Starting phenix.real_space_refine on Sun Apr 27 02:30:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n3a_9349/04_2025/6n3a_9349.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n3a_9349/04_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_9349/04_2025/6n3a_9349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n3a_9349/04_2025/6n3a_9349.map" model { file = "/net/cci-nas-00/data/ceres_data/6n3a_9349/04_2025/6n3a_9349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n3a_9349/04_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-5669/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: 3.16, per 1000 atoms: 0.73 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: 2.41 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.75 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: 1.87 Time building geometry restraints manager: 2.82 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: 0.07 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: 30.450 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.150 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:3.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 4350 Z= 0.333 Angle : 1.143 9.699 5810 Z= 0.553 Chirality : 0.047 0.114 570 Planarity : 0.007 0.055 830 Dihedral : 14.532 76.417 1600 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.18176 ( 112) hydrogen bonds : angle 8.49767 ( 336) covalent geometry : bond 0.00785 ( 4350) covalent geometry : angle 1.14299 ( 5810) *********************** 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 : 1.263 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: 0.2430 time to fit residues: 69.9231 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 : 0.628 ------------------------------------------------------------------------------- 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 = 0.159630 restraints weight = 5148.608| |-----------------------------------------------------------------------------| r_work (start): 0.4781 rms_B_bonded: 2.63 r_work: 0.4711 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4610 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.4610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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= 0.217 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 Details of bonding type rmsd hydrogen bonds : bond 0.03065 ( 112) hydrogen bonds : angle 5.96582 ( 336) covalent geometry : bond 0.00485 ( 4350) covalent geometry : angle 0.72954 ( 5810) *********************** 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 : 0.561 Fit side-chains REVERT: A 317 SER cc_start: 0.8726 (m) cc_final: 0.8521 (t) REVERT: A 336 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8158 (tmm) REVERT: B 317 SER cc_start: 0.8738 (m) cc_final: 0.8537 (t) REVERT: B 336 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8240 (tmm) REVERT: C 323 MET cc_start: 0.8148 (tpp) cc_final: 0.7502 (tpp) REVERT: C 337 MET cc_start: 0.8802 (ttt) cc_final: 0.8578 (ttt) REVERT: D 317 SER cc_start: 0.9067 (m) cc_final: 0.8866 (t) REVERT: D 323 MET cc_start: 0.8223 (tpp) cc_final: 0.7586 (tpp) REVERT: D 337 MET cc_start: 0.8782 (ttt) cc_final: 0.8536 (ttt) REVERT: E 336 MET cc_start: 0.8984 (tmm) cc_final: 0.8652 (tmm) REVERT: F 323 MET cc_start: 0.8132 (tpp) cc_final: 0.7714 (tpp) REVERT: G 345 ASN cc_start: 0.8209 (m-40) cc_final: 0.7788 (m-40) REVERT: H 345 ASN cc_start: 0.8173 (m-40) cc_final: 0.7766 (m-40) REVERT: I 317 SER cc_start: 0.9004 (m) cc_final: 0.8633 (t) REVERT: J 317 SER cc_start: 0.9006 (m) cc_final: 0.8619 (t) REVERT: J 323 MET cc_start: 0.7868 (tpp) cc_final: 0.7614 (tpp) REVERT: K 347 SER cc_start: 0.8229 (t) cc_final: 0.7981 (m) REVERT: L 347 SER cc_start: 0.8453 (t) cc_final: 0.8202 (m) REVERT: R 347 SER cc_start: 0.8586 (t) cc_final: 0.8345 (m) outliers start: 14 outliers final: 6 residues processed: 178 average time/residue: 0.1046 time to fit residues: 25.4539 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 : 0.471 ------------------------------------------------------------------------------- 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: 3.9990 chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 30.0000 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 0.2980 chunk 45 optimal weight: 8.