Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:31:17 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3a_9349/11_2022/6n3a_9349.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3a_9349/11_2022/6n3a_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_9349/11_2022/6n3a_9349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3a_9349/11_2022/6n3a_9349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3a_9349/11_2022/6n3a_9349.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3a_9349/11_2022/6n3a_9349.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.873 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/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: 2.69, per 1000 atoms: 0.62 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: 1.52 Conformation dependent library (CDL) restraints added in 774.2 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: 0.34 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: 1.07 Time building geometry restraints manager: 1.67 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 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. 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: 0.010 Normalize map: mean=0, sd=1: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.840 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.030 Process input model: 15.840 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 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 % 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 *********************** 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 : 0.512 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1062 time to fit residues: 30.5153 Evaluate side-chains 170 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.502 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6436 ------------------------------------------------------------------------------- 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: 20.0000 chunk 45 optimal weight: 8.9990 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: 9.9990 chunk 18 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN ** C 358 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** D 356 GLN ** D 358 ASN ** 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 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 ASN ** 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 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 356 GLN ** H 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 ASN I 354 GLN I 356 GLN ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 ASN J 354 GLN 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2970 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= 0.325 Angle : 0.730 8.161 5810 Z= 0.362 Chirality : 0.043 0.138 570 Planarity : 0.004 0.037 830 Dihedral : 7.757 39.656 590 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer Outliers : 4.09 % 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: -5.23 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.12), residues: 560 *********************** 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 177 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 0.495 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 163 average time/residue: 0.1108 time to fit residues: 24.4935 Evaluate side-chains 149 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 0.498 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0481 time to fit residues: 1.4428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 20.0000 chunk 16 optimal weight: 0.0010 chunk 45 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 58 optimal weight: 0.4980 chunk 48 optimal weight: 0.0570 chunk 18 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 40.0000 overall best weight: 0.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 GLN ** 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 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 319 ASN ** I 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 ASN I 354 GLN J 319 ASN ** J 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 ASN J 354 GLN K 346 GLN L 346 GLN M 346 GLN N 346 GLN O 346 GLN P 346 GLN S 346 GLN T 346 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 4350 Z= 0.140 Angle : 0.649 7.533 5810 Z= 0.313 Chirality : 0.040 0.136 570 Planarity : 0.003 0.026 830 Dihedral : 5.865 31.048 590 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.13 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.12), residues: 560 *********************** 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 181 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 177 time to evaluate : 0.505 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 177 average time/residue: 0.1149 time to fit residues: 27.2857 Evaluate side-chains 151 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 30.0000 chunk 28 optimal weight: 20.0000 chunk 6 optimal weight: 50.0000 chunk 26 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 54 optimal weight: 50.0000 chunk 57 optimal weight: 30.0000 chunk 51 optimal weight: 8.9990 chunk 15 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 32 optimal weight: 0.0670 overall best weight: 9.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN ** F 344 GLN ** 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 ** G 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 344 GLN ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 346 GLN ** H 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3891 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= 0.411 Angle : 0.771 9.041 5810 Z= 0.370 Chirality : 0.040 0.123 570 Planarity : 0.003 0.027 830 Dihedral : 7.031 40.013 590 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer Outliers : 3.41 % 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: -5.16 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.12), residues: 560 *********************** 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 156 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 0.485 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 147 average time/residue: 0.1207 time to fit residues: 23.9006 Evaluate side-chains 137 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 129 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0454 time to fit residues: 1.1331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 40 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 52 optimal weight: 40.0000 chunk 14 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 ** G 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 354 GLN S 344 GLN T 344 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4048 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= 0.396 Angle : 0.796 13.151 5810 Z= 0.372 Chirality : 0.041 0.149 570 Planarity : 0.004 0.028 830 Dihedral : 6.963 39.469 590 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 *********************** 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 139 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 134 average time/residue: 0.1088 time to fit residues: 19.7613 Evaluate side-chains 131 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 0.476 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0582 time to fit residues: 0.8976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 26 optimal weight: 30.0000 chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 6 optimal weight: 50.0000 chunk 33 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 ASN ** 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 319 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** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 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** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 