Starting phenix.real_space_refine on Sat Jul 4 03:57:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l2w_23143/07_2026/7l2w_23143.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l2w_23143/07_2026/7l2w_23143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l2w_23143/07_2026/7l2w_23143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l2w_23143/07_2026/7l2w_23143.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7l2w_23143/07_2026/7l2w_23143.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l2w_23143/07_2026/7l2w_23143.cif" model { file = "/net/cci-nas-00/data/ceres_data/7l2w_23143/07_2026/7l2w_23143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l2w_23143/07_2026/7l2w_23143.cif" } resolution = 3.16 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 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= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 100 5.16 5 Na 1 4.78 5 C 11648 2.51 5 N 2816 2.21 5 O 3168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17737 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "D" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "B" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "C" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "A" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 122 Unusual residues: {'6EU': 1, '6IY': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Unusual residues: {' NA': 1, '6EU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 168 Unusual residues: {'6EU': 2, '6IY': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.29, per 1000 atoms: 0.24 Number of scatterers: 17737 At special positions: 0 Unit cell: (124.415, 132.765, 111.055, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 4 15.00 Na 1 11.00 O 3168 8.00 N 2816 7.00 C 11648 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: 1.56 Conformation dependent library (CDL) restraints added in 667.9 milliseconds 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4056 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 4 sheets defined 64.1% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 203 through 211 Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.724A pdb=" N LYS A 237 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 324 through 328 removed outlier: 3.517A pdb=" N GLU A 327 " --> pdb=" O LYS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 410 through 414 Processing helix chain 'A' and resid 415 through 429 Processing helix chain 'A' and resid 429 through 454 Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 510 through 532 Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.972A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 557 removed outlier: 3.550A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 599 removed outlier: 4.217A pdb=" N ALA A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 Processing helix chain 'A' and resid 655 through 671 Processing helix chain 'A' and resid 672 through 689 removed outlier: 3.854A pdb=" N ASN A 676 " --> pdb=" O ILE A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 712 Processing helix chain 'D' and resid 203 through 211 Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.772A pdb=" N LYS D 237 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 286 through 294 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 324 through 328 removed outlier: 3.525A pdb=" N GLU D 327 " --> pdb=" O LYS D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 354 removed outlier: 3.816A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 410 through 414 removed outlier: 3.596A pdb=" N LEU D 413 " --> pdb=" O HIS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.731A pdb=" N PHE D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 removed outlier: 3.634A pdb=" N ILE D 433 " --> pdb=" O PHE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 551 removed outlier: 4.039A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 555 Processing helix chain 'D' and resid 562 through 599 removed outlier: 4.255A pdb=" N ALA D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 642 Processing helix chain 'D' and resid 655 through 671 Processing helix chain 'D' and resid 672 through 689 removed outlier: 3.877A pdb=" N ASN D 676 " --> pdb=" O ILE D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 712 removed outlier: 3.821A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 270 Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 354 removed outlier: 4.033A pdb=" N GLN B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 410 through 414 removed outlier: 3.596A pdb=" N LEU B 413 " --> pdb=" O HIS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.639A pdb=" N PHE B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 removed outlier: 3.596A pdb=" N ILE B 433 " --> pdb=" O PHE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 510 through 532 Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.613A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 Processing helix chain 'B' and resid 563 through 599 removed outlier: 3.692A pdb=" N VAL B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 Processing helix chain 'B' and resid 655 through 671 Processing helix chain 'B' and resid 672 through 689 removed outlier: 3.832A pdb=" N ASN B 676 " --> pdb=" O ILE B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 712 removed outlier: 4.191A pdb=" N LYS B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 211 Processing helix chain 'C' and resid 213 through 223 Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 270 Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 324 through 328 removed outlier: 3.509A pdb=" N GLU C 327 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 410 through 414 Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.634A pdb=" N PHE C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 removed outlier: 3.729A pdb=" N ILE C 433 " --> pdb=" O