Starting phenix.real_space_refine on Sun Mar 10 19:21:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3a_9349/03_2024/6n3a_9349.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3a_9349/03_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_9349/03_2024/6n3a_9349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3a_9349/03_2024/6n3a_9349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3a_9349/03_2024/6n3a_9349.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3a_9349/03_2024/6n3a_9349.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4310 Number of models: 1 Model: "" Number of chains: 20 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: "B" 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: "C" 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: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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} Chain: "L" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 72 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 72 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 72 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "O" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 72 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 72 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 72 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 72 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 72 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "T" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 72 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Time building chain proxies: 2.50, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 1.70 Conformation dependent library (CDL) restraints added in 908.1 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: 0.56 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: 1.05 Time building geometry restraints manager: 1.80 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: 96.63 - 104.09: 120 104.09 - 111.55: 1628 111.55 - 119.01: 1642 119.01 - 126.47: 2360 126.47 - 133.93: 60 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 2.520 nonbonded pdb=" O SER E 332 " pdb=" NE2 GLN O 344 " model vdw 2.469 2.520 nonbonded pdb=" O SER G 332 " pdb=" NE2 GLN Q 344 " model vdw 2.469 2.520 nonbonded pdb=" O SER I 332 " pdb=" NE2 GLN S 344 " model vdw 2.470 2.520 nonbonded pdb=" O SER J 332 " pdb=" NE2 GLN T 344 " model vdw 2.470 2.520 ... (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 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: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.550 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.390 ------------------------------------------------------------------------------- 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 : 0.473 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: 0.1110 time to fit residues: 31.7583 Evaluate side-chains 170 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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: 3.9990 chunk 45 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 GLN ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 356 GLN ** G 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 356 GLN ** H 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 356 GLN ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 353 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: 0.7492 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4350 Z= 0.228 Angle : 0.676 7.820 5810 Z= 0.334 Chirality : 0.042 0.141 570 Planarity : 0.004 0.037 830 Dihedral : 7.180 34.891 590 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.41 % Allowed : 18.64 % Favored : 77.95 % 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: -5.19 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP J 334 PHE 0.010 0.002 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 194 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 179 time to evaluate : 0.516 Fit side-chains REVERT: A 317 SER cc_start: 0.8477 (m) cc_final: 0.8215 (t) REVERT: A 336 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7953 (tmm) REVERT: B 317 SER cc_start: 0.8474 (m) cc_final: 0.8211 (t) REVERT: B 336 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.7955 (tmm) REVERT: C 317 SER cc_start: 0.8829 (m) cc_final: 0.8624 (t) REVERT: C 323 MET cc_start: 0.7525 (tpp) cc_final: 0.6965 (tpp) REVERT: D 317 SER cc_start: 0.8832 (m) cc_final: 0.8627 (t) REVERT: D 323 MET cc_start: 0.7544 (tpp) cc_final: 0.6978 (tpp) REVERT: D 360 GLN cc_start: 0.8337 (tp40) cc_final: 0.8058 (tp-100) REVERT: E 317 SER cc_start: 0.8820 (m) cc_final: 0.8532 (t) REVERT: E 322 MET cc_start: 0.8771 (mtp) cc_final: 0.8254 (mtp) REVERT: E 336 MET cc_start: 0.8690 (tmm) cc_final: 0.8340 (tmm) REVERT: F 317 SER cc_start: 0.8843 (m) cc_final: 0.8550 (t) REVERT: F 322 MET cc_start: 0.8796 (mtp) cc_final: 0.8120 (mtp) REVERT: G 345 ASN cc_start: 0.7602 (m-40) cc_final: 0.7395 (m110) REVERT: I 317 SER cc_start: 0.8826 (m) cc_final: 0.8391 (t) REVERT: I 