Starting phenix.real_space_refine on Thu Mar 6 01:09:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p6d_13226/03_2025/7p6d_13226.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p6d_13226/03_2025/7p6d_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/cci-nas-00/data/ceres_data/7p6d_13226/03_2025/7p6d_13226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p6d_13226/03_2025/7p6d_13226.map" model { file = "/net/cci-nas-00/data/ceres_data/7p6d_13226/03_2025/7p6d_13226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p6d_13226/03_2025/7p6d_13226.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4340 Number of models: 1 Model: "" Number of chains: 1 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} Restraints were copied for chains: C, B, E, D Time building chain proxies: 2.47, per 1000 atoms: 0.57 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 834.4 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: 0.84 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: 1.31 Time building geometry restraints manager: 1.11 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: 0.00 - 1.15: 5464 1.15 - 2.29: 301 2.29 - 3.44: 90 3.44 - 4.59: 5 4.59 - 5.74: 10 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 3.040 nonbonded pdb=" O GLY B 303 " pdb=" OG SER C 305 " model vdw 2.579 3.040 nonbonded pdb=" O GLY A 303 " pdb=" OG SER E 305 " model vdw 2.584 3.040 nonbonded pdb=" OG1 THR A 386 " pdb=" N ASP A 387 " model vdw 2.587 3.120 nonbonded pdb=" OG1 THR E 386 " pdb=" N ASP E 387 " model vdw 2.588 3.120 ... (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 Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.630 Find NCS groups from input model: 0.130 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.950 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.485 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1421 time to fit residues: 11.8491 Evaluate side-chains 43 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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: 9.9990 chunk 41 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 16 optimal weight: 0.0000 chunk 26 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 overall best weight: 5.1992 ------------------------------------------------------------------------------- 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** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.3689 r_free = 0.3689 target = 0.097304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.080357 restraints weight = 6749.765| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.88 r_work: 0.3347 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 4395 Z= 0.416 Angle : 0.634 4.891 5870 Z= 0.342 Chirality : 0.054 0.141 660 Planarity : 0.003 0.028 755 Dihedral : 5.099 16.178 585 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.26 % Favored : 92.04 % Rotamer: Outliers : 0.61 % Allowed : 5.66 % Favored : 93.74 % 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: -2.65 (0.32), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS C 299 PHE 0.017 0.004 PHE B 346 TYR 0.009 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 54 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.484 Fit side-chains REVERT: A 385 LYS cc_start: 0.7274 (tttt) cc_final: 0.6875 (tptp) REVERT: B 349 ARG cc_start: 0.8053 (mtt-85) cc_final: 0.7082 (mtt-85) REVERT: B 362 HIS cc_start: 0.9013 (t70) cc_final: 0.8737 (t-170) REVERT: C 338 GLU cc_start: 0.8324 (tt0) cc_final: 0.7571 (mt-10) REVERT: C 349 ARG cc_start: 0.8063 (mtt-85) cc_final: 0.7833 (mtp85) REVERT: D 349 ARG cc_start: 0.8064 (mtt-85) cc_final: 0.7623 (mtm180) REVERT: E 276 GLN cc_start: 0.7903 (mt0) cc_final: 0.6963 (mp10) outliers start: 3 outliers final: 2 residues processed: 54 average time/residue: 0.1835 time to fit residues: 12.7282 Evaluate side-chains 45 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 276 GLN 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 5 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 HIS C 374 HIS D 362 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.099659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.082918 restraints weight = 6635.631| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.87 r_work: 0.3370 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 4395 Z= 0.177 Angle : 0.499 5.803 5870 Z= 0.262 Chirality : 0.051 0.127 660 Planarity : 0.002 0.015 755 Dihedral : 4.448 13.243 585 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.61 % Allowed : 8.89 % Favored : 90.51 % 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: -2.65 (0.31), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS A 299 PHE 0.009 0.002 PHE E 378 TYR 0.010 0.002 TYR E 310 ARG 0.001 