PHE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.958A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 557 removed outlier: 3.521A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 575 removed outlier: 3.724A pdb=" N VAL C 567 " --> pdb=" O GLY C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 599 removed outlier: 4.386A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 642 Processing helix chain 'C' and resid 655 through 671 Processing helix chain 'C' and resid 672 through 689 removed outlier: 3.838A pdb=" N ASN C 676 " --> pdb=" O ILE C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 712 Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 373 removed outlier: 5.331A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 368 through 373 removed outlier: 6.789A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ALA D 373 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 368 through 373 removed outlier: 6.675A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ALA B 373 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 368 through 373 removed outlier: 6.754A pdb=" N SER C 379 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA C 373 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) 1002 hydrogen bonds defined for protein. 2907 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: 2.77 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2720 1.30 - 1.43: 5153 1.43 - 1.56: 10122 1.56 - 1.69: 9 1.69 - 1.81: 164 Bond restraints: 18168 Sorted by residual: bond pdb=" CBK 6EU A 901 " pdb=" OAF 6EU A 901 " ideal model delta sigma weight residual 1.329 1.454 -0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" CBK 6EU B 901 " pdb=" OAF 6EU B 901 " ideal model delta sigma weight residual 1.329 1.454 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" CBK 6EU C 903 " pdb=" OAF 6EU C 903 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" CBK 6EU C 901 " pdb=" OAF 6EU C 901 " ideal model delta sigma weight residual 1.329 1.452 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C13 6IY C 902 " pdb=" O6 6IY C 902 " ideal model delta sigma weight residual 1.333 1.421 -0.088 2.00e-02 2.50e+03 1.92e+01 ... (remaining 18163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 24443 4.49 - 8.98: 157 8.98 - 13.47: 10 13.47 - 17.96: 2 17.96 - 22.45: 4 Bond angle restraints: 24616 Sorted by residual: angle pdb=" O3 6IY A 903 " pdb=" P 6IY A 903 " pdb=" O4 6IY A 903 " ideal model delta sigma weight residual 123.06 100.61 22.45 3.00e+00 1.11e-01 5.60e+01 angle pdb=" O3 6IY C 902 " pdb=" P 6IY C 902 " pdb=" O4 6IY C 902 " ideal model delta sigma weight residual 123.06 100.73 22.33 3.00e+00 1.11e-01 5.54e+01 angle pdb=" O3 6IY A 902 " pdb=" P 6IY A 902 " pdb=" O4 6IY A 902 " ideal model delta sigma weight residual 123.06 100.86 22.20 3.00e+00 1.11e-01 5.48e+01 angle pdb=" O3 6IY C 904 " pdb=" P 6IY C 904 " pdb=" O4 6IY C 904 " ideal model delta sigma weight residual 123.06 102.01 21.05 3.00e+00 1.11e-01 4.92e+01 angle pdb=" C14 6IY C 902 " pdb=" C13 6IY C 902 " pdb=" O6 6IY C 902 " ideal model delta sigma weight residual 110.42 126.01 -15.59 3.00e+00 1.11e-01 2.70e+01 ... (remaining 24611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.24: 10390 28.24 - 56.49: 201 56.49 - 84.73: 47 84.73 - 112.98: 23 112.98 - 141.22: 3 Dihedral angle restraints: 10664 sinusoidal: 4344 harmonic: 6320 Sorted by residual: dihedral pdb=" CA PHE A 712 " pdb=" C PHE A 712 " pdb=" N LEU A 713 " pdb=" CA LEU A 713 " ideal model delta harmonic sigma weight residual 180.00 155.26 24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA VAL B 415 " pdb=" C VAL B 415 " pdb=" N GLU B 416 " pdb=" CA GLU B 416 " ideal model delta harmonic sigma weight residual -180.00 -156.61 -23.39 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA VAL C 415 " pdb=" C VAL C 415 " pdb=" N GLU C 416 " pdb=" CA GLU C 416 " ideal model delta harmonic sigma weight residual -180.00 -156.63 -23.37 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 10661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2510 0.087 - 0.174: 238 0.174 - 0.261: 0 0.261 - 0.348: 0 0.348 - 0.435: 4 Chirality restraints: 2752 Sorted by residual: chirality pdb=" CAO 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" CAR 6EU A 901 " pdb=" CAW 6EU A 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.67 0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CAO 6EU C 903 " pdb=" CAJ 6EU C 903 " pdb=" CAR 6EU C 903 " pdb=" CAW 6EU C 903 " both_signs ideal model delta sigma weight residual False -2.24 -2.67 0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" CAO 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAR 6EU B 901 " pdb=" CAW 6EU B 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.67 0.43 2.00e-01 2.50e+01 4.62e+00 ... (remaining 2749 not shown) Planarity restraints: 3020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 544 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C SER B 544 " 0.045 2.00e-02 2.50e+03 pdb=" O SER B 544 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU B 545 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 545 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.37e+00 pdb=" C LEU B 545 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU B 545 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 546 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 544 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.00e+00 pdb=" C SER A 544 " -0.042 2.00e-02 2.50e+03 pdb=" O SER A 544 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A 545 " 0.014 2.00e-02 2.50e+03 ... (remaining 3017 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 215 2.64 - 3.20: 16813 3.20 - 3.77: 26414 3.77 - 4.33: 36361 4.33 - 4.90: 61644 Nonbonded interactions: 141447 Sorted by model distance: nonbonded pdb=" OG1 THR C 731 " pdb=" OD1 ASP C 733 " model vdw 2.075 3.040 nonbonded pdb=" OG1 THR B 731 " pdb=" OD1 ASP B 733 " model vdw 2.093 3.040 nonbonded pdb=" OG1 THR A 731 " pdb=" OD1 ASP A 733 " model vdw 2.116 3.040 nonbonded pdb=" OG1 THR D 731 " pdb=" OD1 ASP D 733 " model vdw 2.128 3.040 nonbonded pdb=" O LYS C 688 " pdb=" NE2 GLN C 691 " model vdw 2.231 3.120 ... (remaining 141442 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 193 through 751) selection = (chain 'B' and resid 193 through 751) selection = (chain 'C' and resid 193 through 751) 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: 0.010 Normalize map: mean=0, sd=1: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.460 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 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 : 0.011 0.125 18168 Z= 0.500 Angle : 1.031 22.453 24616 Z= 0.510 Chirality : 0.053 0.435 2752 Planarity : 0.005 0.044 3020 Dihedral : 14.261 141.220 6608 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.47 % Allowed : 1.79 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.18), residues: 2136 helix: 1.51 (0.14), residues: 1248 sheet: -0.60 (0.55), residues: 64 loop : -1.34 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 739 TYR 0.037 0.003 TYR A 653 PHE 0.030 0.003 PHE A 712 TRP 0.013 0.002 TRP D 372 HIS 0.007 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.01108 / 0.50 (18168) covalent geometry : angle 1.03069 / 0.51 (24616) hydrogen bonds : bond 0.15828 / 10.56 ( 1002) hydrogen bonds : angle 5.23510 / 3.77 ( 2907) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 533 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 GLN cc_start: 0.8297 (mt0) cc_final: 0.7752 (mt0) REVERT: A 378 HIS cc_start: 0.7815 (p-80) cc_final: 0.6428 (p-80) REVERT: A 397 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8056 (mt-10) REVERT: A 506 LEU cc_start: 0.9123 (tp) cc_final: 0.8845 (tp) REVERT: A 650 THR cc_start: 0.8997 (p) cc_final: 0.8545 (m) REVERT: D 234 ASP cc_start: 0.8458 (m-30) cc_final: 0.8211 (p0) REVERT: D 389 THR cc_start: 0.8792 (m) cc_final: 0.8532 (p) REVERT: D 424 ASP cc_start: 0.8816 (t70) cc_final: 0.8289 (t0) REVERT: D 506 LEU cc_start: 0.9108 (tp) cc_final: 0.8870 (tp) REVERT: D 571 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8658 (mmtp) REVERT: D 740 TRP cc_start: 0.8549 (m100) cc_final: 0.8258 (m100) REVERT: B 253 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8330 (p) REVERT: B 378 HIS cc_start: 0.7967 (p-80) cc_final: 0.7123 (p-80) REVERT: B 389 THR cc_start: 0.8799 (m) cc_final: 0.8479 (p) REVERT: B 424 ASP cc_start: 0.8882 (t70) cc_final: 0.8548 (t70) REVERT: B 740 TRP cc_start: 0.8723 (m100) cc_final: 0.8245 (m100) REVERT: B 745 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: C 253 SER cc_start: 0.8708 (OUTLIER) cc_final: 0.8437 (p) REVERT: C 378 HIS cc_start: 0.7992 (p-80) cc_final: 0.7210 (p-80) REVERT: C 389 THR cc_start: 0.8859 (m) cc_final: 0.8629 (p) REVERT: C 506 LEU cc_start: 0.9133 (tp) cc_final: 0.8914 (tp) REVERT: C 571 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8594 (mmtt) REVERT: C 740 TRP cc_start: 0.8480 (m100) cc_final: 0.7758 (m100) outliers start: 9 outliers final: 0 residues processed: 541 average time/residue: 0.1576 time to fit residues: 124.3169 Evaluate side-chains 393 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 390 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain C residue 253 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 393 ASN A 700 GLN D 393 ASN B 206 HIS B 289 HIS B 393 ASN B 410 HIS C 393 ASN C 700 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.150562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.098786 restraints weight = 28918.252| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.63 r_work: 0.2946 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18168 Z= 0.153 Angle : 0.598 10.830 24616 Z= 0.313 Chirality : 0.039 0.149 2752 Planarity : 0.004 0.046 3020 Dihedral : 11.057 83.474 2540 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.32 % Allowed : 7.75 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.19), residues: 2136 helix: 2.37 (0.14), residues: 1292 sheet: -0.11 (0.54), residues: 64 loop : -1.24 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 355 TYR 0.021 0.001 TYR C 309 PHE 0.022 0.001 PHE A 712 TRP 0.013 0.001 TRP B 740 HIS 0.003 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (18168) covalent geometry : angle 0.59762 / 0.31 (24616) hydrogen bonds : bond 0.05786 / 3.90 ( 1002) hydrogen bonds : angle 3.93177 / 2.88 ( 2907) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 431 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8113 (p0) REVERT: A 378 HIS cc_start: 0.8114 (p-80) cc_final: 0.7908 (p-80) REVERT: A 397 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8229 (mt-10) REVERT: A 491 ARG cc_start: 0.8631 (mmm160) cc_final: 0.8376 (mmm160) REVERT: A 650 THR cc_start: 0.9264 (p) cc_final: 0.8836 (m) REVERT: D 234 ASP cc_start: 0.8547 (m-30) cc_final: 0.8111 (p0) REVERT: D 389 THR cc_start: 0.8769 (m) cc_final: 0.8432 (p) REVERT: D 424 ASP cc_start: 0.9107 (t70) cc_final: 0.8533 (t0) REVERT: D 578 CYS cc_start: 0.9149 (m) cc_final: 0.8876 (t) REVERT: D 740 TRP cc_start: 0.8347 (m100) cc_final: 0.8056 (m100) REVERT: B 374 TYR cc_start: 0.7285 (m-80) cc_final: 0.6643 (m-80) REVERT: B 389 THR cc_start: 0.8743 (m) cc_final: 0.8416 (p) REVERT: B 424 ASP cc_start: 0.9200 (t70) cc_final: 0.8821 (t70) REVERT: B 471 ASP cc_start: 0.8594 (m-30) cc_final: 0.8186 (t0) REVERT: B 694 LYS cc_start: 0.8903 (mtmt) cc_final: 0.8693 (tptt) REVERT: B 740 TRP cc_start: 0.8614 (m100) cc_final: 0.7910 (m100) REVERT: C 280 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7474 (ttm110) REVERT: C 389 THR cc_start: 0.8865 (m) cc_final: 0.8546 (p) REVERT: C 424 ASP cc_start: 0.9221 (t70) cc_final: 0.8852 (t0) REVERT: C 571 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8891 (mmtt) outliers start: 25 outliers final: 9 residues processed: 440 average time/residue: 0.1357 time to fit residues: 91.1225 Evaluate side-chains 388 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 