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** ** 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 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 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** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4295 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= 0.368 Angle : 0.816 12.681 5810 Z= 0.378 Chirality : 0.040 0.125 570 Planarity : 0.004 0.026 830 Dihedral : 6.815 36.543 590 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.23 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.12), residues: 560 *********************** 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 140 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 133 average time/residue: 0.1192 time to fit residues: 21.3397 Evaluate side-chains 129 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 0.506 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0616 time to fit residues: 0.8500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 36 optimal weight: 0.4980 chunk 35 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 4350 Z= 0.217 Angle : 0.781 13.158 5810 Z= 0.357 Chirality : 0.040 0.128 570 Planarity : 0.003 0.024 830 Dihedral : 5.982 31.531 590 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.15 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.12), residues: 560 *********************** 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 144 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 139 time to evaluate : 0.494 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 140 average time/residue: 0.1176 time to fit residues: 21.9784 Evaluate side-chains 135 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 0.507 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0641 time to fit residues: 0.9952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 52 optimal weight: 50.0000 chunk 55 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 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 319 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** ** 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** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 360 GLN ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 360 GLN ** I 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 4350 Z= 0.313 Angle : 0.858 17.811 5810 Z= 0.380 Chirality : 0.039 0.126 570 Planarity : 0.003 0.025 830 Dihedral : 6.051 32.826 590 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.13 (0.16), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.13), residues: 560 *********************** 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 132 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 0.507 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 130 average time/residue: 0.1201 time to fit residues: 20.7855 Evaluate side-chains 131 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0620 time to fit residues: 0.8540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 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 319 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** ** 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** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 360 GLN ** I 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 4350 Z= 0.323 Angle : 0.878 16.999 5810 Z= 0.390 Chirality : 0.040 0.126 570 Planarity : 0.004 0.026 830 Dihedral : 6.127 32.640 590 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer Outliers : 0.91 % 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: -5.12 (0.17), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.13), residues: 560 *********************** 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 133 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 129 time to evaluate : 0.500 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 130 average time/residue: 0.1179 time to fit residues: 20.5333 Evaluate side-chains 132 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 0.492 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0607 time to fit residues: 0.9355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 29 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 ASN ** 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 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 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 319 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** ** 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** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 360 GLN ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 360 GLN ** I 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.042 4350 Z= 0.374 Angle : 0.932 17.327 5810 Z= 0.412 Chirality : 0.040 0.129 570 Planarity : 0.004 0.025 830 Dihedral : 6.313 33.971 590 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer Outliers : 0.91 % 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: -5.15 (0.17), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.13), residues: 560 ********************** 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 136 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 133 average time/residue: 0.1269 time to fit residues: 22.5180 Evaluate side-chains 133 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0619 time to fit residues: 0.7293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 5.9990 chunk 6 optimal weight: 50.0000 chunk 8 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 1 optimal weight: 50.0000 chunk 38 optimal weight: 0.6980 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 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 319 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** ** 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** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 360 GLN ** I 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5130 r_free = 0.5130 target = 0.195328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.163645 restraints weight = 5405.438| |-----------------------------------------------------------------------------| r_work (start): 0.4874 rms_B_bonded: 2.82 r_work: 0.4867 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.4859 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work: 0.4851 rms_B_bonded: 2.63 restraints_weight: 0.1250 r_work: 0.4843 rms_B_bonded: 2.67 restraints_weight: 0.0625 r_work: 0.4835 rms_B_bonded: 2.74 restraints_weight: 0.0312 r_work: 0.4826 rms_B_bonded: 2.83 restraints_weight: 0.0156 r_work: 0.4817 rms_B_bonded: 2.94 restraints_weight: 0.0078 r_work: 0.4807 rms_B_bonded: 3.06 restraints_weight: 0.0039 r_work: 0.4797 rms_B_bonded: 3.21 restraints_weight: 0.0020 r_work: 0.4787 rms_B_bonded: 3.38 restraints_weight: 0.0010 r_work: 0.4776 rms_B_bonded: 3.56 restraints_weight: 0.0005 r_work: 0.4764 rms_B_bonded: 3.78 restraints_weight: 0.0002 r_work: 0.4751 rms_B_bonded: 4.02 restraints_weight: 0.0001 r_work: 0.4738 rms_B_bonded: 4.29 restraints_weight: 0.0001 r_work: 0.4724 rms_B_bonded: 4.59 restraints_weight: 0.0000 r_work: 0.4709 rms_B_bonded: 4.92 restraints_weight: 0.0000 r_work (final): 0.4709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 4350 Z= 0.304 Angle : 0.903 17.061 5810 Z= 0.398 Chirality : 0.040 0.126 570 Planarity : 0.003 0.025 830 Dihedral : 6.133 32.307 590 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer Outliers : 2.05 % 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: -5.15 (0.17), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.13), residues: 560 =============================================================================== Job complete usr+sys time: 1061.07 seconds wall clock time: 20 minutes 44.76 seconds (1244.76 seconds total)