Starting phenix.real_space_refine on Sun Mar 10 19:24:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6d_13226/03_2024/7p6d_13226.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6d_13226/03_2024/7p6d_13226.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/7p6d_13226/03_2024/7p6d_13226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6d_13226/03_2024/7p6d_13226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6d_13226/03_2024/7p6d_13226.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6d_13226/03_2024/7p6d_13226.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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.001 sd= 0.005 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 10 5.16 5 C 2695 2.51 5 N 810 2.21 5 O 825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4340 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 868 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "B" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 868 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "C" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 868 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "D" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 868 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "E" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 868 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Time building chain proxies: 2.71, per 1000 atoms: 0.62 Number of scatterers: 4340 At special positions: 0 Unit cell: (114.66, 88.92, 43.29, 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 10 16.00 O 825 8.00 N 810 7.00 C 2695 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: 1.27 Conformation dependent library (CDL) restraints added in 859.6 milliseconds 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1010 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 42.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 275 through 283 removed outlier: 7.070A pdb=" N GLN C 276 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE B 277 " --> pdb=" O GLN C 276 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE C 278 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASN B 279 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS C 280 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS B 281 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N GLN A 276 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N ASN C 279 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N ILE A 278 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 10.431A pdb=" N LYS C 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LYS A 280 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ASP C 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 282 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLN E 276 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE A 277 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE E 278 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASN A 279 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS E 280 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS A 281 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 9.178A pdb=" N GLN D 276 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N ASN E 279 " --> pdb=" O GLN D 276 " (cutoff:3.500A) removed outlier: 9.153A pdb=" N ILE D 278 " --> pdb=" O ASN E 279 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N LYS E 281 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LYS D 280 " --> pdb=" O LYS E 281 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ASP E 283 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU D 282 " --> pdb=" O ASP E 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 293 through 299 removed outlier: 6.826A pdb=" N SER B 293 " --> pdb=" O LYS C 294 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N ASN C 296 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ASP B 295 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N LYS C 298 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE B 297 " --> pdb=" O LYS C 298 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER A 293 " --> pdb=" O LYS E 294 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ASN E 296 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASP A 295 " --> pdb=" O ASN E 296 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N LYS E 298 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE A 297 " --> pdb=" O LYS E 298 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.511A pdb=" N GLN B 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N TYR C 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL B 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.934A pdb=" N VAL B 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 317 through 321 removed outlier: 6.472A pdb=" N