377 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 716 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 193 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 183 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 228 GLN D 393 ASN D 700 GLN ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS B 700 GLN C 206 HIS C 410 HIS C 700 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.151222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.099816 restraints weight = 29552.690| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.70 r_work: 0.2955 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18168 Z= 0.150 Angle : 0.559 9.776 24616 Z= 0.290 Chirality : 0.039 0.181 2752 Planarity : 0.004 0.046 3020 Dihedral : 9.784 89.579 2536 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.64 % Allowed : 9.44 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.19), residues: 2136 helix: 2.71 (0.14), residues: 1288 sheet: 0.24 (0.55), residues: 64 loop : -1.29 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 499 TYR 0.013 0.001 TYR D 309 PHE 0.019 0.001 PHE A 712 TRP 0.009 0.001 TRP A 372 HIS 0.004 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (18168) covalent geometry : angle 0.55915 / 0.29 (24616) hydrogen bonds : bond 0.05015 / 3.36 ( 1002) hydrogen bonds : angle 3.74318 / 2.74 ( 2907) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 412 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.8760 (m-30) cc_final: 0.8166 (p0) REVERT: A 397 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8156 (mt-10) REVERT: A 491 ARG cc_start: 0.8650 (mmm160) cc_final: 0.8268 (mmm160) REVERT: A 494 GLN cc_start: 0.9024 (tt0) cc_final: 0.8608 (tm-30) REVERT: A 650 THR cc_start: 0.9265 (p) cc_final: 0.8876 (m) REVERT: D 234 ASP cc_start: 0.8468 (m-30) cc_final: 0.8090 (p0) REVERT: D 389 THR cc_start: 0.8782 (m) cc_final: 0.8436 (p) REVERT: D 424 ASP cc_start: 0.9177 (t70) cc_final: 0.8703 (t0) REVERT: D 466 LYS cc_start: 0.9185 (mtmm) cc_final: 0.8983 (mmtt) REVERT: D 471 ASP cc_start: 0.8709 (m-30) cc_final: 0.8374 (t0) REVERT: D 578 CYS cc_start: 0.9185 (m) cc_final: 0.8984 (t) REVERT: D 740 TRP cc_start: 0.8425 (m100) cc_final: 0.8077 (m100) REVERT: B 260 GLN cc_start: 0.6228 (mt0) cc_final: 0.5893 (mt0) REVERT: B 374 TYR cc_start: 0.7223 (m-80) cc_final: 0.6517 (m-80) REVERT: B 389 THR cc_start: 0.8704 (m) cc_final: 0.8342 (p) REVERT: B 405 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8513 (mp0) REVERT: B 424 ASP cc_start: 0.9208 (t70) cc_final: 0.8810 (t70) REVERT: B 471 ASP cc_start: 0.8568 (m-30) cc_final: 0.8175 (t0) REVERT: B 694 LYS cc_start: 0.8978 (mtmt) cc_final: 0.8610 (tptt) REVERT: B 740 TRP cc_start: 0.8641 (m100) cc_final: 0.7929 (m100) REVERT: C 288 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8476 (mt) REVERT: C 389 THR cc_start: 0.8842 (m) cc_final: 0.8503 (p) REVERT: C 471 ASP cc_start: 0.8817 (m-30) cc_final: 0.8573 (t0) REVERT: C 571 LYS cc_start: 0.9082 (mmtt) cc_final: 0.8847 (mmtt) outliers start: 31 outliers final: 13 residues processed: 422 average time/residue: 0.1299 time to fit residues: 84.5240 Evaluate side-chains 403 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 389 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 632 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 100 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 170 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 HIS D 270 ASN ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 HIS C 700 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.148415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.096585 restraints weight = 29478.653| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.68 r_work: 0.2906 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 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 : 0.006 0.058 18168 Z= 0.260 Angle : 0.611 10.086 24616 Z= 0.317 Chirality : 0.041 0.146 2752 Planarity : 0.004 0.042 3020 Dihedral : 9.718 87.734 2536 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.27 % Allowed : 11.02 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.19), residues: 2136 helix: 2.56 (0.14), residues: 1292 sheet: 0.31 (0.56), residues: 64 loop : -1.40 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 211 TYR 0.015 0.002 TYR D 584 PHE 0.015 0.001 PHE A 712 TRP 0.014 0.001 TRP D 372 HIS 0.011 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.26 (18168) covalent geometry : angle 0.61114 / 0.32 (24616) hydrogen bonds : bond 0.05639 / 3.78 ( 1002) hydrogen bonds : angle 3.93187 / 2.87 ( 2907) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 398 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8151 (p0) REVERT: A 429 PHE cc_start: 0.8024 (m-10) cc_final: 0.7746 (m-10) REVERT: A 491 ARG cc_start: 0.8692 (mmm160) cc_final: 0.8246 (mmm160) REVERT: A 494 GLN cc_start: 0.9098 (tt0) cc_final: 0.8664 (tm-30) REVERT: A 650 THR cc_start: 0.9275 (p) cc_final: 0.8887 (m) REVERT: D 234 ASP cc_start: 0.8503 (m-30) cc_final: 0.8108 (p0) REVERT: D 389 THR cc_start: 0.8865 (m) cc_final: 0.8535 (p) REVERT: D 424 ASP cc_start: 0.9167 (t70) cc_final: 0.8624 (t0) REVERT: D 466 LYS cc_start: 0.9158 (mtmm) cc_final: 0.8896 (mmtt) REVERT: D 471 ASP cc_start: 0.8731 (m-30) cc_final: 0.8380 (t0) REVERT: D 578 CYS cc_start: 0.9231 (m) cc_final: 0.8944 (t) REVERT: D 740 TRP cc_start: 0.8471 (m100) cc_final: 0.8069 (m100) REVERT: B 260 GLN cc_start: 0.6224 (mt0) cc_final: 0.5850 (mt0) REVERT: B 389 THR cc_start: 0.8766 (m) cc_final: 0.8435 (p) REVERT: B 405 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8464 (mp0) REVERT: B 424 ASP cc_start: 0.9208 (t70) cc_final: 0.8787 (t70) REVERT: B 471 ASP cc_start: 0.8553 (m-30) cc_final: 0.8100 (t0) REVERT: B 694 LYS cc_start: 0.9041 (mtmt) cc_final: 0.8697 (tptt) REVERT: B 740 TRP cc_start: 0.8669 (m100) cc_final: 0.8039 (m100) REVERT: C 211 ARG cc_start: 0.8610 (mmm160) cc_final: 0.8337 (mmm160) REVERT: C 288 