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 ** 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 = 0.229180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.173614 restraints weight = 5914.627| |-----------------------------------------------------------------------------| r_work (start): 0.4749 rms_B_bonded: 2.96 r_work: 0.4847 rms_B_bonded: 2.58 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: 0.7823 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4350 Z= 0.148 Angle : 0.663 7.489 5810 Z= 0.324 Chirality : 0.040 0.132 570 Planarity : 0.003 0.027 830 Dihedral : 7.500 50.837 590 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.50 % Allowed : 20.91 % Favored : 76.59 % 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 A 334 PHE 0.007 0.002 PHE J 316 Details of bonding type rmsd hydrogen bonds : bond 0.02560 ( 112) hydrogen bonds : angle 5.40305 ( 336) covalent geometry : bond 0.00331 ( 4350) covalent geometry : angle 0.66260 ( 5810) *********************** 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 179 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 SER cc_start: 0.8758 (OUTLIER) cc_final: 0.8556 (t) REVERT: A 345 ASN cc_start: 0.8409 (m-40) cc_final: 0.8145 (m-40) REVERT: B 317 SER cc_start: 0.8750 (OUTLIER) cc_final: 0.8516 (t) REVERT: B 336 MET cc_start: 0.8636 (tmm) cc_final: 0.7820 (tmm) REVERT: C 336 MET cc_start: 0.8377 (tmm) cc_final: 0.5989 (tmm) REVERT: D 336 MET cc_start: 0.8314 (tmm) cc_final: 0.6032 (tmm) REVERT: F 311 MET cc_start: 0.8410 (ptp) cc_final: 0.8010 (mtm) REVERT: G 345 ASN cc_start: 0.8160 (m-40) cc_final: 0.7633 (m110) REVERT: H 345 ASN cc_start: 0.8246 (m-40) cc_final: 0.7745 (m110) REVERT: I 317 SER cc_start: 0.8993 (m) cc_final: 0.8659 (t) REVERT: J 317 SER cc_start: 0.9010 (m) cc_final: 0.8662 (t) REVERT: J 323 MET cc_start: 0.7894 (tpp) cc_final: 0.7548 (tpp) REVERT: J 360 GLN cc_start: 0.8202 (tp-100) cc_final: 0.5695 (pt0) REVERT: K 347 SER cc_start: 0.8229 (t) cc_final: 0.7914 (m) REVERT: L 347 SER cc_start: 0.8192 (t) cc_final: 0.7927 (m) REVERT: R 347 SER cc_start: 0.8243 (t) cc_final: 0.8026 (m) outliers start: 11 outliers final: 7 residues processed: 168 average time/residue: 0.1072 time to fit residues: 24.3566 Evaluate side-chains 163 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER 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: 0.7980 chunk 3 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 overall best weight: 8.9592 ------------------------------------------------------------------------------- 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 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 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4981 r_free = 0.4981 target = 0.215116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.167108 restraints weight = 6066.958| |-----------------------------------------------------------------------------| r_work (start): 0.4684 rms_B_bonded: 2.94 r_work: 0.4780 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4681 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.4681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 4350 Z= 0.273 Angle : 0.753 8.272 5810 Z= 0.363 Chirality : 0.039 0.123 570 Planarity : 0.003 0.029 830 Dihedral : 7.795 52.434 590 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 3.64 % Allowed : 20.45 % 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: -5.11 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP F 334 PHE 0.008 0.002 PHE A 316 Details of bonding type rmsd hydrogen bonds : bond 0.02561 ( 112) hydrogen bonds : angle 5.26976 ( 336) covalent geometry : bond 0.00620 ( 4350) covalent geometry : angle 0.75277 ( 5810) *********************** 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 160 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 SER