322 MET cc_start: 0.8364 (mtp) cc_final: 0.8161 (mmm) REVERT: I 336 MET cc_start: 0.8335 (tmm) cc_final: 0.7937 (tmm) REVERT: I 354 GLN cc_start: 0.8411 (mt0) cc_final: 0.8156 (mt0) REVERT: J 317 SER cc_start: 0.8827 (m) cc_final: 0.8388 (t) REVERT: J 336 MET cc_start: 0.8343 (tmm) cc_final: 0.7915 (tmm) REVERT: J 354 GLN cc_start: 0.8406 (mt0) cc_final: 0.8143 (mt0) REVERT: K 347 SER cc_start: 0.8081 (t) cc_final: 0.7819 (m) REVERT: L 347 SER cc_start: 0.8115 (t) cc_final: 0.7900 (m) REVERT: R 347 SER cc_start: 0.8341 (t) cc_final: 0.8080 (m) outliers start: 15 outliers final: 4 residues processed: 179 average time/residue: 0.1083 time to fit residues: 26.2915 Evaluate side-chains 165 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 159 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain G residue 339 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: 10.0000 chunk 16 optimal weight: 50.0000 chunk 45 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 58 optimal weight: 0.5980 chunk 48 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 53 optimal weight: 40.0000 overall best weight: 9.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 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 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 358 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 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 4350 Z= 0.407 Angle : 0.760 7.565 5810 Z= 0.371 Chirality : 0.040 0.130 570 Planarity : 0.004 0.031 830 Dihedral : 7.513 43.691 590 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % Rotamer: Outliers : 3.18 % Allowed : 22.73 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.21 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 334 PHE 0.011 0.002 PHE I 313 *********************** 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 161 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.8711 (tmm) cc_final: 0.7730 (tmm) REVERT: B 336 MET cc_start: 0.8831 (tmm) cc_final: 0.7769 (tmm) REVERT: C 336 MET cc_start: 0.8341 (tmm) cc_final: 0.6838 (tmm) REVERT: C 337 MET cc_start: 0.7928 (ttt) cc_final: 0.7429 (ttt) REVERT: D 336 MET cc_start: 0.8305 (tmm) cc_final: 0.6708 (tmm) REVERT: D 337 MET cc_start: 0.8018 (ttt) cc_final: 0.7551 (ttt) REVERT: F 322 MET cc_start: 0.9097 (mtp) cc_final: 0.8710 (mtp) REVERT: F 339 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.7095 (ttp) REVERT: G 345 ASN cc_start: 0.7667 (m-40) cc_final: 0.7284 (m110) REVERT: I 317 SER cc_start: 0.8978 (m) cc_final: 0.8469 (t) REVERT: I 339 MET cc_start: 0.8580 (tpt) cc_final: 0.8193 (tpt) REVERT: J 317 SER cc_start: 0.8973 (m) cc_final: 0.8457 (t) REVERT: K 347 SER cc_start: 0.8177 (t) cc_final: 0.7848 (m) REVERT: L 347 SER cc_start: 0.8202 (t) cc_final: 0.7881 (m) REVERT: R 347 SER cc_start: 0.8384 (t) cc_final: 0.8170 (m) outliers start: 14 outliers final: 11 residues processed: 151 average time/residue: 0.1126 time to fit residues: 22.9447 Evaluate side-chains 153 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 141 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 347 SER Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain H residue 339 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 40.0000 chunk 28 optimal weight: 9.9990 chunk 6 optimal weight: 50.0000 chunk 26 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 54 optimal weight: 30.0000 chunk 57 optimal weight: 8.9990 chunk 51 optimal weight: 30.0000 chunk 15 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 overall best weight: 9.3994 ------------------------------------------------------------------------------- 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 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 358 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 344 GLN ** T 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3546 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= 0.406 Angle : 0.728 8.208 5810 Z= 0.359 Chirality : 0.040 0.133 570 Planarity : 0.003 0.026 830 Dihedral : 7.264 46.097 590 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 3.86 % Allowed : 22.27 % 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: -5.22 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 334 PHE 0.009 0.002 PHE J 313 *********************** 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 fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7869 (tmm) REVERT: B 336 MET cc_start: 0.8613 (tmm) cc_final: 0.7887 (tmm) REVERT: C 336 MET cc_start: 0.8258 (tmm) cc_final: 0.6722 (tmm) REVERT: C 337 MET cc_start: 0.8080 (ttt) cc_final: 0.7657 (ttt) REVERT: D 336 MET cc_start: 0.8293 (tmm) cc_final: 0.6728 (tmm) REVERT: F 322 MET cc_start: 0.9105 (mtp) cc_final: 0.8401 (mtp) REVERT: F 339 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.7421 (ttp) REVERT: G 345 ASN cc_start: 0.7675 (m-40) cc_final: 0.7268 (m110) REVERT: I 317 SER cc_start: 0.9021 (m) cc_final: 0.8517 (t) REVERT: I 322 MET cc_start: 0.8462 (mtp) cc_final: 0.8262 (mmm) REVERT: I 339 MET cc_start: 0.8635 (tpt) cc_final: 0.8131 (tpt) REVERT: I 359 MET cc_start: 0.8552 (ttp) cc_final: 0.8263 (ttp) REVERT: J 317 SER cc_start: 0.9028 (m) cc_final: 0.8544 (t) REVERT: J 360 GLN cc_start: 0.7823 (mm110) cc_final: 0.4892 (pm20) REVERT: K 347 SER cc_start: 0.8305 (t) cc_final: 0.7946 (m) REVERT: R 347 SER cc_start: 0.8475 (t) cc_final: 0.8253 (m) outliers start: 17 outliers final: 13 residues processed: 148 average time/residue: 0.1029 time to fit residues: 20.7742 Evaluate side-chains 151 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 352 ASN Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 347 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 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 0 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 52 optimal weight: 30.0000 chunk 14 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 overall best weight: 7.5390 ------------------------------------------------------------------------------- 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 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 ASN ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 ASN ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 358 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3729 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= 0.338 Angle : 0.697 8.130 5810 Z= 0.337 Chirality : 0.039 0.130 570 Planarity : 0.003 0.024 830 Dihedral : 6.907 45.225 590 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % 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: -5.23 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 334 PHE 0.010 0.002 PHE J 313 *********************** 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 161 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7940 (tmm) REVERT: B 336 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7758 (tmm) REVERT: B 339 MET cc_start: 0.8617 (ttp) cc_final: 0.7343 (ttp) REVERT: C 336 MET cc_start: 0.8353 (tmm) cc_final: 0.6700 (tmm) REVERT: C 337 MET cc_start: 0.7964 (ttt) cc_final: 0.7597 (ttt) REVERT: D 336 MET cc_start: 0.8326 (tmm) cc_final: 0.6639 (tmm) REVERT: E 322 MET cc_start: 0.9053 (mtp) cc_final: 0.8527 (mtt) REVERT: F 339 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.7974 (ttp) REVERT: I 317 SER cc_start: 0.9022 (m) cc_final: 0.8544 (t) REVERT: I 353 ASN cc_start: 0.7714 (t160) cc_final: 0.7325 (t0) REVERT: J 317 SER cc_start: 0.9015 (m) cc_final: 0.8546 (t) REVERT: J 353 ASN cc_start: 0.7837 (t160) cc_final: 0.7348 (t0) REVERT: J 359 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.6869 (ttm) REVERT: J 360 GLN cc_start: 0.7786 (mm110) cc_final: 0.4798 (pm20) REVERT: K 347 SER cc_start: 0.8217 (t) cc_final: 0.7911 (m) REVERT: R 347 SER cc_start: 0.8458 (t) cc_final: 0.8252 (m) outliers start: 21 outliers final: 13 residues processed: 145 average time/residue: 0.1108 time to fit residues: 21.7473 Evaluate side-chains 157 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 336 MET Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain F residue 339 MET 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 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: 9.9990 chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 30.0000 chunk 4 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 40.0000 chunk 6 optimal weight: 50.0000 chunk 33 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- 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 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3873 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= 0.301 Angle : 0.714 11.189 5810 Z= 0.334 Chirality : 0.039 0.129 570 Planarity : 0.003 0.026 830 Dihedral : 6.595 43.465 590 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 4.09 % Allowed : 23.64 % 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: -5.19 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 334 PHE 0.010 0.002 PHE J 313 *********************** 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 fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7931 (tmm) REVERT: B 336 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7833 (tmm) REVERT: D 336 MET cc_start: 0.8383 (tmm) cc_final: 0.6588 (tmm) REVERT: F 311 MET cc_start: 0.8197 (ptp) cc_final: 0.7478 (mtm) REVERT: F 322 MET cc_start: 0.9072 (mtp) cc_final: 0.8542 (mtt) REVERT: F 339 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.7166 (ttp) REVERT: I 317 SER cc_start: 0.8996 (m) cc_final: 0.8546 (t) REVERT: I 339 MET cc_start: 0.8848 (tpt) cc_final: 0.7939 (tpt) REVERT: I 353 ASN cc_start: 0.7681 (t160) cc_final: 0.7302 (t0) REVERT: I 359 MET cc_start: 0.8592 (ttp) cc_final: 0.7750 (ttp) REVERT: J 317 SER cc_start: 0.9019 (m) cc_final: 0.8579 (t) REVERT: J 353 ASN cc_start: 0.7726 (t160) cc_final: 0.7315 (t0) REVERT: J 359 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.6877 (ttm) REVERT: J 360 GLN cc_start: 0.7691 (mm110) cc_final: 0.4703 (pm20) outliers start: 18 outliers final: 11 residues processed: 150 average time/residue: 0.1141 time to fit