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8576 (mt) REVERT: C 389 THR cc_start: 0.8877 (m) cc_final: 0.8585 (p) REVERT: C 471 ASP cc_start: 0.8811 (m-30) cc_final: 0.8591 (t0) REVERT: C 571 LYS cc_start: 0.9100 (mmtt) cc_final: 0.8827 (mmtt) outliers start: 43 outliers final: 29 residues processed: 417 average time/residue: 0.1250 time to fit residues: 80.6238 Evaluate side-chains 411 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 380 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 694 LYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 653 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 94 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 176 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 HIS ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 ASN B 700 GLN ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.150678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.099408 restraints weight = 29110.342| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.68 r_work: 0.2947 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 18168 Z= 0.145 Angle : 0.546 9.081 24616 Z= 0.283 Chirality : 0.038 0.146 2752 Planarity : 0.004 0.044 3020 Dihedral : 9.189 89.318 2536 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.85 % Allowed : 12.29 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.19), residues: 2136 helix: 2.70 (0.14), residues: 1268 sheet: 0.57 (0.59), residues: 64 loop : -1.30 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 717 TYR 0.012 0.001 TYR C 584 PHE 0.015 0.001 PHE A 266 TRP 0.012 0.001 TRP D 372 HIS 0.011 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (18168) covalent geometry : angle 0.54579 / 0.28 (24616) hydrogen bonds : bond 0.04744 / 3.18 ( 1002) hydrogen bonds : angle 3.78476 / 2.77 ( 2907) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 404 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8170 (p0) REVERT: A 308 MET cc_start: 0.9033 (mmm) cc_final: 0.8714 (mmm) REVERT: A 491 ARG cc_start: 0.8684 (mmm160) cc_final: 0.8385 (mmm160) REVERT: A 494 GLN cc_start: 0.9096 (tt0) cc_final: 0.8691 (tm-30) REVERT: A 650 THR cc_start: 0.9286 (p) cc_final: 0.8939 (m) REVERT: D 234 ASP cc_start: 0.8443 (m-30) cc_final: 0.8078 (p0) REVERT: D 389 THR cc_start: 0.8840 (m) cc_final: 0.8514 (p) REVERT: D 424 ASP cc_start: 0.9178 (t70) cc_final: 0.8705 (t0) REVERT: D 471 ASP cc_start: 0.8672 (m-30) cc_final: 0.8430 (t0) REVERT: D 740 TRP cc_start: 0.8427 (m100) cc_final: 0.8132 (m100) REVERT: B 260 GLN cc_start: 0.6094 (mt0) cc_final: 0.5740 (mt0) REVERT: B 324 LYS cc_start: 0.8283 (mttp) cc_final: 0.7874 (mtmt) REVERT: B 389 THR cc_start: 0.8749 (m) cc_final: 0.8401 (p) REVERT: B 405 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8534 (mp0) REVERT: B 412 MET cc_start: 0.9198 (mtp) cc_final: 0.8997 (mtp) REVERT: B 424 ASP cc_start: 0.9214 (t70) cc_final: 0.8786 (t70) REVERT: B 471 ASP cc_start: 0.8555 (m-30) cc_final: 0.8115 (t0) REVERT: B 740 TRP cc_start: 0.8636 (m100) cc_final: 0.7994 (m100) REVERT: C 211 ARG cc_start: 0.8600 (mmm160) cc_final: 0.8386 (mmm160) REVERT: C 288 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8484 (mt) REVERT: C 308 MET cc_start: 0.9280 (tpp) cc_final: 0.9003 (mpp) REVERT: C 389 THR cc_start: 0.8828 (m) cc_final: 0.8529 (p) REVERT: C 471 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8479 (t0) REVERT: C 494 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8558 (tm-30) REVERT: C 571 LYS cc_start: 0.9050 (mmtt) cc_final: 0.8807 (mmtt) outliers start: 35 outliers final: 22 residues processed: 411 average time/residue: 0.1206 time to fit residues: 76.9817 Evaluate side-chains 413 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 387 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 694 LYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 716 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 94 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 208 optimal weight: 6.9990 chunk 83 optimal weight: 0.4980 chunk 138 optimal weight: 0.7980 chunk 168 optimal weight: 8.9990 chunk 196 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 HIS ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.151478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.100451 restraints weight = 28946.289| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.65 r_work: 0.2962 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18168 Z= 0.124 Angle : 0.529 8.804 24616 Z= 0.273 Chirality : 0.038 0.151 2752 Planarity : 0.003 0.043 3020 Dihedral : 8.735 88.783 2536 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.06 % Allowed : 13.03 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.19), residues: 2136 helix: 2.83 (0.14), residues: 1268 sheet: 0.83 (0.62), residues: 64 loop : -1.24 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 499 TYR 0.011 0.001 TYR C 584 PHE 0.014 0.001 PHE A 712 TRP 0.012 0.001 TRP D 372 HIS 0.011 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (18168) covalent geometry : angle 0.52880 / 0.27 (24616) hydrogen bonds : bond 0.04378 / 2.93 ( 1002) hydrogen bonds : angle 3.69572 / 2.71 ( 2907) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 410 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8183 (p0) REVERT: A 308 MET cc_start: 0.8991 (mmm) cc_final: 0.8652 (mmm) REVERT: A 491 ARG cc_start: 0.8690 (mmm160) cc_final: 0.8365 (mmm160) REVERT: A 494 GLN cc_start: 0.9079 (tt0) cc_final: 0.8693 (tm-30) REVERT: A 499 ARG cc_start: 0.8221 (tpp80) cc_final: 0.7903 (tpp80) REVERT: A 650 THR cc_start: 0.9285 (p) cc_final: 0.8969 (m) REVERT: D 234 ASP cc_start: 0.8442 (m-30) cc_final: 0.8056 (p0) REVERT: D 389 THR cc_start: 0.8858 (m) cc_final: 0.8562 (p) REVERT: D 424 ASP cc_start: 0.9177 (t70) cc_final: 0.8811 (t70) REVERT: D 471 ASP cc_start: 0.8643 (m-30) cc_final: 0.8389 (t0) REVERT: D 494 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8575 (tm-30) REVERT: D 498 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8189 (tm-30) REVERT: D 740 TRP cc_start: 0.8388 (m100) cc_final: 0.8152 (m100) REVERT: B 260 GLN cc_start: 0.6279 (mt0) cc_final: 0.5847 (mt0) REVERT: B 324 LYS cc_start: 0.8261 (mttp) cc_final: 0.7835 (mtmt) REVERT: B 389 THR cc_start: 0.8712 (m) cc_final: 0.8366 (p) REVERT: B 405 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8519 (mp0) REVERT: B 424 ASP cc_start: 0.9220 (t70) cc_final: 0.8792 (t70) REVERT: B 471 ASP cc_start: 0.8519 (m-30) cc_final: 0.8060 (t0) REVERT: B 740 TRP cc_start: 0.8546 (m100) cc_final: 0.8049 (m100) REVERT: C 211 ARG cc_start: 0.8644 (mmm160) cc_final: 0.8440 (mmm160) REVERT: C 288 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8527 (mt) REVERT: C 389 THR cc_start: 0.8787 (m) cc_final: 0.8497 (p) REVERT: C 471 ASP cc_start: 0.8707 (m-30) cc_final: 0.8420 (t0) REVERT: C 494 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8642 (tm-30) REVERT: C 571 LYS cc_start: 0.9075 (mmtt) cc_final: 0.8843 (mmtt) outliers start: 39 outliers final: 24 residues processed: 422 average time/residue: 0.1215 time to fit residues: 79.7205 Evaluate side-chains 418 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 390 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 691 GLN Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 694 LYS Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 653 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 186 optimal weight: 9.9990 chunk 192 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 120 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 HIS A 560 GLN D 700 GLN ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 GLN C 700 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.152542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.101738 restraints weight = 29173.890| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.67 r_work: 0.2984 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 18168 Z= 0.110 Angle : 0.532 10.278 24616 Z= 0.271 Chirality : 0.037 0.162 2752 Planarity : 0.003 0.044 3020 Dihedral : 8.304 89.090 2536 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.00 % Allowed : 13.71 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.19), residues: 2136 helix: 2.83 (0.14), residues: 1268 sheet: 1.07 (0.64), residues: 64 loop : -1.16 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 499 TYR 0.012 0.001 TYR C 584 PHE 0.014 0.001 PHE A 266 TRP 0.012 0.001 TRP D 372 HIS 0.011 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (18168) covalent geometry : angle 0.53188 / 0.27 (24616) hydrogen bonds : bond 0.04057 / 2.71 ( 1002) hydrogen bonds : angle 3.66646 / 2.69 ( 2907) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 418 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8184 (p0) REVERT: A 294 VAL cc_start: 0.9054 (OUTLIER) cc_final: 0.8847 (p) REVERT: A 308 MET cc_start: 0.9029 (mmm) cc_final: 0.8657 (mmm) REVERT: A 460 LEU cc_start: 0.8532 (mt) cc_final: 0.8130 (pp) REVERT: A 491 ARG cc_start: 0.8660 (mmm160) cc_final: 0.8317 (mmm160) REVERT: A 494 GLN cc_start: 0.9066 (tt0) cc_final: 0.8686 (tm-30) REVERT: A 499 ARG cc_start: 0.8179 (tpp80) cc_final: 0.7844 (tpp80) REVERT: A 650 THR cc_start: 0.9241 (p) cc_final: 0.8941 (m) REVERT: D 234 ASP cc_start: 0.8422 (m-30) cc_final: 0.8050 (p0) REVERT: D 389 THR cc_start: 0.8854 (m) cc_final: 0.8555 (p) REVERT: D 424 ASP cc_start: 0.9159 (t70) cc_final: 0.8788 (t70) REVERT: D 471 ASP cc_start: 0.8633 (m-30) cc_final: 0.8378 (t0) REVERT: D 494 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8558 (tm-30) REVERT: D 740 TRP cc_start: 0.8342 (m100) cc_final: 0.8124 (m100) REVERT: B 260 GLN cc_start: 0.6192 (mt0) cc_final: 0.5806 (mt0) REVERT: B 324 LYS cc_start: 0.8236 (mttp) cc_final: 0.7806 (mtmt) REVERT: B 389 THR cc_start: 0.8702 (m) cc_final: 0.8336 (p) REVERT: B 405 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8528 (mp0) REVERT: B 424 ASP cc_start: 0.9216 (t70) cc_final: 0.8836 (t70) REVERT: B 542 VAL cc_start: 0.9419 (t) cc_final: 0.9165 (m) REVERT: B 740 TRP cc_start: 0.8487 (m100) cc_final: 0.7955 (m100) REVERT: C 211 ARG cc_start: 0.8713 (mmm160) cc_final: 0.8357 (mmm160) REVERT: C 288 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8447 (mt) REVERT: C 389 THR cc_start: 0.8813 (m) cc_final: 0.8529 (p) REVERT: C 471 ASP cc_start: 0.8668 (m-30) cc_final: 0.8401 (t0) REVERT: C 494 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8651 (tm-30) REVERT: C 498 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8108 (tm-30) REVERT: C 571 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8774 (mmtt) outliers start: 38 outliers final: 23 residues processed: 431 average time/residue: 0.1151 time to fit residues: 77.4643 Evaluate side-chains 424 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 396 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 691 GLN Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 694 LYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 716 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 62 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 190 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 HIS A 700 GLN ** D 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN D 700 GLN ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN C 700 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.151514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.100723 restraints weight = 29027.039| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.64 r_work: 0.2966 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 18168 Z= 0.139 Angle : 0.561 10.031 24616 Z= 0.287 Chirality : 0.038 0.162 2752 Planarity : 0.003 0.043 3020 Dihedral : 8.161 89.478 2536 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.16 % Allowed : 14.50 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.19), residues: 2136 helix: 2.80 (0.14), residues: 1268 sheet: 1.02 (0.65), residues: 64 loop : -1.16 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 