cc_start: 0.9020 (OUTLIER) cc_final: 0.8772 (t) REVERT: A 336 MET cc_start: 0.9140 (tmm) cc_final: 0.8330 (tmm) REVERT: B 317 SER cc_start: 0.9039 (m) cc_final: 0.8802 (t) REVERT: B 336 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.7962 (tmm) REVERT: C 336 MET cc_start: 0.8456 (tmm) cc_final: 0.6423 (tmm) REVERT: D 336 MET cc_start: 0.8193 (tmm) cc_final: 0.5872 (tmm) REVERT: F 336 MET cc_start: 0.8849 (tmm) cc_final: 0.8003 (tmm) REVERT: G 345 ASN cc_start: 0.8293 (m-40) cc_final: 0.7917 (m-40) REVERT: H 345 ASN cc_start: 0.8307 (m-40) cc_final: 0.7757 (m110) REVERT: I 317 SER cc_start: 0.9106 (m) cc_final: 0.8690 (t) REVERT: I 359 MET cc_start: 0.8712 (ttp) cc_final: 0.8389 (ttp) REVERT: J 317 SER cc_start: 0.9156 (m) cc_final: 0.8772 (t) REVERT: J 323 MET cc_start: 0.7993 (tpp) cc_final: 0.7636 (tpp) REVERT: K 347 SER cc_start: 0.8321 (t) cc_final: 0.7970 (m) REVERT: L 347 SER cc_start: 0.8425 (t) cc_final: 0.8090 (m) REVERT: R 347 SER cc_start: 0.8360 (t) cc_final: 0.8104 (m) outliers start: 16 outliers final: 11 residues processed: 145 average time/residue: 0.1080 time to fit residues: 21.3322 Evaluate side-chains 154 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 352 ASN 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 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: 40.0000 chunk 34 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 41 optimal weight: 40.0000 chunk 31 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 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** ** 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** I 354 GLN ** 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 = 0.5038 r_free = 0.5038 target = 0.222991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.172123 restraints weight = 6076.502| |-----------------------------------------------------------------------------| r_work (start): 0.4739 rms_B_bonded: 2.92 r_work: 0.4814 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4706 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.4706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4350 Z= 0.215 Angle : 0.707 10.085 5810 Z= 0.338 Chirality : 0.039 0.126 570 Planarity : 0.003 0.027 830 Dihedral : 7.571 51.421 590 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 3.86 % Allowed : 20.68 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.11 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 334 PHE 0.009 0.002 PHE C 316 Details of bonding type rmsd hydrogen bonds : bond 0.02351 ( 112) hydrogen bonds : angle 5.09608 ( 336) covalent geometry : bond 0.00490 ( 4350) covalent geometry : angle 0.70708 ( 5810) *********************** 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 164 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 SER cc_start: 0.9038 (m) cc_final: 0.8795 (t) REVERT: A 336 MET cc_start: 0.9144 (tmm) cc_final: 0.8440 (tmm) REVERT: B 336 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8012 (tmm) REVERT: C 336 MET cc_start: 0.8592 (tmm) cc_final: 0.7029 (tmm) REVERT: E 322 MET cc_start: 0.8963 (mtp) cc_final: 0.8744 (mtt) REVERT: F 322 MET cc_start: 0.8907 (mtp) cc_final: 0.8603 (mtp) REVERT: F 336 MET cc_start: 0.8721 (tmm) cc_final: 0.7706 (tmm) REVERT: G 345 ASN cc_start: 0.8298 (m-40) cc_final: 0.7675 (m110) REVERT: H 345 ASN cc_start: 0.8285 (m-40) cc_final: 0.7637 (m110) REVERT: I 317 SER cc_start: 0.9108 (m) cc_final: 0.8701 (t) REVERT: I 359 MET cc_start: 0.8539 (ttp) cc_final: 0.7786 (ttp) REVERT: J 317 SER cc_start: 0.9061 (m) cc_final: 0.8613 (t) REVERT: J 323 MET cc_start: 0.8047 (tpp) cc_final: 0.7634 (tpp) REVERT: J 359 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7173 (ttm) REVERT: K 347 SER cc_start: 0.8220 (t) cc_final: 0.7867 (m) REVERT: L 347 SER cc_start: 0.8349 (t) cc_final: 0.8059 (m) REVERT: R 347 SER cc_start: 0.8328 (t) cc_final: 0.8074 (m) outliers start: 17 outliers final: 15 residues processed: 148 average time/residue: 0.1065 time to fit residues: 21.4132 Evaluate side-chains 160 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 SER 