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 46 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.751 Fit side-chains REVERT: B 349 ARG cc_start: 0.7928 (mtt-85) cc_final: 0.6749 (mtt-85) REVERT: B 371 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7462 (mt) REVERT: C 338 GLU cc_start: 0.8300 (tt0) cc_final: 0.7540 (mt-10) REVERT: C 349 ARG cc_start: 0.7870 (mtt-85) cc_final: 0.7652 (mtp85) REVERT: D 349 ARG cc_start: 0.8144 (mtt-85) cc_final: 0.7699 (mtm180) REVERT: E 276 GLN cc_start: 0.7886 (mt0) cc_final: 0.7639 (mt0) REVERT: E 349 ARG cc_start: 0.7835 (mtt-85) cc_final: 0.7579 (mtp85) outliers start: 3 outliers final: 2 residues processed: 46 average time/residue: 0.1662 time to fit residues: 10.5165 Evaluate side-chains 41 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 371 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 overall best weight: 6.7788 ------------------------------------------------------------------------------- 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** ** C 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 = 0.3637 r_free = 0.3637 target = 0.094067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.077092 restraints weight = 6948.499| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.81 r_work: 0.3285 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 4395 Z= 0.526 Angle : 0.665 5.864 5870 Z= 0.361 Chirality : 0.055 0.138 660 Planarity : 0.003 0.019 755 Dihedral : 5.354 15.959 585 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.85 % Favored : 90.97 % Rotamer: Outliers : 2.02 % Allowed : 11.92 % Favored : 86.06 % 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: -2.92 (0.31), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS B 330 PHE 0.019 0.004 PHE B 378 TYR 0.012 0.003 TYR A 310 ARG 0.002 0.000 ARG B 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 49 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.968 Fit side-chains REVERT: A 349 ARG cc_start: 0.8164 (mtt-85) cc_final: 0.7826 (mtp85) REVERT: B 349 ARG cc_start: 0.8137 (mtt-85) cc_final: 0.7119 (mtt-85) REVERT: C 338 GLU cc_start: 0.8242 (tt0) cc_final: 0.7520 (mt-10) REVERT: C 349 ARG cc_start: 0.8164 (mtt-85) cc_final: 0.7917 (mtp85) REVERT: D 349 ARG cc_start: 0.8233 (mtt-85) cc_final: 0.7814 (mtm180) REVERT: E 276 GLN cc_start: 0.8015 (mt0) cc_final: 0.7767 (mt0) REVERT: E 349 ARG cc_start: 0.8205 (mtt-85) cc_final: 0.7802 (mtt90) outliers start: 10 outliers final: 7 residues processed: 49 average time/residue: 0.2396 time to fit residues: 15.6386 Evaluate side-chains 45 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 276 GLN Chi-restraints excluded: chain D residue 371 ILE 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 40 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.097512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.080610 restraints weight = 6925.045| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.91 r_work: 0.3337 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4395 Z= 0.231 Angle : 0.522 6.038 5870 Z= 0.275 Chirality : 0.051 0.131 660 Planarity : 0.002 0.018 755 Dihedral : 4.702 13.798 585 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.02 % Allowed : 11.52 % Favored : 86.46 % 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: -2.84 (0.31), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 299 PHE 0.010 0.002 PHE E 378 TYR 0.012 0.003 TYR A 310 ARG 0.001 0.000 ARG C 379 *********************** 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 50 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.548 Fit side-chains REVERT: B 349 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.7042 (mtt-85) REVERT: B 371 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7462 (mt) REVERT: C 349 ARG cc_start: 0.8011 (mtt-85) cc_final: 0.7757 (mtp85) REVERT: D 349 ARG cc_start: 0.8227 (mtt-85) cc_final: 0.7730 (mtm180) REVERT: D 371 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7494 (mp) REVERT: E 276 GLN cc_start: 0.7966 (mt0) cc_final: 0.7749 (mt0) outliers start: 10 outliers final: 5 residues processed: 49 average time/residue: 0.1541 time to fit residues: 10.1715 Evaluate side-chains 46 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 371 ILE 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 13 optimal weight: 8.9990 chunk 31 optimal weight: 30.0000 chunk 7 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 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 C 362 HIS E 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.095601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.078612 restraints weight = 6853.674| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.86 r_work: 0.3314 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2855 