575 TYR 0.012 0.001 TYR C 584 PHE 0.011 0.001 PHE A 712 TRP 0.013 0.001 TRP D 372 HIS 0.011 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (18168) covalent geometry : angle 0.56059 / 0.29 (24616) hydrogen bonds : bond 0.04303 / 2.88 ( 1002) hydrogen bonds : angle 3.75755 / 2.75 ( 2907) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 399 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8184 (p0) REVERT: A 460 LEU cc_start: 0.8492 (mt) cc_final: 0.8116 (pp) REVERT: A 491 ARG cc_start: 0.8651 (mmm160) cc_final: 0.8159 (mmm160) REVERT: A 494 GLN cc_start: 0.9061 (tt0) cc_final: 0.8707 (tm-30) REVERT: A 650 THR cc_start: 0.9238 (p) cc_final: 0.8944 (m) REVERT: D 234 ASP cc_start: 0.8445 (m-30) cc_final: 0.8056 (p0) REVERT: D 389 THR cc_start: 0.8844 (m) cc_final: 0.8554 (p) REVERT: D 424 ASP cc_start: 0.9166 (t70) cc_final: 0.8793 (t70) REVERT: D 465 LEU cc_start: 0.8776 (tp) cc_final: 0.7517 (tt) REVERT: D 471 ASP cc_start: 0.8644 (m-30) cc_final: 0.8071 (t0) REVERT: D 494 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8583 (tm-30) REVERT: D 498 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8391 (tm-30) REVERT: D 740 TRP cc_start: 0.8372 (m100) cc_final: 0.8119 (m100) REVERT: B 260 GLN cc_start: 0.6244 (mt0) cc_final: 0.5858 (mt0) REVERT: B 324 LYS cc_start: 0.8232 (mttp) cc_final: 0.7800 (mtmt) REVERT: B 389 THR cc_start: 0.8729 (m) cc_final: 0.8377 (p) REVERT: B 405 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8510 (mp0) REVERT: B 424 ASP cc_start: 0.9216 (t70) cc_final: 0.8789 (t70) REVERT: B 471 ASP cc_start: 0.8614 (m-30) cc_final: 0.8401 (t0) REVERT: B 694 LYS cc_start: 0.8886 (mtmm) cc_final: 0.8372 (tptt) REVERT: B 740 TRP cc_start: 0.8555 (m100) cc_final: 0.8022 (m100) REVERT: C 211 ARG cc_start: 0.8697 (mmm160) cc_final: 0.8328 (mmm160) REVERT: C 260 GLN cc_start: 0.6758 (OUTLIER) cc_final: 0.6471 (mm-40) REVERT: C 288 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8438 (mt) REVERT: C 310 ASN cc_start: 0.9187 (t0) cc_final: 0.8976 (m-40) REVERT: C 389 THR cc_start: 0.8839 (m) cc_final: 0.8565 (p) REVERT: C 471 ASP cc_start: 0.8627 (m-30) cc_final: 0.8397 (t0) REVERT: C 494 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8702 (tm-30) REVERT: C 499 ARG cc_start: 0.8206 (tpp80) cc_final: 0.7951 (tpp80) REVERT: C 571 LYS cc_start: 0.9024 (mmtt) cc_final: 0.8779 (mmtt) outliers start: 41 outliers final: 29 residues processed: 415 average time/residue: 0.1242 time to fit residues: 80.0815 Evaluate side-chains 425 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 391 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 691 GLN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 694 LYS Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 716 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 59 optimal weight: 0.6980 chunk 179 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 173 optimal weight: 3.9990 chunk 109 optimal weight: 0.0870 chunk 197 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 181 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 HIS ** D 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN C 700 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.153239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.102366 restraints weight = 29026.114| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.68 r_work: 0.2992 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 18168 Z= 0.108 Angle : 0.557 10.796 24616 Z= 0.284 Chirality : 0.038 0.201 2752 Planarity : 0.003 0.046 3020 Dihedral : 7.894 89.063 2536 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.95 % Allowed : 14.61 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.19), residues: 2136 helix: 2.85 (0.14), residues: 1264 sheet: 1.11 (0.65), residues: 64 loop : -1.13 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 499 TYR 0.012 0.001 TYR C 738 PHE 0.011 0.001 PHE A 266 TRP 0.011 0.001 TRP D 372 HIS 0.012 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (18168) covalent geometry : angle 0.55666 / 0.28 (24616) hydrogen bonds : bond 0.03964 / 2.65 ( 1002) hydrogen bonds : angle 3.71095 / 2.72 ( 2907) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 413 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8181 (p0) REVERT: A 308 MET cc_start: 0.8973 (mmm) cc_final: 0.8714 (mmm) REVERT: A 460 LEU cc_start: 0.8517 (mt) cc_final: 0.8154 (pp) REVERT: A 491 ARG cc_start: 0.8661 (mmm160) cc_final: 0.8321 (mmm160) REVERT: A 494 GLN cc_start: 0.9064 (tt0) cc_final: 0.8720 (tm-30) REVERT: A 650 THR cc_start: 0.9222 (p) cc_final: 0.8954 (m) REVERT: D 234 ASP cc_start: 0.8435 (m-30) cc_final: 0.8055 (p0) REVERT: D 389 THR cc_start: 0.8839 (m) cc_final: 0.8563 (p) REVERT: D 424 ASP cc_start: 0.9166 (t70) cc_final: 0.8794 (t70) REVERT: D 465 LEU cc_start: 0.8766 (tp) cc_final: 0.7555 (tt) REVERT: D 471 ASP cc_start: 0.8625 (m-30) cc_final: 0.8067 (t0) REVERT: D 494 GLN cc_start: 0.8947 (tt0) cc_final: 0.8603 (tm-30) REVERT: D 498 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8422 (tm-30) REVERT: D 740 TRP cc_start: 0.8330 (m100) cc_final: 0.8129 (m100) REVERT: B 324 LYS cc_start: 0.8237 (mttp) cc_final: 0.7798 (mtmt) REVERT: B 389 THR cc_start: 0.8707 (m) cc_final: 0.8355 (p) REVERT: B 405 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8529 (mp0) REVERT: B 424 ASP cc_start: 0.9226 (t70) cc_final: 0.8821 (t70) REVERT: B 471 ASP cc_start: 0.8551 (m-30) cc_final: 0.8273 (t0) REVERT: B 498 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8484 (tm-30) REVERT: B 542 VAL cc_start: 0.9426 (t) cc_final: 0.9209 (m) REVERT: B 694 LYS cc_start: 0.8806 (mtmm) cc_final: 0.8345 (tptt) REVERT: B 739 ARG cc_start: 0.6851 (mtt180) cc_final: 0.6604 (mtt180) REVERT: B 740 TRP cc_start: 0.8525 (m100) cc_final: 0.8035 (m100) REVERT: C 211 ARG cc_start: 0.8708 (mmm160) cc_final: 0.8350 (mmm160) REVERT: C 260 GLN cc_start: 0.6723 (OUTLIER) cc_final: 0.6369 (mm-40) REVERT: C 288 