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 53 optimal weight: 40.0000 chunk 35 optimal weight: 9.9990 chunk 21 optimal weight: 40.0000 chunk 56 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 46 optimal weight: 0.0470 chunk 55 optimal weight: 9.9990 chunk 51 optimal weight: 50.0000 overall best weight: 6.4086 ------------------------------------------------------------------------------- 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 = 0.5045 r_free = 0.5045 target = 0.222968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.170521 restraints weight = 6009.567| |-----------------------------------------------------------------------------| r_work (start): 0.4731 rms_B_bonded: 2.92 r_work: 0.4813 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4709 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.4709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 4350 Z= 0.206 Angle : 0.700 10.045 5810 Z= 0.332 Chirality : 0.039 0.125 570 Planarity : 0.003 0.026 830 Dihedral : 7.320 50.133 590 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 4.09 % Allowed : 21.14 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.11 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 334 PHE 0.008 0.002 PHE C 316 Details of bonding type rmsd hydrogen bonds : bond 0.02197 ( 112) hydrogen bonds : angle 4.99626 ( 336) covalent geometry : bond 0.00468 ( 4350) covalent geometry : angle 0.69985 ( 5810) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 SER cc_start: 0.9035 (m) cc_final: 0.8766 (t) REVERT: A 336 MET cc_start: 0.9163 (tmm) cc_final: 0.8961 (tmm) REVERT: B 336 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8053 (tmm) REVERT: C 336 MET cc_start: 0.8639 (tmm) cc_final: 0.7013 (tmm) REVERT: E 322 MET cc_start: 0.9050 (mtp) cc_final: 0.8578 (mtt) REVERT: F 311 MET cc_start: 0.8496 (ptp) cc_final: 0.8178 (mtm) REVERT: G 345 ASN cc_start: 0.8235 (m-40) cc_final: 0.7793 (m-40) REVERT: H 345 ASN cc_start: 0.8225 (m-40) cc_final: 0.7812 (m-40) REVERT: I 317 SER cc_start: 0.9059 (m) cc_final: 0.8649 (t) REVERT: J 317 SER cc_start: 0.9021 (m) cc_final: 0.8572 (t) REVERT: J 323 MET cc_start: 0.8072 (tpp) cc_final: 0.7651 (tpp) REVERT: J 359 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7159 (ttm) REVERT: K 347 SER cc_start: 0.8306 (t) cc_final: 0.7977 (m) REVERT: L 347 SER cc_start: 0.8351 (t) cc_final: 0.8054 (m) REVERT: R 347 SER cc_start: 0.8516 (t) cc_final: 0.8269 (m) outliers start: 18 outliers final: 16 residues processed: 146 average time/residue: 0.1098 time to fit residues: 21.7785 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 : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 SER 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 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 347 SER Chi-restraints excluded: chain H residue 350 SER Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain M residue 339 MET Chi-restraints excluded: chain N residue 339 MET Chi-restraints excluded: chain O residue 347 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 50.0000 chunk 52 optimal weight: 9.9990 chunk 6 optimal weight: 50.0000 chunk 25 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 59 optimal weight: 0.5980 chunk 35 optimal weight: 20.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- 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** D 319 ASN ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 354 GLN ** K 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5071 r_free = 0.5071 target = 0.222442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4936 r_free = 0.4936 target = 0.171686 restraints weight = 5971.259| |-----------------------------------------------------------------------------| r_work (start): 0.4771 rms_B_bonded: 2.96 r_work: 0.4855 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4747 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.4747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4350 Z= 0.182 Angle : 0.699 11.983 5810 Z= 0.327 Chirality : 0.038 0.124 570 Planarity : 0.003 0.026 830 Dihedral : 7.169 50.263 590 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 3.64 % Allowed : 22.95 % 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: -5.10 (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 Details of bonding type rmsd hydrogen bonds : bond 0.02187 ( 112) hydrogen bonds : angle 4.98299 ( 336) covalent geometry : bond 0.00415 ( 4350) covalent geometry : angle 0.69929 ( 5810) *********************** 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 161 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 SER cc_start: 0.8995 (m) cc_final: 0.8732 (t) REVERT: A 336 MET cc_start: 0.9101 (tmm) cc_final: 0.7678 (tmm) REVERT: B 317 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8675 (t) REVERT: B 336 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8063 (tmm) REVERT: C 336 MET cc_start: 0.8617 (tmm) cc_final: 0.6934 (tmm) REVERT: E 336 MET cc_start: 0.9006 (tmm) cc_final: 0.8783 (tmm) REVERT: F 311 MET cc_start: 0.8526 (ptp) cc_final: 0.8277 (mtm) REVERT: G 345 ASN cc_start: 0.8238 (m-40) cc_final: 0.7810 (m-40) REVERT: H 345 ASN cc_start: 0.8239 (m-40) cc_final: 0.7838 (m-40) REVERT: I 317 SER cc_start: 0.9022 (m) cc_final: 0.8615 (t) REVERT: J 317 SER cc_start: 0.9015 (m) cc_final: 0.8588 (t) REVERT: J 323 MET cc_start: 0.7837 (tpp) cc_final: 0.7395 (tpp) REVERT: K 347 SER cc_start: 0.8270 (t) cc_final: 0.7910 (m) REVERT: L 347 SER cc_start: 0.8365 (t) cc_final: 0.8063 (m) REVERT: R 345 ASN cc_start: 0.7734 (m-40) cc_final: 0.7512 (m-40) REVERT: R 347 SER cc_start: 0.8524 (t) cc_final: 0.8312 (m) outliers start: 16 outliers final: 13 residues processed: 146 average time/residue: 0.1771 time to fit residues: 35.1134 Evaluate side-chains 159 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 SER 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 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 347 SER Chi-restraints excluded: chain H residue 350 SER 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: 6.9990 chunk 39 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 53 optimal weight: 40.0000 chunk 42 optimal weight: 9.9990 chunk 31 optimal weight: 0.0070 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 overall best weight: 3.4006 ------------------------------------------------------------------------------- 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** ** 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** ** 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 = 0.5150 r_free = 0.5150 target = 0.227447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5009 r_free = 0.5009 target = 0.176930 restraints weight = 5822.343| |-----------------------------------------------------------------------------| r_work (start): 0.4855 rms_B_bonded: 3.01 r_work: 0.4942 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.4835 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.4835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4350 Z= 0.139 Angle : 0.687 14.956 5810 Z= 0.318 Chirality : 0.038 0.126 570 Planarity : 0.003 0.024 830 Dihedral : 6.683 42.172 590 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.64 % Allowed : 22.50 % 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: -5.06 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 334 PHE 0.007 0.001 PHE C 316 Details of bonding type rmsd hydrogen bonds : bond 0.02374 ( 112) hydrogen bonds : angle 5.05408 ( 336) covalent geometry : bond 0.00317 ( 4350) covalent geometry : angle 0.68700 ( 5810) *********************** 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 166 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 317 SER cc_start: 0.8792 (m) cc_final: 0.8528 (t) REVERT: A 336 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8124 (tmm) REVERT: B 317 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8529 (t) REVERT: B 336 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8025 (tmm) REVERT: C 336 MET cc_start: 0.8518 (tmm) cc_final: 0.6682 (tmm) REVERT: E 323 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7808 (tpt) REVERT: F 311 MET