5085 r_free = 0.5085 target = 0.227340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4959 r_free = 0.4959 target = 0.173530 restraints weight = 5901.355| |-----------------------------------------------------------------------------| r_work (start): 0.4783 rms_B_bonded: 2.90 r_work: 0.4888 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4781 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.4781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4350 Z= 0.265 Angle : 0.737 14.350 5810 Z= 0.335 Chirality : 0.038 0.123 570 Planarity : 0.003 0.025 830 Dihedral : 7.005 49.857 590 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 4.32 % Allowed : 20.68 % Favored : 75.00 % 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: -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 TRP 0.012 0.002 TRP E 334 PHE 0.007 0.002 PHE C 316 *********************** 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 163 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 336 MET cc_start: 0.9234 (tmm) cc_final: 0.8983 (tmm) REVERT: B 317 SER cc_start: 0.8956 (m) cc_final: 0.8674 (t) REVERT: B 336 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8074 (tmm) REVERT: C 336 MET cc_start: 0.8560 (tmm) cc_final: 0.6791 (tmm) REVERT: D 336 MET cc_start: 0.8383 (tmm) cc_final: 0.5923 (tmm) REVERT: E 323 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7822 (tpt) REVERT: F 311 MET cc_start: 0.8465 (ptp) cc_final: 0.8246 (mtm) REVERT: G 345 ASN cc_start: 0.8268 (m-40) cc_final: 0.7689 (m110) REVERT: H 345 ASN cc_start: 0.8266 (m-40) cc_final: 0.7660 (m110) REVERT: I 317 SER cc_start: 0.9017 (m) cc_final: 0.8700 (t) REVERT: I 336 MET cc_start: 0.7303 (tmm) cc_final: 0.6391 (tpt) REVERT: J 317 SER cc_start: 0.9004 (m) cc_final: 0.8615 (t) REVERT: J 323 MET cc_start: 0.7772 (tpp) cc_final: 0.7186 (tpp) REVERT: J 334 TRP cc_start: 0.8655 (m-90) cc_final: 0.7335 (m-90) REVERT: K 347 SER cc_start: 0.8343 (t) cc_final: 0.8005 (m) REVERT: L 347 SER cc_start: 0.8398 (t) cc_final: 0.8121 (m) outliers start: 19 outliers final: 16 residues processed: 146 average time/residue: 0.1163 time to fit residues: 22.8495 Evaluate side-chains 160 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 350 SER Chi-restraints excluded: chain F residue 323 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 O residue 347 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 5.9990 chunk 6 optimal weight: 50.0000 chunk 26 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 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** ** G 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** ** M 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5048 r_free = 0.5048 target = 0.221669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.169689 restraints weight = 6035.394| |-----------------------------------------------------------------------------| r_work (start): 0.4759 rms_B_bonded: 2.93 r_work: 0.4844 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4740 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.4740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4350 Z= 0.328 Angle : 0.789 16.261 5810 Z= 0.356 Chirality : 0.039 0.124 570 Planarity : 0.003 0.026 830 Dihedral : 7.063 44.034 590 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 4.32 % Allowed : 21.59 % Favored : 74.09 % 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: -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 TRP 0.013 0.002 TRP F 334 PHE 0.008 0.002 PHE C 316 *********************** 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: 19 poor density : 139 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 336 MET cc_start: 0.9211 (tmm) cc_final: 0.8931 (tmm) REVERT: A 339 MET cc_start: 0.8832 (ttp) cc_final: 0.7862 (ttp) REVERT: B 317 SER cc_start: 0.9021 (m) cc_final: 0.8706 (t) REVERT: C 336 MET cc_start: 0.8561 (tmm) cc_final: 0.6762 (tmm) REVERT: D 336 MET cc_start: 0.8486 (tmm) cc_final: 0.6081 (tmm) REVERT: E 336 MET cc_start: 0.9036 (tmm) cc_final: 0.8734 (tmm) REVERT: F 311 MET cc_start: 0.8575 (ptp) cc_final: 0.8201 (mtm) REVERT: G 345 ASN cc_start: 0.8256 (m-40) cc_final: 0.7838 (m-40) REVERT: H 345 ASN cc_start: 0.8272 (m-40) cc_final: 0.7872 (m-40) REVERT: I 317 SER cc_start: 0.9065 (m) cc_final: 0.8695 (t) REVERT: I 336 MET cc_start: 0.7379 (tmm) cc_final: 0.6402 (tpt) REVERT: J 317 SER cc_start: 0.9006 (m) cc_final: 0.8580 (t) REVERT: J 323 MET cc_start: 0.7878 (tpp) cc_final: 0.7377 (tpp) REVERT: J 334 TRP cc_start: 0.8677 (m-90) cc_final: 0.7399 (m-90) REVERT: J 336 MET cc_start: 0.7664 (tmm) cc_final: 0.6437 (tpt) REVERT: J 359 MET cc_start: 0.8287 (ttp) cc_final: 0.7889 (ttp) REVERT: K 347 SER cc_start: 0.8296 (t) cc_final: 0.7914 (m) REVERT: L 347 SER cc_start: 0.8336 (t) cc_final: 0.8025 (m) outliers start: 19 outliers final: 