Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:31:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6d_13226/11_2022/7p6d_13226.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6d_13226/11_2022/7p6d_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_13226/11_2022/7p6d_13226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6d_13226/11_2022/7p6d_13226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6d_13226/11_2022/7p6d_13226.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6d_13226/11_2022/7p6d_13226.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= 0.001 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 Convert atoms to be neutral 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-4778/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: 2.93, per 1000 atoms: 0.68 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: 2.04 Conformation dependent library (CDL) restraints added in 818.8 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: 0.36 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: 1.07 Time building geometry restraints manager: 2.19 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 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. 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: 0.400 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: 2.540 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.030 Process input model: 16.710 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 % 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 *********************** 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 : 0.796 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1349 time to fit residues: 11.3107 Evaluate side-chains 43 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7489 ------------------------------------------------------------------------------- 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: 0.9990 chunk 43 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8014 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.047 4395 Z= 0.534 Angle : 0.677 4.896 5870 Z= 0.370 Chirality : 0.055 0.148 660 Planarity : 0.004 0.033 755 Dihedral : 5.327 16.689 585 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.88 % Allowed : 7.79 % Favored : 91.33 % Rotamer Outliers : 1.62 % 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: -2.70 (0.32), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.24), residues: 565 *********************** 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 61 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.539 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 60 average time/residue: 0.1702 time to fit residues: 13.1413 Evaluate side-chains 47 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.522 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0492 time to fit residues: 1.2074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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** B 374 HIS ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS D 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.029 4395 Z= 0.359 Angle : 0.582 5.601 5870 Z= 0.314 Chirality : 0.052 0.130 660 Planarity : 0.003 0.031 755 Dihedral : 5.028 15.014 585 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 2.83 % 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: -2.77 (0.31), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.24), residues: 565 *********************** 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 56 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.549 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 56 average time/residue: 0.1536 time to fit residues: 11.5029 Evaluate side-chains 47 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.540 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0446 time to fit residues: 1.3865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 25 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 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 276 GLN A 351 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.039 4395 Z= 0.491 Angle : 0.647 5.317 5870 Z= 0.350 Chirality : 0.054 0.148 660 Planarity : 0.003 0.023 755 Dihedral : 5.393 16.625 585 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer Outliers : 2.63 % 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: -2.98 (0.31), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.24), residues: 565 *********************** 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 55 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 0.706 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 52 average time/residue: 0.1624 time to fit residues: 11.1502 Evaluate side-chains 49 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.538 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0416 time to fit residues: 1.3673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 4395 Z= 0.358 Angle : 0.583 5.396 5870 Z= 0.311 Chirality : 0.052 0.132 660 Planarity : 0.003 0.020 755 Dihedral : 5.058 15.316 585 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.31), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.23), residues: 565 *********************** 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 49 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.550 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 48 average time/residue: 0.1695 time to fit residues: 10.7990 Evaluate side-chains 44 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.560 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0435 time to fit residues: 1.1834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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: 0.8061 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.039 4395 Z= 0.464 Angle : 0.642 5.112 5870 Z= 0.343 Chirality : 0.054 0.149 660 Planarity : 0.003 0.029 755 Dihedral : 5.323 16.335 585 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer Outliers : 2.02 % 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: -3.07 (0.31), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.23), residues: 565 *********************** 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 55 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.608 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 53 average time/residue: 0.1817 time to fit residues: 12.3399 Evaluate side-chains 48 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.564 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0441 time to fit residues: 1.2991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 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** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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: 0.8047 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 4395 Z= 0.374 Angle : 0.626 7.204 5870 Z= 0.326 Chirality : 0.053 0.136 660 Planarity : 0.003 0.028 755 Dihedral : 5.081 15.232 585 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer Outliers : 1.62 % 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 *********************** 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 49 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.557 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 48 average time/residue: 0.1677 time to fit residues: 10.6475 Evaluate side-chains 43 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.577 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0432 time to fit residues: 1.0365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN ** C 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: 0.8025 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 4395 Z= 0.269 Angle : 0.577 7.450 5870 Z= 0.293 Chirality : 0.052 0.138 660 Planarity : 0.002 0.019 755 Dihedral : 4.828 14.351 585 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer Outliers : 0.61 % 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: -2.96 (0.31), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.23), residues: 565 *********************** 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 47 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.555 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 46 average time/residue: 0.1746 time to fit residues: 10.5477 Evaluate side-chains 43 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0416 time to fit residues: 0.9068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN ** C 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: 0.8056 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.034 4395 Z= 0.402 Angle : 0.632 7.232 5870 Z= 0.329 Chirality : 0.053 0.136 660 Planarity : 0.003 0.023 755 Dihedral : 5.108 14.993 585 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.80 % Favored : 89.20 % Rotamer Outliers : 1.21 % 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: -3.06 (0.31), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.23), residues: 565 *********************** 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 50 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.535 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 48 average time/residue: 0.1653 time to fit residues: 10.4477 Evaluate side-chains 45 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.559 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0433 time to fit residues: 1.0435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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: 0.7993 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.018 4395 Z= 0.172 Angle : 0.547 8.413 5870 Z= 0.270 Chirality : 0.051 0.138 660 Planarity : 0.002 0.017 755 Dihedral : 4.538 12.948 585 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % 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: -2.86 (0.30), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.23), residues: 565 ********************** 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 40 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.562 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1886 time to fit residues: 9.8519 Evaluate side-chains 39 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.555 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3848 r_free = 0.3848 target = 0.105354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.088437 restraints weight = 6131.183| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.80 r_work: 0.3610 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work: 0.3590 rms_B_bonded: 2.57 restraints_weight: 0.1250 r_work: 0.3580 rms_B_bonded: 2.61 restraints_weight: 0.0625 r_work: 0.3569 rms_B_bonded: 2.68 restraints_weight: 0.0312 r_work: 0.3557 rms_B_bonded: 2.78 restraints_weight: 0.0156 r_work: 0.3545 rms_B_bonded: 2.89 restraints_weight: 0.0078 r_work: 0.3533 rms_B_bonded: 3.03 restraints_weight: 0.0039 r_work: 0.3520 rms_B_bonded: 3.18 restraints_weight: 0.0020 r_work: 0.3506 rms_B_bonded: 3.36 restraints_weight: 0.0010 r_work: 0.3491 rms_B_bonded: 3.56 restraints_weight: 0.0005 r_work: 0.3476 rms_B_bonded: 3.79 restraints_weight: 0.0002 r_work: 0.3459 rms_B_bonded: 4.04 restraints_weight: 0.0001 r_work: 0.3442 rms_B_bonded: 4.32 restraints_weight: 0.0001 r_work: 0.3423 rms_B_bonded: 4.64 restraints_weight: 0.0000 r_work: 0.3403 rms_B_bonded: 4.99 restraints_weight: 0.0000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.048 4395 Z= 0.593 Angle : 0.715 6.880 5870 Z= 0.382 Chirality : 0.056 0.189 660 Planarity : 0.004 0.054 755 Dihedral : 5.502 16.316 585 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.63 % Favored : 86.02 % Rotamer Outliers : 0.61 % 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: -3.19 (0.31), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.23), residues: 565 =============================================================================== Job complete usr+sys time: 982.93 seconds wall clock time: 18 minutes 56.05 seconds (1136.05 seconds total)