cc_start: 0.8377 (ptp) cc_final: 0.8047 (mtm) REVERT: F 322 MET cc_start: 0.8201 (mtt) cc_final: 0.7739 (mtt) REVERT: F 336 MET cc_start: 0.8664 (tmm) cc_final: 0.7466 (tmm) REVERT: G 345 ASN cc_start: 0.8268 (m-40) cc_final: 0.7734 (m110) REVERT: H 345 ASN cc_start: 0.8253 (m-40) cc_final: 0.7708 (m110) REVERT: I 317 SER cc_start: 0.8969 (m) cc_final: 0.8640 (t) REVERT: I 334 TRP cc_start: 0.8818 (m-90) cc_final: 0.7305 (m-10) REVERT: I 336 MET cc_start: 0.7621 (tmm) cc_final: 0.6415 (tpp) REVERT: J 317 SER cc_start: 0.8954 (m) cc_final: 0.8581 (t) REVERT: J 323 MET cc_start: 0.7628 (tpp) cc_final: 0.7081 (tpp) REVERT: J 334 TRP cc_start: 0.8624 (m-90) cc_final: 0.7413 (m-90) REVERT: K 347 SER cc_start: 0.8142 (t) cc_final: 0.7798 (m) REVERT: L 347 SER cc_start: 0.8345 (t) cc_final: 0.8048 (m) REVERT: R 347 SER cc_start: 0.8523 (t) cc_final: 0.8276 (m) outliers start: 16 outliers final: 11 residues processed: 150 average time/residue: 0.1151 time to fit residues: 23.3150 Evaluate side-chains 160 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 317 SER 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 9.9990 chunk 6 optimal weight: 50.0000 chunk 26 optimal weight: 0.9990 chunk 45 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** ** 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 = 0.5066 r_free = 0.5066 target = 0.220850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.170603 restraints weight = 6003.736| |-----------------------------------------------------------------------------| r_work (start): 0.4770 rms_B_bonded: 2.98 r_work: 0.4861 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4759 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.4759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4350 Z= 0.211 Angle : 0.771 15.578 5810 Z= 0.353 Chirality : 0.038 0.123 570 Planarity : 0.003 0.026 830 Dihedral : 6.893 39.075 590 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 3.64 % Allowed : 23.41 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.08 (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 0.014 0.002 TRP F 334 PHE 0.008 0.002 PHE C 316 Details of bonding type rmsd hydrogen bonds : bond 0.02487 ( 112) hydrogen bonds : angle 5.01930 ( 336) covalent geometry : bond 0.00483 ( 4350) covalent geometry : angle 0.77099 ( 5810) *********************** 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 160 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 SER cc_start: 0.9002 (m) cc_final: 0.8731 (t) REVERT: A 336 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.7678 (tmm) REVERT: B 317 SER cc_start: 0.9013 (m) cc_final: 0.8713 (t) REVERT: B 339 MET cc_start: 0.8913 (tmm) cc_final: 0.8684 (tmm) REVERT: C 336 MET cc_start: 0.8544 (tmm) cc_final: 0.6705 (tmm) REVERT: F 311 MET cc_start: 0.8540 (ptp) cc_final: 0.8171 (mtm) REVERT: F 322 MET cc_start: 0.8551 (mtt) cc_final: 0.7896 (mtt) REVERT: G 345 ASN cc_start: 0.8291 (m-40) cc_final: 0.7926 (m-40) REVERT: H 345 ASN cc_start: 0.8262 (m-40) cc_final: 0.7901 (m-40) REVERT: I 317 SER cc_start: 0.9009 (m) cc_final: 0.8622 (t) REVERT: I 336 MET cc_start: 0.7927 (tmm) cc_final: 0.6560 (tpt) REVERT: J 317 SER cc_start: 0.9012 (m) cc_final: 0.8592 (t) REVERT: J 323 MET cc_start: 0.7690 (tpp) cc_final: 0.7260 (tpp) REVERT: J 334 TRP cc_start: 0.8700 (m-90) cc_final: 0.7450 (m-90) REVERT: K 347 SER cc_start: 0.8248 (t) cc_final: 0.7908 (m) REVERT: L 347 SER cc_start: 0.8391 (t) cc_final: 0.8079 (m) REVERT: R 347 SER cc_start: 0.8568 (t) cc_final: 0.8343 (m) outliers start: 16 outliers final: 13 residues processed: 144 average time/residue: 0.1177 time to fit residues: 23.2003 Evaluate side-chains 157 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 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 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 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: 7.9990 chunk 19 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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 = 0.5158 r_free = 0.5158 target = 