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8499 (mt) REVERT: C 389 THR cc_start: 0.8841 (m) cc_final: 0.8565 (p) REVERT: C 471 ASP cc_start: 0.8621 (m-30) cc_final: 0.8392 (t0) REVERT: C 494 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8697 (tm-30) REVERT: C 498 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8128 (tm-30) REVERT: C 571 LYS cc_start: 0.9048 (mmtt) cc_final: 0.8815 (mmtt) REVERT: C 740 TRP cc_start: 0.8520 (m100) cc_final: 0.7578 (m100) outliers start: 37 outliers final: 25 residues processed: 423 average time/residue: 0.1225 time to fit residues: 80.9771 Evaluate side-chains 428 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 399 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 691 GLN Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 694 LYS Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 653 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 187 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 HIS ** D 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN C 700 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.152087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.101385 restraints weight = 29064.303| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.66 r_work: 0.2973 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18168 Z= 0.140 Angle : 0.579 10.499 24616 Z= 0.297 Chirality : 0.039 0.235 2752 Planarity : 0.003 0.042 3020 Dihedral : 7.822 89.537 2536 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.00 % Allowed : 14.77 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.19), residues: 2136 helix: 2.82 (0.14), residues: 1264 sheet: 1.03 (0.64), residues: 64 loop : -1.16 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 499 TYR 0.013 0.001 TYR C 584 PHE 0.010 0.001 PHE A 712 TRP 0.011 0.001 TRP D 372 HIS 0.012 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (18168) covalent geometry : angle 0.57941 / 0.30 (24616) hydrogen bonds : bond 0.04305 / 2.88 ( 1002) hydrogen bonds : angle 3.79113 / 2.78 ( 2907) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 407 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8157 (p0) REVERT: A 308 MET cc_start: 0.9024 (mmm) cc_final: 0.8765 (mmm) REVERT: A 460 LEU cc_start: 0.8536 (mt) cc_final: 0.8165 (pp) REVERT: A 491 ARG cc_start: 0.8661 (mmm160) cc_final: 0.8171 (mmm160) REVERT: A 494 GLN cc_start: 0.9117 (tt0) cc_final: 0.8801 (tm-30) REVERT: A 650 THR cc_start: 0.9233 (p) cc_final: 0.8965 (m) REVERT: D 234 ASP cc_start: 0.8430 (m-30) cc_final: 0.8054 (p0) REVERT: D 389 THR cc_start: 0.8865 (m) cc_final: 0.8608 (p) REVERT: D 424 ASP cc_start: 0.9176 (t70) cc_final: 0.8809 (t70) REVERT: D 465 LEU cc_start: 0.8765 (tp) cc_final: 0.7538 (tt) REVERT: D 471 ASP cc_start: 0.8640 (m-30) cc_final: 0.8079 (t0) REVERT: D 494 GLN cc_start: 0.8967 (tt0) cc_final: 0.8620 (tm-30) REVERT: D 498 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8367 (tm-30) REVERT: D 740 TRP cc_start: 0.8366 (m100) cc_final: 0.8136 (m100) REVERT: B 324 LYS cc_start: 0.8248 (mttp) cc_final: 0.7805 (mtmt) REVERT: B 389 THR cc_start: 0.8743 (m) cc_final: 0.8401 (p) REVERT: B 405 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8502 (mp0) REVERT: B 424 ASP cc_start: 0.9227 (t70) cc_final: 0.8810 (t70) REVERT: B 471 ASP cc_start: 0.8598 (m-30) cc_final: 0.8358 (t0) REVERT: B 498 GLN cc_start: 0.8729 (tm-30) cc_final: 0.8522 (tm-30) REVERT: B 694 LYS cc_start: 0.8800 (mtmm) cc_final: 0.8355 (tptt) REVERT: B 739 ARG cc_start: 0.6910 (mtt180) cc_final: 0.6680 (mtt180) REVERT: B 740 TRP cc_start: 0.8522 (m100) cc_final: 0.8128 (m100) REVERT: C 211 ARG cc_start: 0.8687 (mmm160) cc_final: 0.8329 (mmm160) REVERT: C 260 GLN cc_start: 0.6887 (OUTLIER) cc_final: 0.6525 (mm-40) REVERT: C 288 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8502 (mt) REVERT: C 389 THR cc_start: 0.8844 (m) cc_final: 0.8568 (p) REVERT: C 471 ASP cc_start: 0.8614 (m-30) cc_final: 0.8373 (t0) REVERT: C 494 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8734 (tm-30) REVERT: C 498 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8198 (tm-30) REVERT: C 571 LYS cc_start: 0.9052 (mmtt) cc_final: 0.8812 (mmtt) REVERT: C 740 TRP cc_start: 0.8465 (m100) cc_final: 0.7548 (m100) outliers start: 38 outliers final: 30 residues processed: 420 average time/residue: 0.1184 time to fit residues: 78.0935 Evaluate side-chains 431 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 397 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 691 GLN Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 694 LYS Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 653 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 14 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 165 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 HIS ** D 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN C 700 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.152744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.102221 restraints weight = 29087.430| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.67 r_work: 0.2989 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18168 Z= 0.121 Angle : 0.578 10.666 24616 Z= 0.295 Chirality : 0.039 0.229 2752 Planarity : 0.003 0.046 3020 Dihedral : 7.654 88.621 2536 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.79 % Allowed : 15.45 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.19), residues: 2136 helix: 2.81 (0.14), residues: 1264 sheet: 1.11 (0.64), residues: 64 loop : -1.15 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 499 TYR 0.014 0.001 TYR B 738 PHE 0.011 0.001 PHE A 266 TRP 0.013 0.001 TRP D 372 HIS 0.013 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (18168) covalent geometry : angle 0.57835 / 0.29 (24616) hydrogen bonds : bond 0.04136 / 2.77 ( 1002) hydrogen bonds : angle 3.77764 / 2.77 ( 2907) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4575.70 seconds wall clock time: 79 minutes 7.36 seconds (4747.36 seconds total)