Starting phenix.real_space_refine on Mon Sep 23 17:35:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3a_9349/09_2024/6n3a_9349.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3a_9349/09_2024/6n3a_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3a_9349/09_2024/6n3a_9349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3a_9349/09_2024/6n3a_9349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3a_9349/09_2024/6n3a_9349.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3a_9349/09_2024/6n3a_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-5461/modules/chem_data/mon_lib" Total number of atoms: 4310 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 359 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 72 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Restraints were copied for chains: M, L, O, N, Q, P, S, R, T, C, B, E, D, G, F, I, H, J Time building chain proxies: 1.42, per 1000 atoms: 0.33 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: 1.06 Conformation dependent library (CDL) restraints added in 533.0 milliseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1060 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 48.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'G' and resid 317 through 318 removed outlier: 6.431A pdb=" N SER D 317 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER A 317 " --> pdb=" O ILE D 318 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 321 through 323 removed outlier: 5.783A pdb=" N ALA D 321 " --> pdb=" O MET G 322 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ALA A 321 " --> pdb=" O MET D 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 328 through 335 removed outlier: 6.281A pdb=" N ALA D 329 " --> pdb=" O LEU G 330 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N SER G 332 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN D 331 " --> pdb=" O SER G 332 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N TRP G 334 " --> pdb=" O GLN D 331 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER D 333 " --> pdb=" O TRP G 334 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ALA A 329 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER D 332 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLN A 331 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N TRP D 334 " --> pdb=" O GLN A 331 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER A 333 " --> pdb=" O TRP D 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 338 through 346 removed outlier: 6.518A pdb=" N GLY D 338 " --> pdb=" O MET G 339 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ALA G 341 " --> pdb=" O GLY D 338 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU D 340 " --> pdb=" O ALA G 341 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLN G 343 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER D 342 " --> pdb=" O GLN G 343 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ASN G 345 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLN D 344 " --> pdb=" O ASN G 345 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLY A 338 " --> pdb=" O MET D 339 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ALA D 341 " --> pdb=" O GLY A 338 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 340 " --> pdb=" O ALA D 341 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN D 343 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER A 342 " --> pdb=" O GLN D 343 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N ASN D 345 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLN A 344 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 352 through 359 removed outlier: 6.904A pdb=" N ASN D 353 " --> pdb=" O GLN G 354 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N GLN G 356 " --> pdb=" O ASN D 353 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASN D 355 " --> pdb=" O GLN G 356 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ASN G 358 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLY D 357 " --> pdb=" O ASN G 358 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN A 353 " --> pdb=" O GLN D 354 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N GLN D 356 " --> pdb=" O ASN A 353 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASN A 355 " --> pdb=" O GLN D 356 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ASN D 358 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY A 357 " --> pdb=" O ASN D 358 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN F 353 " --> pdb=" O ASN A 352 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN I 353 " --> pdb=" O ASN F 352 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 317 through 318 removed outlier: 6.438A pdb=" N SER C 317 " --> pdb=" O ILE H 318 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER B 317 " --> pdb=" O ILE C 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 321 through 323 removed outlier: 5.790A pdb=" N ALA C 321 " --> pdb=" O MET H 322 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA B 321 " --> pdb=" O MET C 322 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 328 through 335 removed outlier: 6.288A pdb=" N ALA C 329 " --> pdb=" O LEU H 330 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N SER H 332 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLN C 331 " --> pdb=" O SER H 332 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N TRP H 334 " --> pdb=" O GLN C 331 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER C 333 " --> pdb=" O TRP H 334 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA B 329 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N SER C 332 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN B 331 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N TRP C 334 " --> pdb=" O GLN B 331 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER B 333 " --> pdb=" O TRP C 334 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 338 through 346 removed outlier: 6.520A pdb=" N GLY C 338 " --> pdb=" O MET H 339 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ALA H 341 " --> pdb=" O GLY C 338 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU C 340 " --> pdb=" O ALA H 341 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN H 343 " --> pdb=" O LEU C 340 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER C 342 " --> pdb=" O GLN H 343 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ASN H 345 " --> pdb=" O SER C 342 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLN C 344 " --> pdb=" O ASN H 345 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY B 338 " --> pdb=" O MET C 339 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ALA C 341 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU B 340 " --> pdb=" O ALA C 341 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLN C 343 " --> pdb=" O LEU B 340 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER B 342 " --> pdb=" O GLN C 343 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N ASN C 345 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLN B 344 " --> pdb=" O ASN C 345 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 352 through 359 removed outlier: 6.903A pdb=" N ASN C 353 " --> pdb=" O GLN H 354 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N GLN H 356 " --> pdb=" O ASN C 353 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ASN C 355 " --> pdb=" O GLN H 356 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ASN H 358 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY C 357 " --> pdb=" O ASN H 358 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASN B 353 " --> pdb=" O GLN C 354 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N GLN C 356 " --> pdb=" O ASN B 353 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASN B 355 " --> pdb=" O GLN C 356 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ASN C 358 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLY B 357 " --> pdb=" O ASN C 358 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN E 353 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN J 353 " --> pdb=" O ASN E 352 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 340 through 344 removed outlier: 7.182A pdb=" N ALA K 341 " --> pdb=" O SER P 342 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLN P 344 " --> pdb=" O ALA K 341 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLN K 343 " --> pdb=" O GLN P 344 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA P 341 " --> pdb=" O SER S 342 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N GLN S 344 " --> pdb=" O ALA P 341 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN P 343 " --> pdb=" O GLN S 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 340 through 344 removed outlier: 7.190A pdb=" N ALA L 341 " --> pdb=" O SER O 342 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N GLN O 344 " --> pdb=" O ALA L 341 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN L 343 " --> pdb=" O GLN O 344 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ALA O 341 " --> pdb=" O SER T 342 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N GLN T 344 " --> pdb=" O ALA O 341 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLN O 343 " --> pdb=" O GLN T 344 " (cutoff:3.500A) 112 hydrogen bonds defined for protein. 