0.231938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5037 r_free = 0.5037 target = 0.178890 restraints weight = 5857.569| |-----------------------------------------------------------------------------| r_work (start): 0.4874 rms_B_bonded: 2.96 r_work: 0.4967 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4859 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.4859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4350 Z= 0.141 Angle : 0.782 16.069 5810 Z= 0.348 Chirality : 0.038 0.125 570 Planarity : 0.003 0.026 830 Dihedral : 6.397 38.962 590 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.41 % Allowed : 23.64 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.04 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 334 PHE 0.007 0.001 PHE C 316 Details of bonding type rmsd hydrogen bonds : bond 0.02568 ( 112) hydrogen bonds : angle 5.01499 ( 336) covalent geometry : bond 0.00325 ( 4350) covalent geometry : angle 0.78207 ( 5810) ********************** 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 159 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.496 Fit side-chains REVERT: A 317 SER cc_start: 0.8784 (m) cc_final: 0.8468 (t) REVERT: B 317 SER cc_start: 0.8775 (m) cc_final: 0.8511 (t) REVERT: B 339 MET cc_start: 0.8794 (tmm) cc_final: 0.8539 (tmm) REVERT: E 323 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7787 (tpt) REVERT: F 311 MET cc_start: 0.8481 (ptp) cc_final: 0.8220 (mtm) REVERT: F 322 MET cc_start: 0.7956 (mtt) cc_final: 0.7607 (mtt) REVERT: G 345 ASN cc_start: 0.8261 (m-40) cc_final: 0.7720 (m110) REVERT: H 345 ASN cc_start: 0.8223 (m-40) cc_final: 0.7702 (m110) REVERT: I 317 SER cc_start: 0.8930 (m) cc_final: 0.8621 (t) REVERT: I 322 MET cc_start: 0.7998 (mmm) cc_final: 0.7648 (mtp) REVERT: I 334 TRP cc_start: 0.8817 (m-90) cc_final: 0.7441 (m-90) REVERT: I 336 MET cc_start: 0.7602 (tmm) cc_final: 0.6503 (tpt) REVERT: J 317 SER cc_start: 0.8920 (m) cc_final: 0.8586 (t) REVERT: J 323 MET cc_start: 0.7572 (tpp) cc_final: 0.7028 (tpp) REVERT: J 334 TRP cc_start: 0.8654 (m-90) cc_final: 0.7500 (m-90) REVERT: J 336 MET cc_start: 0.7175 (tmm) cc_final: 0.6050 (tpp) REVERT: K 347 SER cc_start: 0.8252 (t) cc_final: 0.7909 (m) REVERT: L 347 SER cc_start: 0.8347 (t) cc_final: 0.8047 (m) REVERT: R 347 SER cc_start: 0.8570 (t) cc_final: 0.8316 (m) outliers start: 15 outliers final: 13 residues processed: 144 average time/residue: 0.1149 time to fit residues: 22.1931 Evaluate side-chains 157 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 15 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 55 optimal weight: 50.0000 chunk 50 optimal weight: 30.0000 chunk 24 optimal weight: 9.9990 overall best weight: 8.1994 ------------------------------------------------------------------------------- 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** ** 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 = 0.5061 r_free = 0.5061 target = 0.217358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.168212 restraints weight = 5979.248| |-----------------------------------------------------------------------------| r_work (start): 0.4737 rms_B_bonded: 2.91 r_work: 0.4820 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4715 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.4715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 4350 Z= 0.259 Angle : 0.880 18.458 5810 Z= 0.389 Chirality : 0.039 0.122 570 Planarity : 0.004 0.026 830 Dihedral : 6.988 39.064 590 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 3.41 % Allowed : 24.32 % Favored : 72.27 % 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: -5.08 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 334 PHE 0.009 0.002 PHE C 316 Details of bonding type rmsd hydrogen bonds : bond 0.02599 ( 112) hydrogen bonds : angle 5.07194 ( 336) covalent geometry : bond 0.00592 ( 4350) covalent geometry : angle 0.87991 ( 5810) =============================================================================== Job complete usr+sys time: 2827.86 seconds wall clock time: 50 minutes 43.17 seconds (3043.17 seconds total)