residues: 22.9888 Evaluate side-chains 154 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain F residue 339 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 57 optimal weight: 30.0000 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 26 optimal weight: 30.0000 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN ** G 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4350 Z= 0.253 Angle : 0.708 11.436 5810 Z= 0.326 Chirality : 0.039 0.131 570 Planarity : 0.003 0.024 830 Dihedral : 6.198 40.461 590 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 3.64 % Allowed : 25.45 % Favored : 70.91 % 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 0.012 0.002 TRP I 334 PHE 0.006 0.002 PHE D 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 155 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 SER cc_start: 0.8894 (m) cc_final: 0.8550 (t) REVERT: A 336 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7551 (tmm) REVERT: B 317 SER cc_start: 0.8893 (m) cc_final: 0.8544 (t) REVERT: B 336 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7364 (tmm) REVERT: D 337 MET cc_start: 0.7872 (ttt) cc_final: 0.7348 (ttt) REVERT: F 339 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8155 (ttp) REVERT: G 322 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8073 (mtp) REVERT: H 322 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8089 (mtp) REVERT: I 317 SER cc_start: 0.8934 (m) cc_final: 0.8474 (t) REVERT: I 353 ASN cc_start: 0.7697 (t160) cc_final: 0.7312 (t0) REVERT: I 359 MET cc_start: 0.8552 (ttp) cc_final: 0.8021 (ttp) REVERT: J 317 SER cc_start: 0.8958 (m) cc_final: 0.8510 (t) REVERT: J 353 ASN cc_start: 0.7726 (t160) cc_final: 0.7326 (t0) REVERT: J 359 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.6843 (ttm) outliers start: 16 outliers final: 9 residues processed: 143 average time/residue: 0.1121 time to fit residues: 21.6874 Evaluate side-chains 152 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 322 MET Chi-restraints excluded: chain G residue 339 MET 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 J residue 359 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: 9.9990 chunk 5 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 52 optimal weight: 30.0000 chunk 55 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 16 optimal weight: 30.0000 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** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 358 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4350 Z= 0.306 Angle : 0.753 14.990 5810 Z= 0.343 Chirality : 0.039 0.127 570 Planarity : 0.003 0.025 830 Dihedral : 6.246 39.804 590 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 4.77 % Allowed : 25.00 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.20 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 334 PHE 0.009 0.002 PHE J 313 *********************** 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 160 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 336 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7442 (tmm) REVERT: A 339 MET cc_start: 0.8558 (tmm) cc_final: 0.7378 (ttp) REVERT: B 317 SER cc_start: 0.8927 (m) cc_final: 0.8579 (t) REVERT: B 336 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7752 (tmm) REVERT: D 337 MET cc_start: 0.7848 (ttt) cc_final: 0.7342 (ttt) REVERT: F 339 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.7421 (ttp) REVERT: G 322 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8058 (mtp) REVERT: H 322 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8040 (mtp) REVERT: I 317 SER cc_start: 0.8943 (m) cc_final: 0.8483 (t) REVERT: I 339 MET cc_start: 0.8820 (tpt) cc_final: 0.8010 (tpt) REVERT: I 353 ASN cc_start: 0.7692 (t160) cc_final: 0.7298 (t0) REVERT: J 317 SER cc_start: 0.8980 (m) cc_final: 0.8535 (t) REVERT: J 353 ASN cc_start: 0.7747 (t160) cc_final: 0.7305 (t0) REVERT: J 359 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7448 (ttp) REVERT: J 360 GLN cc_start: 0.7692 (mm110) cc_final: 0.4716 (pm20) outliers start: 21 outliers final: 13 residues processed: 144 average time/residue: 0.1129 time to fit residues: 21.9693 Evaluate side-chains 157 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 336 MET Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 322 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 47 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** ** D 345 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** E 354 GLN ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 358 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4350 Z= 0.352 Angle : 0.813 16.788 5810 Z= 0.368 Chirality : 0.040 0.127 570 Planarity : 0.003 0.026 830 Dihedral : 6.409 40.335 590 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 5.00 % Allowed : 25.45 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.19 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 160 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7993 (tmm) REVERT: B 336 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7686 (tmm) REVERT: F 322 MET cc_start: 0.8987 (mtp) cc_final: 0.8744 (mtt) REVERT: F 339 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.7824 (ttp) REVERT: G 322 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8073 (mtp) REVERT: H 322 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8083 (mtp) REVERT: I 317 SER cc_start: 0.8994 (m) cc_final: 0.8541 (t) REVERT: I 353 ASN cc_start: 0.7831 (t160) cc_final: 0.7378 (t0) REVERT: J 317 SER cc_start: 0.8988 (m) cc_final: 0.8536 (t) REVERT: J 336 MET cc_start: 0.7553 (tmm) cc_final: 0.6157 (tpt) REVERT: J 353 ASN cc_start: 0.7760 (t160) cc_final: 0.7292 (t0) REVERT: J 359 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.6825 (ttm) REVERT: P 346 GLN cc_start: 0.8471 (tm130) cc_final: 0.7144 (tm-30) outliers start: 22 outliers final: 11 residues processed: 142 average time/residue: 0.1156 time to fit residues: 22.1481 Evaluate side-chains 154 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 336 MET Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 322 MET Chi-restraints excluded: chain G residue 339 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 358 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4212 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= 0.250 Angle : 0.788 18.136 5810 Z= 0.351 Chirality : 0.039 0.129 570 Planarity : 0.003 0.025 830 Dihedral : 5.887 37.513 590 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.41 % Allowed : 27.27 % Favored : 69.32 % 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: -5.17 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.94 (0.12), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 334 PHE 0.007 0.002 PHE J 313 ********************** 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 157 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 SER cc_start: 0.8751 (m) cc_final: 0.8424 (t) REVERT: B 317 SER cc_start: 0.8764 (m) cc_final: 0.8432 (t) REVERT: B 336 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7711 (tmm) REVERT: D 337 MET cc_start: 0.7522 (ttt) cc_final: 0.6980 (ttt) REVERT: E 311 MET cc_start: 0.8552 (ptp) cc_final: 0.8057 (mtm) REVERT: F 322 MET cc_start: 0.8930 (mtp) cc_final: 0.8695 (mtt) REVERT: F 339 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.7151 (ttp) REVERT: G 322 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8037 (mtp) REVERT: H 322 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8041 (mtp) REVERT: I 317 SER cc_start: 0.8916 (m) cc_final: 0.8482 (t) REVERT: I 339 MET cc_start: 0.8796 (tpt) cc_final: 0.7984 (tpt) REVERT: J 317 SER cc_start: 0.8883 (m) cc_final: 0.8448 (t) REVERT: J 322 MET cc_start: 0.8088 (mmm) cc_final: 0.7486 (mmt) REVERT: J 336 MET cc_start: 0.7040 (tmm) cc_final: 0.6141 (tpp) REVERT: J 353 ASN cc_start: 0.7738 (t160) cc_final: 0.7330 (t0) REVERT: J 359 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.6644 (ttm) outliers start: 15 outliers final: 8 residues processed: 145 average time/residue: 0.1135 time to fit residues: 22.1821 Evaluate side-chains 150 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 137 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 322 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 J residue 359 MET Chi-restraints excluded: chain O residue 347 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 10.0000 chunk 6 optimal weight: 50.0000 chunk 8 optimal weight: 20.0000 chunk 41 optimal weight: 40.0000 chunk 2 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 54 optimal weight: 40.0000 chunk 32 optimal weight: 0.0000 chunk 40 optimal weight: 9.9990 chunk 1 optimal weight: 50.0000 chunk 38 optimal weight: 7.9990 overall best weight: 7.5994 ------------------------------------------------------------------------------- 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** E 354 GLN ** F 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 358 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** ** 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 = 0.5025 r_free = 0.5025 target = 0.218378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.168201 restraints weight = 5948.676| |-----------------------------------------------------------------------------| r_work (start): 0.4738 rms_B_bonded: 2.83 r_work: 0.4833 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4733 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.4733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4350 Z= 0.354 Angle : 0.855 18.417 5810 Z= 0.380 Chirality : 0.040 0.126 570 Planarity : 0.003 0.026 830 Dihedral : 6.235 39.065 590 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 3.64 % Allowed : 27.05 % Favored : 69.32 % 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: -5.19 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (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 =============================================================================== Job complete usr+sys time: 1158.30 seconds wall clock time: 21 minutes 41.15 seconds (1301.15 seconds total)