336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.95 Time building geometry restraints manager: 1.20 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.140 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.600 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 4350 Z= 0.514 Angle : 1.143 9.699 5810 Z= 0.553 Chirality : 0.047 0.114 570 Planarity : 0.007 0.055 830 Dihedral : 14.532 76.417 1600 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.23 (0.15), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.11), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP E 334 PHE 0.018 0.008 PHE J 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 0.463 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: 0.1057 time to fit residues: 30.5109 Evaluate side-chains 170 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 4350 Z= 0.320 Angle : 0.730 7.823 5810 Z= 0.364 Chirality : 0.042 0.137 570 Planarity : 0.004 0.036 830 Dihedral : 8.154 45.418 590 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 3.18 % Allowed : 19.32 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.22 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP J 334 PHE 0.011 0.003 PHE A 316 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 178 time to evaluate : 0.464 Fit side-chains REVERT: A 317 SER cc_start: 0.8575 (m) cc_final: 0.8289 (t) REVERT: A 336 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.7991 (tmm) REVERT: B 317 SER cc_start: 0.8574 (m) cc_final: 0.8289 (t) REVERT: B 336 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8009 (tmm) REVERT: B 360 GLN cc_start: 0.8549 (tp40) cc_final: 0.8323 (tp-100) REVERT: C 317 SER cc_start: 0.8934 (m) cc_final: 0.8679 (t) REVERT: C 323 MET cc_start: 0.7528 (tpp) cc_final: 0.6885 (tpp) REVERT: C 337 MET cc_start: 0.8558 (ttt) cc_final: 0.8301 (ttt) REVERT: D 317 SER cc_start: 0.8937 (m) cc_final: 0.8680 (t) REVERT: D 323 MET cc_start: 0.7596 (tpp) cc_final: 0.6964 (tpp) REVERT: D 337 MET cc_start: 0.8532 (ttt) cc_final: 0.8246 (ttt) REVERT: E 317 SER cc_start: 0.8992 (m) cc_final: 0.8741 (t) REVERT: E 336 MET cc_start: 0.8677 (tmm) cc_final: 0.8347 (tmm) REVERT: F 317 SER cc_start: 0.8934 (m) cc_final: 0.8657 (t) REVERT: F 323 MET cc_start: 0.7545 (tpp) cc_final: 0.7128 (tpp) REVERT: G 345 ASN cc_start: 0.7983 (m-40) cc_final: 0.7488 (m-40) REVERT: H 345 ASN cc_start: 0.7972 (m-40) cc_final: 0.7486 (m-40) REVERT: I 317 SER cc_start: 0.8897 (m) cc_final: 0.8424 (t) REVERT: I 354 GLN cc_start: 0.8462 (mt0) cc_final: 0.8238 (mt0) REVERT: J 317 SER cc_start: 0.8901 (m) cc_final: 0.8412 (t) REVERT: J 323 MET cc_start: 0.7299 (tpp) cc_final: 0.7074 (tpp) REVERT: J 354 GLN cc_start: 0.8435 (mt0) cc_final: 0.8229 (mt0) REVERT: K 347 SER cc_start: 0.8004 (t) cc_final: 0.7773 (m) REVERT: L 347 SER cc_start: 0.8148 (t) cc_final: 0.7929 (m) REVERT: R 347 SER cc_start: 0.8371 (t) cc_final: 0.8147 (m) outliers start: 14 outliers final: 6 residues processed: 178 average time/residue: 0.1060 time to fit residues: 25.6206 Evaluate side-chains 168 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 30 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 37 optimal weight: 30.0000 chunk 15 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 53 optimal weight: 50.0000 overall best weight: 9.1990 ------------------------------------------------------------------------------- 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 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** I 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 4350 Z= 0.408 Angle : 0.758 7.641 5810 Z= 0.373 Chirality : 0.041 0.130 570 Planarity : 0.004 0.029 830 Dihedral : 8.299 53.834 590 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % 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: -5.17 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 334 PHE 0.010 0.002 PHE J 