18 residues processed: 141 average time/residue: 0.1107 time to fit residues: 21.1865 Evaluate side-chains 157 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 350 SER Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 337 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 O residue 347 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 40 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 59 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- 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 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 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** ** G 353 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** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5089 r_free = 0.5089 target = 0.223722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.171950 restraints weight = 5911.307| |-----------------------------------------------------------------------------| r_work (start): 0.4780 rms_B_bonded: 2.94 r_work: 0.4871 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4767 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.4767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4350 Z= 0.290 Angle : 0.811 16.456 5810 Z= 0.362 Chirality : 0.039 0.123 570 Planarity : 0.003 0.026 830 Dihedral : 6.870 42.820 590 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 4.09 % Allowed : 22.05 % Favored : 73.86 % 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: -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 TRP 0.012 0.002 TRP E 334 PHE 0.008 0.002 PHE C 316 ********************** 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 158 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.473 Fit side-chains REVERT: A 339 MET cc_start: 0.8778 (ttp) cc_final: 0.7798 (ttp) REVERT: B 317 SER cc_start: 0.8976 (m) cc_final: 0.8680 (t) REVERT: E 323 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7921 (tpt) REVERT: F 311 MET cc_start: 0.8545 (ptp) cc_final: 0.8189 (mtm) REVERT: G 345 ASN cc_start: 0.8238 (m-40) cc_final: 0.7623 (m110) REVERT: H 345 ASN cc_start: 0.8243 (m-40) cc_final: 0.7622 (m110) REVERT: I 317 SER cc_start: 0.8995 (m) cc_final: 0.8622 (t) REVERT: I 336 MET cc_start: 0.7309 (tmm) cc_final: 0.6304 (tpt) REVERT: J 317 SER cc_start: 0.8988 (m) cc_final: 0.8580 (t) REVERT: J 323 MET cc_start: 0.7848 (tpp) cc_final: 0.7285 (tpp) REVERT: J 334 TRP cc_start: 0.8657 (m-90) cc_final: 0.7417 (m-90) REVERT: J 336 MET cc_start: 0.7386 (tmm) cc_final: 0.6503 (tpp) REVERT: K 347 SER cc_start: 0.8298 (t) cc_final: 0.7944 (m) REVERT: L 347 SER cc_start: 0.8340 (t) cc_final: 0.8028 (m) outliers start: 18 outliers final: 17 residues processed: 142 average time/residue: 0.1163 time to fit residues: 22.3473 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 : 0.492 ------------------------------------------------------------------------------- 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 350 SER Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 337 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 O residue 347 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 15 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 31 optimal weight: 0.0970 chunk 59 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 55 optimal weight: 40.0000 chunk 50 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 overall best weight: 6.8186 ------------------------------------------------------------------------------- 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 353 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** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 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** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5059 r_free = 0.5059 target = 0.223011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.170100 restraints weight = 6007.565| |-----------------------------------------------------------------------------| r_work (start): 0.4765 rms_B_bonded: 2.92 r_work: 0.4844 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4741 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.4741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4350 Z= 0.333 Angle : 0.845 18.479 5810 Z= 0.374 Chirality : 0.039 0.123 570 Planarity : 0.003 0.026 830 Dihedral : 6.909 39.175 590 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.07 % Favored : 88.93 % Rotamer: Outliers : 4.09 % Allowed : 22.50 % Favored : 73.41 % 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: -5.12 (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 TRP 0.014 0.002 TRP F 334 PHE 0.008 0.002 PHE C 316 =============================================================================== Job complete usr+sys time: 2490.75 seconds wall clock time: 44 minutes 42.12 seconds (2682.12 seconds total)