LYS B 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N SER C 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR B 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LYS A 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N SER E 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR A 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.803A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE D 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 336 through 341 removed outlier: 6.506A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL D 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N LYS E 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL D 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 344 through 345 removed outlier: 6.885A pdb=" N LEU A 344 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU D 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.529A pdb=" N LYS B 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 358 through 362 removed outlier: 6.344A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP D 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N THR E 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE D 360 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 369 through 374 removed outlier: 6.299A pdb=" N LYS B 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N GLU C 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE B 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N HIS C 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR B 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 377 through 385 removed outlier: 6.881A pdb=" N THR B 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N GLU C 380 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG B 379 " --> pdb=" O GLU C 380 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ALA C 382 " --> pdb=" O ARG B 379 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASN B 381 " --> pdb=" O ALA C 382 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ALA C 384 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS B 383 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR A 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N GLU E 380 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG A 379 " --> pdb=" O GLU E 380 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ALA E 382 " --> pdb=" O ARG A 379 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN A 381 " --> pdb=" O ALA E 382 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ALA E 384 " --> pdb=" O ASN A 381 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS A 383 " --> pdb=" O ALA E 384 " (cutoff:3.500A) 86 hydrogen bonds defined for protein. 258 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: 1.08 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1455 1.34 - 1.46: 583 1.46 - 1.57: 2347 1.57 - 1.69: 0 1.69 - 1.81: 10 Bond restraints: 4395 Sorted by residual: bond pdb=" N VAL D 275 " pdb=" CA VAL D 275 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.24e-02 6.50e+03 8.16e+00 bond pdb=" N VAL A 275 " pdb=" CA VAL A 275 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.24e-02 6.50e+03 7.81e+00 bond pdb=" N VAL B 275 " pdb=" CA VAL B 275 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.24e-02 6.50e+03 7.72e+00 bond pdb=" N VAL C 275 " pdb=" CA VAL C 275 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.24e-02 6.50e+03 7.72e+00 bond pdb=" N VAL E 275 " pdb=" CA VAL E 275 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.24e-02 6.50e+03 7.67e+00 ... (remaining 4390 not shown) Histogram of bond angle deviations from ideal: 102.68 - 108.39: 313 108.39 - 114.10: 2501 114.10 - 119.81: 1002 119.81 - 125.52: 2009 125.52 - 131.22: 45 Bond angle restraints: 5870 Sorted by residual: angle pdb=" CA VAL B 275 " pdb=" C VAL B 275 " pdb=" O VAL B 275 " ideal model delta sigma weight residual 120.53 117.28 3.25 1.07e+00 8.73e-01 9.24e+00 angle pdb=" CA VAL E 275 " pdb=" C VAL E 275 " pdb=" O VAL E 275 " ideal model delta sigma weight residual 120.53 117.29 3.24 1.07e+00 8.73e-01 9.18e+00 angle pdb=" CA VAL C 275 " pdb=" C VAL C 275 " pdb=" O VAL C 275 " ideal model delta sigma weight residual 120.53 117.31 3.22 1.07e+00 8.73e-01 9.07e+00 angle pdb=" CA VAL A 275 " pdb=" C VAL A 275 " pdb=" O VAL A 275 " ideal model delta sigma weight residual 120.53 117.32 3.21 1.07e+00 8.73e-01 9.00e+00 angle pdb=" CA VAL D 275 " pdb=" C VAL D 275 " pdb=" O VAL D 275 " ideal model delta sigma weight residual 120.53 117.34 3.19 1.07e+00 8.73e-01 8.90e+00 ... (remaining 5865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 2530 16.00 - 32.00: 150 32.00 - 47.99: 35 47.99 - 63.99: 0 63.99 - 79.99: 5 Dihedral angle restraints: 2720 sinusoidal: 1135 harmonic: 1585 Sorted by residual: dihedral pdb=" CB GLU A 342 " pdb=" CG GLU A 342 " pdb=" CD