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= 0.362 Angle : 0.585 5.935 5870 Z= 0.310 Chirality : 0.052 0.131 660 Planarity : 0.003 0.017 755 Dihedral : 4.987 15.392 585 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 2.63 % Allowed : 11.92 % Favored : 85.45 % 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 (0.30), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 330 PHE 0.014 0.003 PHE B 378 TYR 0.013 0.003 TYR A 310 ARG 0.002 0.000 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 55 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.516 Fit side-chains REVERT: A 325 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6963 (tt) REVERT: A 349 ARG cc_start: 0.8189 (mtt-85) cc_final: 0.7872 (mtp85) REVERT: B 349 ARG cc_start: 0.7978 (mtt-85) cc_final: 0.7057 (mtt-85) REVERT: C 338 GLU cc_start: 0.8307 (tt0) cc_final: 0.7578 (mt-10) REVERT: C 349 ARG cc_start: 0.8075 (mtt-85) cc_final: 0.7835 (mtp85) REVERT: D 349 ARG cc_start: 0.8273 (mtt-85) cc_final: 0.7871 (mtm180) REVERT: D 371 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7606 (mp) REVERT: E 276 GLN cc_start: 0.7986 (mt0) cc_final: 0.7760 (mt0) outliers start: 13 outliers final: 9 residues processed: 52 average time/residue: 0.1636 time to fit residues: 11.0816 Evaluate side-chains 52 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 276 GLN Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 371 ILE 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 35 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.096222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.079258 restraints weight = 6818.064| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.80 r_work: 0.3321 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4395 Z= 0.315 Angle : 0.570 6.092 5870 Z= 0.299 Chirality : 0.052 0.131 660 Planarity : 0.002 0.017 755 Dihedral : 4.839 14.523 585 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.63 % Allowed : 11.92 % Favored : 85.45 % 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: -2.99 (0.30), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 330 PHE 0.012 0.003 PHE B 378 TYR 0.013 0.003 TYR A 310 ARG 0.003 0.000 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 53 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.500 Fit side-chains REVERT: A 349 ARG cc_start: 0.8242 (mtt-85) cc_final: 0.7965 (mtp85) REVERT: B 349 ARG cc_start: 0.8082 (mtt-85) cc_final: 0.7131 (mtt-85) REVERT: C 349 ARG cc_start: 0.8133 (mtt-85) cc_final: 0.7909 (mtp85) REVERT: D 349 ARG cc_start: 0.8295 (mtt-85) cc_final: 0.7923 (mtm180) REVERT: D 371 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7652 (mp) REVERT: E 276 GLN cc_start: 0.8045 (mt0) cc_final: 0.7825 (mt0) REVERT: E 349 ARG cc_start: 0.8253 (mtt90) cc_final: 0.7948 (mtt90) outliers start: 13 outliers final: 9 residues processed: 50 average time/residue: 0.1704 time to fit residues: 11.0591 Evaluate side-chains 50 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 276 GLN Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D 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 45 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.097509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.080467 restraints weight = 6731.763| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.86 r_work: 0.3341 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4395 Z= 0.227 Angle : 0.535 6.210 5870 Z= 0.274 Chirality : 0.051 0.132 660 Planarity : 0.002 0.016 755 Dihedral : 4.600 13.672 585 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.42 % Allowed : 11.72 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.30), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 330 PHE 0.010 0.002 PHE E 378 TYR 0.014 0.003 TYR A 310 ARG 0.002 0.000 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 56 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.503 Fit side-chains REVERT: A 349 ARG cc_start: 0.8134 (mtt-85) cc_final: 0.7835 (mtp85) REVERT: B 349 ARG cc_start: 0.8051 (mtt-85) cc_final: 0.7181 (mtt-85) REVERT: B 371 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7542 (mt) REVERT: B 385 LYS cc_start: 0.7340 (tttt) cc_final: 0.6911 (tptp) REVERT: C 349 ARG cc_start: 0.8064 (mtt-85) cc_final: 0.7825 (mtp85) REVERT: D 349 ARG cc_start: 0.8277 (mtt-85) cc_final: 0.7873 (mtm180) REVERT: D 371 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7655 (mp) REVERT: E 276 GLN cc_start: 0.8008 (mt0) cc_final: 0.7800 (mt0) REVERT: E 349 ARG cc_start: 0.8222 (mtt90) cc_final: 0.7910 (mtt90) outliers start: 12 outliers final: 9 residues processed: 53 average time/residue: 0.1743 time to fit residues: 11.8776 Evaluate side-chains 54 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 276 GLN Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 