316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.8608 (tmm) cc_final: 0.8087 (tmm) REVERT: B 336 MET cc_start: 0.8839 (tmm) cc_final: 0.7512 (tmm) REVERT: C 336 MET cc_start: 0.8269 (tmm) cc_final: 0.6718 (tmm) REVERT: D 336 MET cc_start: 0.8189 (tmm) cc_final: 0.6537 (tmm) REVERT: G 345 ASN cc_start: 0.8014 (m-40) cc_final: 0.7381 (m110) REVERT: H 345 ASN cc_start: 0.8046 (m-40) cc_final: 0.7420 (m110) REVERT: I 317 SER cc_start: 0.8954 (m) cc_final: 0.8434 (t) REVERT: J 317 SER cc_start: 0.8953 (m) cc_final: 0.8428 (t) REVERT: J 323 MET cc_start: 0.7536 (tpp) cc_final: 0.7257 (tpp) REVERT: K 347 SER cc_start: 0.8186 (t) cc_final: 0.7852 (m) REVERT: L 347 SER cc_start: 0.8255 (t) cc_final: 0.7963 (m) REVERT: R 347 SER cc_start: 0.8258 (t) cc_final: 0.8014 (m) outliers start: 16 outliers final: 13 residues processed: 153 average time/residue: 0.1125 time to fit residues: 23.3538 Evaluate side-chains 154 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 352 ASN Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain O residue 347 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 30.0000 chunk 28 optimal weight: 7.9990 chunk 6 optimal weight: 50.0000 chunk 26 optimal weight: 30.0000 chunk 36 optimal weight: 40.0000 chunk 54 optimal weight: 50.0000 chunk 57 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- 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** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 354 GLN ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 354 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 4350 Z= 0.380 Angle : 0.735 8.873 5810 Z= 0.357 Chirality : 0.040 0.137 570 Planarity : 0.003 0.029 830 Dihedral : 8.015 52.538 590 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 3.86 % Allowed : 21.82 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 : -3.91 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP F 334 PHE 0.009 0.002 PHE I 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7828 (tmm) REVERT: B 336 MET cc_start: 0.8890 (tmm) cc_final: 0.7988 (tmm) REVERT: B 360 GLN cc_start: 0.8137 (mm110) cc_final: 0.7914 (mm110) REVERT: C 336 MET cc_start: 0.8452 (tmm) cc_final: 0.6347 (tmm) REVERT: D 336 MET cc_start: 0.8311 (tmm) cc_final: 0.6826 (tmm) REVERT: G 345 ASN cc_start: 0.8029 (m-40) cc_final: 0.7454 (m110) REVERT: H 345 ASN cc_start: 0.8035 (m-40) cc_final: 0.7470 (m110) REVERT: I 317 SER cc_start: 0.9013 (m) cc_final: 0.8545 (t) REVERT: I 359 MET cc_start: 0.8464 (ttp) cc_final: 0.7476 (ttp) REVERT: J 317 SER cc_start: 0.8998 (m) cc_final: 0.8528 (t) REVERT: J 323 MET cc_start: 0.7278 (tpp) cc_final: 0.6986 (tpp) REVERT: J 359 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.6517 (ttm) REVERT: K 347 SER cc_start: 0.8210 (t) cc_final: 0.7926 (m) REVERT: L 347 SER cc_start: 0.8283 (t) cc_final: 0.8003 (m) REVERT: R 347 SER cc_start: 0.8315 (t) cc_final: 0.8052 (m) outliers start: 17 outliers final: 15 residues processed: 150 average time/residue: 0.1100 time to fit residues: 22.4238 Evaluate side-chains 158 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 347 SER Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain M residue 339 MET Chi-restraints excluded: chain N residue 339 MET Chi-restraints excluded: chain O residue 347 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 52 optimal weight: 40.0000 chunk 14 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 40.0000 chunk 34 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3850 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= 0.349 Angle : 0.708 9.117 5810 Z= 0.342 Chirality : 0.039 0.130 570 Planarity : 0.003 0.027 830 Dihedral : 7.782 52.136 590 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 4.77 % Allowed : 20.91 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.14 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 334 PHE 0.008 0.002 PHE I 316 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7822 (tmm) REVERT: B 336 MET cc_start: 0.8799 (tmm) cc_final: 0.7761 (tmm) REVERT: C 336 MET cc_start: 0.8499 (tmm) cc_final: 0.6816 (tmm) REVERT: D 336 MET cc_start: 0.8332 (tmm) cc_final: 0.6802 (tmm) REVERT: G 345 ASN cc_start: 0.8029 (m-40) cc_final: 0.7422 (m110) REVERT: H 345 ASN cc_start: 0.8035 (m-40) cc_final: 0.7438 (m110) REVERT: I 317 SER cc_start: 0.9007 (m) cc_final: 0.8547 (t) REVERT: I 359 MET cc_start: 0.8429 (ttp) cc_final: 0.7505 (ttp) REVERT: J 317 SER cc_start: 0.8989 (m) cc_final: 0.8531 (t) REVERT: J 323 MET cc_start: 0.7368 (tpp) cc_final: 0.6990 (tpp) REVERT: J 359 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.6538 (ttm) REVERT: K 347 SER cc_start: 0.8299 (t) cc_final: 0.7971 (m) REVERT: L 347 SER cc_start: 0.8307 (t) cc_final: 0.8035 (m) REVERT: R 347 SER cc_start: 0.8486 (t) cc_final: 0.8267 (m) outliers start: 21 outliers final: 15 residues processed: 156 average time/residue: 0.1117 time to fit residues: 23.7732 Evaluate side-chains 162 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 347 SER Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain M residue 339 MET Chi-restraints excluded: chain N residue 339 MET Chi-restraints excluded: chain O residue 347 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 4 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 6 optimal weight: 50.0000 chunk 33 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4350 Z= 0.336 Angle : 0.725 10.851 5810 Z= 0.342 Chirality : 0.039 0.130 570 Planarity : 0.003 0.027 830 Dihedral : 7.578 51.624 590 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 4.32 % Allowed : 21.82 % 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: -5.13 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 334 PHE 0.007 0.002 PHE J 316 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7878 (tmm) REVERT: B 336 MET cc_start: 0.8756 (tmm) cc_final: 0.7838 (tmm) REVERT: D 336 MET cc_start: 0.8338 (tmm) cc_final: 0.6734 (tmm) REVERT: E 317 SER cc_start: 0.9104 (m) cc_final: 0.8825 (t) REVERT: F 317 SER cc_start: 0.9117 (m) cc_final: 0.8840 (t) REVERT: G 345 ASN cc_start: 0.7998 (m-40) cc_final: 0.7536 (m-40) REVERT: H 345 ASN cc_start: 0.8003 (m-40) cc_final: 0.7518 (m-40) REVERT: I 317 SER cc_start: 0.8994 (m) cc_final: 0.8532 (t) REVERT: I 334 TRP cc_start: 0.8588 (m-90) cc_final: 0.7489 (m-90) REVERT: J 317 SER cc_start: 0.8987 (m) cc_final: 0.8521 (t) REVERT: J 323 MET cc_start: 0.7473 (tpp) cc_final: 0.7097 (tpp) REVERT: J 360 GLN cc_start: 0.7792 (mm110) cc_final: 0.4876 (pm20) REVERT: K 347 SER cc_start: 0.8293 (t) cc_final: 0.7988 (m) REVERT: L 347 SER cc_start: 0.8227 (t) cc_final: 0.7932 (m) REVERT: R 347 SER cc_start: 0.8483 (t) cc_final: 0.8255 (m) outliers start: 19 outliers final: 16 residues processed: 152 average time/residue: 0.0867 time to fit residues: 17.9920 Evaluate side-chains 163 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 347 SER Chi-restraints excluded: chain H residue 350 SER Chi-restraints excluded: chain J residue 311 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 32 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 26 optimal weight: 40.0000 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 overall best weight: 5.9790 ------------------------------------------------------------------------------- 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** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4350 Z= 0.298 Angle : 0.744 13.055 5810 Z= 0.344 Chirality : 0.039 0.130 570 Planarity : 0.003 0.026 830 Dihedral : 7.324 48.959 590 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 3.64 % Allowed : 23.86 % Favored : 72.50 % 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: -5.14 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 334 PHE 0.006 0.002 PHE C 316 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 336 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7897 (tmm) REVERT: B 336 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8255 (tmm) REVERT: C 336 MET cc_start: 0.8268 (tmm) cc_final: 0.6523 (tmm) REVERT: D 336 MET cc_start: 0.8283 (tmm) cc_final: 0.6507 (tmm) REVERT: E 317 SER cc_start: 0.9095 (m) cc_final: 0.8824 (t) REVERT: F 317 SER cc_start: 0.9102 (m) cc_final: 0.8828 (t) REVERT: G 345 ASN cc_start: 0.8032 (m-40) cc_final: 0.7546 (m-40) REVERT: H 322 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8237 (mtp) REVERT: H 345 ASN cc_start: 0.8029 (m-40) cc_final: 0.7565 (m-40) REVERT: I 317 SER cc_start: 0.8984 (m) cc_final: 0.8537 (t) REVERT: J 317 SER cc_start: 0.8970 (m) cc_final: 0.8522 (t) REVERT: J 323 MET cc_start: 0.7321 (tpp) cc_final: 0.6940 (tpp) REVERT: J 334 TRP cc_start: 0.8581 (m-90) cc_final: 0.7368 (m-90) REVERT: J 360 GLN cc_start: 0.7690 (mm110) cc_final: 0.4779 (pm20) REVERT: K 347 SER cc_start: 0.8307 (t) cc_final: 0.7997 (m) REVERT: L 347 SER