GLU A 342 " pdb=" OE1 GLU A 342 " ideal model delta sinusoidal sigma weight residual 0.00 -79.99 79.99 1 3.00e+01 1.11e-03 8.81e+00 dihedral pdb=" CB GLU E 342 " pdb=" CG GLU E 342 " pdb=" CD GLU E 342 " pdb=" OE1 GLU E 342 " ideal model delta sinusoidal sigma weight residual 0.00 -79.98 79.98 1 3.00e+01 1.11e-03 8.81e+00 dihedral pdb=" CB GLU D 342 " pdb=" CG GLU D 342 " pdb=" CD GLU D 342 " pdb=" OE1 GLU D 342 " ideal model delta sinusoidal sigma weight residual 0.00 -79.98 79.98 1 3.00e+01 1.11e-03 8.81e+00 ... (remaining 2717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 410 0.037 - 0.074: 130 0.074 - 0.112: 83 0.112 - 0.149: 32 0.149 - 0.186: 5 Chirality restraints: 660 Sorted by residual: chirality pdb=" CA VAL E 275 " pdb=" N VAL E 275 " pdb=" C VAL E 275 " pdb=" CB VAL E 275 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.64e-01 chirality pdb=" CA VAL C 275 " pdb=" N VAL C 275 " pdb=" C VAL C 275 " pdb=" CB VAL C 275 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.58e-01 chirality pdb=" CA VAL D 275 " pdb=" N VAL D 275 " pdb=" C VAL D 275 " pdb=" CB VAL D 275 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.51e-01 ... (remaining 657 not shown) Planarity restraints: 755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 361 " 0.003 2.00e-02 2.50e+03 6.27e-03 3.93e-01 pdb=" C THR A 361 " -0.011 2.00e-02 2.50e+03 pdb=" O THR A 361 " 0.004 2.00e-02 2.50e+03 pdb=" N HIS A 362 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 300 " -0.010 5.00e-02 4.00e+02 1.56e-02 3.89e-01 pdb=" N PRO E 301 " 0.027 5.00e-02 4.00e+02 pdb=" CA PRO E 301 " -0.008 5.00e-02 4.00e+02 pdb=" CD PRO E 301 " -0.009 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR D 361 " 0.003 2.00e-02 2.50e+03 6.21e-03 3.85e-01 pdb=" C THR D 361 " -0.011 2.00e-02 2.50e+03 pdb=" O THR D 361 " 0.004 2.00e-02 2.50e+03 pdb=" N HIS D 362 " 0.004 2.00e-02 2.50e+03 ... (remaining 752 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.04: 2321 3.04 - 3.51: 3873 3.51 - 3.97: 6583 3.97 - 4.44: 6965 4.44 - 4.90: 12089 Nonbonded interactions: 31831 Sorted by model distance: nonbonded pdb=" OG SER A 305 " pdb=" O GLY C 303 " model vdw 2.575 2.440 nonbonded pdb=" O GLY B 303 " pdb=" OG SER C 305 " model vdw 2.579 2.440 nonbonded pdb=" O GLY A 303 " pdb=" OG SER E 305 " model vdw 2.584 2.440 nonbonded pdb=" OG1 THR A 386 " pdb=" N ASP A 387 " model vdw 2.587 2.520 nonbonded pdb=" OG1 THR E 386 " pdb=" N ASP E 387 " model vdw 2.588 2.520 ... (remaining 31826 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' } 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: 0.460 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: 2.410 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.450 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 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 : 0.003 0.035 4395 Z= 0.209 Angle : 0.655 5.737 5870 Z= 0.382 Chirality : 0.054 0.186 660 Planarity : 0.002 0.016 755 Dihedral : 11.405 79.990 1710 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.54 (0.31), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 299 PHE 0.006 0.001 PHE B 378 TYR 0.003 0.001 TYR D 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.539 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1464 time to fit residues: 12.2151 Evaluate side-chains 43 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 9.9990 chunk 16 optimal weight: 0.0670 chunk 26 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 overall best weight: 5.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 4395 Z= 0.431 Angle : 0.629 4.923 5870 Z= 0.342 Chirality : 0.054 0.144 660 Planarity : 0.003 0.031 755 Dihedral : 5.109 16.378 585 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.79 % Favored : 91.86 % Rotamer: Outliers : 1.01 % Allowed : 7.47 % Favored : 91.52 % 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: -2.63 (0.32), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS C 299 PHE 0.018 0.004 PHE C 346 TYR 0.010 0.002 TYR E 310 ARG 0.002 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: D 293 SER cc_start: 0.8352 (t) cc_final: 0.7930 (m) outliers start: 5 outliers final: 3 residues processed: 58 average time/residue: 0.1712 time to fit residues: 12.7861 Evaluate side-chains 46 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 377 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN B 362 HIS B 374 HIS C 362 HIS C 374 HIS D 362 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 4395 Z= 0.311 Angle : 0.552 5.671 5870 Z= 0.297 Chirality : 0.051 0.127 660 Planarity : 0.003 0.020 755 Dihedral : 4.835 14.699 585 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.83 % Allowed : 11.52 % Favored : 85.66 % 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: -2.71 (0.31), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS A 299 PHE 