344 LEU 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 8 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 31 optimal weight: 30.0000 chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 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 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.095967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.078932 restraints weight = 6866.254| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.81 r_work: 0.3304 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4395 Z= 0.375 Angle : 0.604 6.275 5870 Z= 0.316 Chirality : 0.052 0.133 660 Planarity : 0.003 0.018 755 Dihedral : 4.941 14.946 585 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 2.22 % Allowed : 12.32 % Favored : 85.45 % 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 (0.30), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (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 0.013 0.003 TYR A 310 ARG 0.002 0.001 ARG E 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 55 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.530 Fit side-chains REVERT: A 349 ARG cc_start: 0.8372 (mtt-85) cc_final: 0.7886 (mtt-85) REVERT: B 349 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.7167 (mtt-85) REVERT: B 385 LYS cc_start: 0.7305 (tttt) cc_final: 0.6898 (tptp) REVERT: C 349 ARG cc_start: 0.8163 (mtt-85) cc_final: 0.7799 (mtp85) REVERT: D 274 LYS cc_start: 0.8502 (mptt) cc_final: 0.7882 (mmtm) REVERT: D 349 ARG cc_start: 0.8368 (mtt-85) cc_final: 0.7947 (mtm180) REVERT: D 371 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7667 (mp) REVERT: E 276 GLN cc_start: 0.8038 (mt0) cc_final: 0.7809 (mt0) REVERT: E 349 ARG cc_start: 0.8251 (mtt90) cc_final: 0.8009 (mtt90) outliers start: 11 outliers final: 10 residues processed: 52 average time/residue: 0.1831 time to fit residues: 12.1606 Evaluate side-chains 54 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 276 GLN Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 344 LEU 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 51 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 27 optimal weight: 0.2980 chunk 14 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.096755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.079685 restraints weight = 6725.035| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.82 r_work: 0.3330 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4395 Z= 0.290 Angle : 0.578 8.151 5870 Z= 0.296 Chirality : 0.052 0.134 660 Planarity : 0.002 0.018 755 Dihedral : 4.774 14.138 585 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.42 % Allowed : 12.12 % Favored : 85.45 % 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: -3.04 (0.30), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.011 0.003 PHE E 378 TYR 0.013 0.003 TYR A 310 ARG 0.002 0.000 ARG E 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 55 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.538 Fit side-chains REVERT: A 349 ARG cc_start: 0.8288 (mtt-85) cc_final: 0.7830 (mtt-85) REVERT: B 349 ARG cc_start: 0.8021 (mtt-85) cc_final: 0.7142 (mtt-85) REVERT: B 385 LYS cc_start: 0.7270 (tttt) cc_final: 0.6865 (tptp) REVERT: C 349 ARG cc_start: 0.8127 (mtt-85) cc_final: 0.7790 (mtp85) REVERT: D 349 ARG cc_start: 0.8336 (mtt-85) cc_final: 0.7931 (mtm180) REVERT: D 371 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7643 (mp) REVERT: E 276 GLN cc_start: 0.8003 (mt0) cc_final: 0.7780 (mt0) REVERT: E 349 ARG cc_start: 0.8329 (mtt90) cc_final: 0.8024 (mtt90) outliers start: 12 outliers final: 10 residues processed: 52 average time/residue: 0.1850 time to fit residues: 12.2781 Evaluate side-chains 53 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 276 GLN Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 344 LEU 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 38 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.095503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.078351 restraints weight = 6815.775| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.84 r_work: 0.3320 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3047 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= 0.358 Angle : 0.608 7.664 5870 Z= 0.315 Chirality : 0.052 0.136 660 Planarity : 0.003 0.019 755 Dihedral : 4.908 15.172 585 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 2.22 % Allowed : 12.32 % Favored : 85.45 % 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: -3.10 (0.30), residues: 565 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 330 PHE 0.013 0.003 PHE B 378 TYR 0.013 0.003 TYR A 310 ARG 0.002 0.001 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2733.14 seconds wall clock time: 48 minutes 54.96 seconds (2934.96 seconds total)