cc_start: 0.8237 (t) cc_final: 0.7942 (m) REVERT: R 347 SER cc_start: 0.8494 (t) cc_final: 0.8272 (m) outliers start: 16 outliers final: 13 residues processed: 150 average time/residue: 0.1122 time to fit residues: 22.7102 Evaluate side-chains 161 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER 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 E residue 323 MET 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 347 SER Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 347 SER Chi-restraints excluded: chain H residue 350 SER Chi-restraints excluded: chain N residue 339 MET Chi-restraints excluded: chain O residue 347 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 52 optimal weight: 40.0000 chunk 55 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4167 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= 0.295 Angle : 0.762 14.181 5810 Z= 0.349 Chirality : 0.039 0.129 570 Planarity : 0.003 0.026 830 Dihedral : 7.106 45.199 590 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 4.09 % Allowed : 23.18 % Favored : 72.73 % 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 : -3.91 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 334 PHE 0.006 0.002 PHE D 316 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 336 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7992 (tmm) REVERT: B 336 MET cc_start: 0.8534 (tmm) cc_final: 0.7724 (tmm) REVERT: E 317 SER cc_start: 0.9090 (m) cc_final: 0.8823 (t) REVERT: F 317 SER cc_start: 0.9090 (m) cc_final: 0.8823 (t) REVERT: G 345 ASN cc_start: 0.8033 (m-40) cc_final: 0.7589 (m-40) REVERT: H 322 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8144 (mtp) REVERT: H 345 ASN cc_start: 0.8027 (m-40) cc_final: 0.7585 (m-40) REVERT: I 317 SER cc_start: 0.8968 (m) cc_final: 0.8535 (t) REVERT: J 317 SER cc_start: 0.8956 (m) cc_final: 0.8523 (t) REVERT: J 323 MET cc_start: 0.7278 (tpp) cc_final: 0.6865 (tpp) REVERT: J 334 TRP cc_start: 0.8559 (m-90) cc_final: 0.7397 (m-90) REVERT: K 347 SER cc_start: 0.8268 (t) cc_final: 0.7952 (m) REVERT: L 347 SER cc_start: 0.8198 (t) cc_final: 0.7896 (m) REVERT: R 347 SER cc_start: 0.8507 (t) cc_final: 0.8275 (m) outliers start: 18 outliers final: 15 residues processed: 148 average time/residue: 0.1113 time to fit residues: 22.2194 Evaluate side-chains 160 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain C 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 350 SER Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 347 SER Chi-restraints excluded: chain H residue 350 SER Chi-restraints excluded: chain J residue 311 MET Chi-restraints excluded: chain N residue 339 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 10.0000 chunk 50 optimal weight: 50.0000 chunk 53 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 59 optimal weight: 0.1980 chunk 55 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 overall best weight: 5.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4350 Z= 0.303 Angle : 0.808 16.818 5810 Z= 0.364 Chirality : 0.039 0.129 570 Planarity : 0.003 0.026 830 Dihedral : 6.955 39.070 590 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 4.77 % Allowed : 21.82 % 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: -5.13 (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 0.013 0.002 TRP F 334 PHE 0.006 0.002 PHE D 316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: B 323 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7159 (tpp) REVERT: B 336 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7702 (tmm) REVERT: D 336 MET cc_start: 0.8167 (tmm) cc_final: 0.6358 (tmm) REVERT: E 317 SER cc_start: 0.9086 (m) cc_final: 0.8819 (t) REVERT: F 317 SER cc_start: 0.9083 (m) cc_final: 0.8819 (t) REVERT: G 345 ASN cc_start: 0.8037 (m-40) cc_final: 0.7581 (m-40) REVERT: H 322 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8141 (mtp) REVERT: H 345 ASN cc_start: 0.8032 (m-40) cc_final: 0.7583 (m-40) REVERT: I 317 SER cc_start: 0.8953 (m) cc_final: 0.8538 (t) REVERT: I 334 TRP cc_start: 0.8555 (m-90) cc_final: 0.7473 (m-90) REVERT: I 336 MET cc_start: 0.7634 (tmm) cc_final: 0.6050 (tpt) REVERT: J 317 SER cc_start: 0.8945 (m) cc_final: 0.8527 (t) REVERT: J 323 MET cc_start: 0.7195 (tpp) cc_final: 0.6818 (tpp) REVERT: J 334 TRP cc_start: 0.8563 (m-90) cc_final: 0.7451 (m-90) REVERT: J 336 MET cc_start: 0.7169 (tmm) cc_final: 0.6228 (tpt) REVERT: K 347 SER