0.013 0.003 PHE E 378 TYR 0.010 0.002 TYR E 310 ARG 0.002 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: C 368 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.7722 (m-40) REVERT: D 293 SER cc_start: 0.8171 (t) cc_final: 0.7836 (m) outliers start: 14 outliers final: 7 residues processed: 56 average time/residue: 0.1445 time to fit residues: 10.8544 Evaluate side-chains 51 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain E residue 377 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4395 Z= 0.299 Angle : 0.547 6.598 5870 Z= 0.289 Chirality : 0.051 0.128 660 Planarity : 0.002 0.017 755 Dihedral : 4.854 15.079 585 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.64 % Allowed : 12.53 % Favored : 83.84 % 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: -2.79 (0.31), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 330 PHE 0.012 0.003 PHE B 378 TYR 0.012 0.003 TYR A 310 ARG 0.004 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 42 time to evaluate : 0.538 Fit side-chains REVERT: B 368 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7627 (m110) REVERT: C 368 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7700 (m-40) REVERT: D 293 SER cc_start: 0.8200 (t) cc_final: 0.7818 (m) outliers start: 18 outliers final: 15 residues processed: 59 average time/residue: 0.1632 time to fit residues: 12.6391 Evaluate side-chains 59 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 42 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 276 GLN Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 279 ASN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain E residue 377 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 351 GLN ** E 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 4395 Z= 0.521 Angle : 0.656 5.036 5870 Z= 0.357 Chirality : 0.054 0.141 660 Planarity : 0.003 0.022 755 Dihedral : 5.370 16.129 585 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 5.05 % Allowed : 13.33 % Favored : 81.62 % 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: -3.03 (0.30), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS C 330 PHE 0.018 0.004 PHE B 378 TYR 0.013 0.003 TYR E 310 ARG 0.005 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 40 time to evaluate : 0.439 Fit side-chains REVERT: C 368 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.7746 (m-40) outliers start: 25 outliers final: 19 residues processed: 62 average time/residue: 0.1471 time to fit residues: 11.9614 Evaluate side-chains 60 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 40 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 276 GLN Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 279 ASN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain E residue 377 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4395 Z= 0.370 Angle : 0.584 5.300 5870 Z= 0.312 Chirality : 0.052 0.132 660 Planarity : 0.003 0.017 755 Dihedral : 5.060 14.833 585 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.25 % Allowed : 13.54 % Favored : 81.21 % 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: -3.02 (0.30), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 330 PHE 0.014 0.003 PHE B 378 TYR 0.014 0.003 TYR A 310 ARG 0.005 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 42 time to evaluate : 0.560 Fit side-chains REVERT: D 279 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.7384 (m-40) outliers start: 26 outliers final: 20 residues processed: 63 average time/residue: 0.1577 time to fit residues: 13.0551 Evaluate side-chains 63 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 42 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 276 GLN Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 279 ASN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain E residue 377 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 53 optimal weight: 30.0000 chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.051 4395 Z= 0.609 Angle : 0.711 5.046 5870 Z= 0.387 Chirality : 0.056 0.145 660 Planarity : 0.004 0.023 755 Dihedral : 5.577 16.536 585 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.92 % Favored : 87.08 % Rotamer: Outliers : 5.86 % Allowed : 13.54 % Favored : 80.61 % 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: -3.30 (0.30), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS C 330 PHE 0.022 0.005 PHE D 378 TYR 0.015 0.003 TYR A 310 ARG 0.006 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 45 time to evaluate : 0.461 Fit side-chains REVERT: D 279 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.7509 (m-40) REVERT: D 359 ASN cc_start: 0.7764 (OUTLIER) cc_final: 0.7331 (m-40) outliers start: 29 outliers final: 25 residues processed: 70 average time/residue: 0.1661 time to fit residues: 15.2007 Evaluate side-chains 69 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 42 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain D residue 276 GLN Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain E residue 279 ASN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 377 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 4395 Z= 0.314 Angle : 0.594 7.321 5870 Z= 0.308 Chirality : 0.052 0.138 660 Planarity : 0.002 0.018 755 Dihedral : 5.019 14.443 585 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 4.85 % Allowed : 15.15 % Favored : 80.00 % 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: -3.14 (0.30), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 330 PHE 0.012 0.003 PHE D 378 TYR 0.014 0.003 TYR E 310 ARG 0.006 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 41 time to evaluate : 0.540 Fit side-chains REVERT: D 279 ASN cc_start: 0.7636 (OUTLIER) cc_final: 0.7337 (m-40) REVERT: D 342 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6694 (mm-30) outliers start: 24 outliers final: 20 residues processed: 61 average time/residue: 0.1407 time to fit residues: 11.4742 Evaluate side-chains 63 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 41 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 276 GLN Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain E residue 377 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 46 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4395 Z= 0.407 Angle : 0.636 7.215 5870 Z= 0.331 Chirality : 0.053 0.136 660 Planarity : 0.003 0.020 755 Dihedral : 5.197 15.116 585 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 5.25 % Allowed : 14.75 % Favored : 80.00 % 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: -3.20 (0.30), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 330 PHE 0.016 0.004 PHE D 378 TYR 0.014 0.003 TYR A 310 ARG 0.007 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 45 time to evaluate : 0.549 Fit side-chains REVERT: B 349 ARG cc_start: 0.5706 (mmt-90) cc_final: 0.5050 (mtt-85) REVERT: D 279 ASN cc_start: 0.7680 (OUTLIER) cc_final: 0.7427 (m-40) REVERT: D 342 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6742 (mm-30) REVERT: D 359 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7311 (m-40) outliers start: 26 outliers final: 23 residues processed: 67 average time/residue: 0.1502 time to fit residues: 13.2813 Evaluate side-chains 70 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 44 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain D residue 276 GLN Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain E residue 279 ASN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain E residue 377 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4395 Z= 0.236 Angle : 0.569 8.185 5870 Z= 0.287 Chirality : 0.051 0.139 660 Planarity : 0.002 0.022 755 Dihedral : 4.796 13.757 585 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.65 % Allowed : 15.35 % Favored : 80.00 % 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: -3.06 (0.30), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 299 PHE 0.010 0.002 PHE D 378 TYR 0.014 0.003 TYR A 310 ARG 0.007 0.001 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 45 time to evaluate : 0.481 Fit side-chains REVERT: B 349 ARG cc_start: 0.5539 (mmt-90) cc_final: 0.4876 (mtt-85) REVERT: D 279 ASN cc_start: 0.7593 (OUTLIER) cc_final: 0.7298 (m-40) REVERT: D 342 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6599 (mm-30) REVERT: D 359 ASN cc_start: 0.7678 (OUTLIER) cc_final: 0.7298 (m-40) outliers start: 23 outliers final: 18 residues processed: 65 average time/residue: 0.1497 time to fit residues: 12.7420 Evaluate side-chains 65 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 44 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain D residue 276 GLN Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 279 ASN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain E residue 377 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 38 optimal weight: 0.2980 chunk 2 optimal weight: 9.9990 chunk 31 optimal weight: 30.0000 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.107375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.090262 restraints weight = 6069.956| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.72 r_work: 0.3519 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4395 Z= 0.405 Angle : 0.631 7.408 5870 Z= 0.328 Chirality : 0.053 0.137 660 Planarity : 0.003 0.030 755 Dihedral : 5.134 15.017 585 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 4.44 % Allowed : 15.35 % Favored : 80.20 % 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: -3.18 (0.30), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 330 PHE 0.016 0.003 PHE D 378 TYR 0.014 0.003 TYR A 310 ARG 0.006 0.001 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1079.65 seconds wall clock time: 20 minutes 37.19 seconds (1237.19 seconds total)