cc_start: 0.8272 (t) cc_final: 0.7955 (m) REVERT: L 347 SER cc_start: 0.8197 (t) cc_final: 0.7895 (m) REVERT: R 347 SER cc_start: 0.8513 (t) cc_final: 0.8277 (m) outliers start: 21 outliers final: 16 residues processed: 147 average time/residue: 0.1122 time to fit residues: 22.3406 Evaluate side-chains 161 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 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 347 SER Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 347 SER Chi-restraints excluded: chain H residue 350 SER Chi-restraints excluded: chain J residue 311 MET Chi-restraints excluded: chain N residue 339 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 50 optimal weight: 50.0000 chunk 14 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 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** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4350 Z= 0.339 Angle : 0.843 18.239 5810 Z= 0.380 Chirality : 0.040 0.129 570 Planarity : 0.004 0.027 830 Dihedral : 7.001 38.156 590 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 4.32 % Allowed : 22.05 % Favored : 73.64 % 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: -5.16 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 334 PHE 0.007 0.002 PHE D 316 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: B 323 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7169 (tpp) REVERT: B 336 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7630 (tmm) REVERT: D 337 MET cc_start: 0.7964 (ttt) cc_final: 0.7478 (ttt) REVERT: E 317 SER cc_start: 0.9093 (m) cc_final: 0.8816 (t) REVERT: F 317 SER cc_start: 0.9096 (m) cc_final: 0.8823 (t) REVERT: G 345 ASN cc_start: 0.8069 (m-40) cc_final: 0.7605 (m-40) REVERT: H 322 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8149 (mtp) REVERT: H 345 ASN cc_start: 0.8029 (m-40) cc_final: 0.7572 (m-40) REVERT: I 317 SER cc_start: 0.8958 (m) cc_final: 0.8537 (t) REVERT: I 334 TRP cc_start: 0.8572 (m-90) cc_final: 0.7499 (m-90) REVERT: I 336 MET cc_start: 0.7293 (tmm) cc_final: 0.6000 (tpt) REVERT: J 317 SER cc_start: 0.8949 (m) cc_final: 0.8526 (t) REVERT: J 323 MET cc_start: 0.7311 (tpp) cc_final: 0.6911 (tpp) REVERT: J 334 TRP cc_start: 0.8586 (m-90) cc_final: 0.7437 (m-90) REVERT: J 336 MET cc_start: 0.7265 (tmm) cc_final: 0.6283 (tpp) REVERT: K 347 SER cc_start: 0.8290 (t) cc_final: 0.7967 (m) REVERT: L 347 SER cc_start: 0.8209 (t) cc_final: 0.7899 (m) REVERT: R 347 SER cc_start: 0.8540 (t) cc_final: 0.8294 (m) outliers start: 19 outliers final: 16 residues processed: 147 average time/residue: 0.1062 time to fit residues: 21.1911 Evaluate side-chains 162 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 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 347 SER Chi-restraints excluded: chain H residue 311 MET Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 347 SER Chi-restraints excluded: chain H residue 350 SER Chi-restraints excluded: chain J residue 311 MET Chi-restraints excluded: chain N residue 339 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 20.0000 chunk 6 optimal weight: 50.0000 chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 1 optimal weight: 50.0000 chunk 38 optimal weight: 10.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- 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** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 GLN ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5133 r_free = 0.5133 target = 0.225424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.174499 restraints weight = 5861.860| |-----------------------------------------------------------------------------| r_work (start): 0.4824 rms_B_bonded: 3.03 r_work: 0.4907 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4796 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.4796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4350 Z= 0.245 Angle : 0.810 17.953 5810 Z= 0.359 Chirality : 0.039 0.129 570 Planarity : 0.003 0.025 830 Dihedral : 6.508 37.420 590 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 3.64 % Allowed : 24.55 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.12 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 334 PHE 0.005 0.001 PHE C 316 =============================================================================== Job complete usr+sys time: 1144.40 seconds wall clock time: 24 minutes 19.33 seconds (1459.33 seconds total)