Starting phenix.real_space_refine on Wed Apr 30 22:51:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q7y_18244/04_2025/8q7y_18244.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q7y_18244/04_2025/8q7y_18244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q7y_18244/04_2025/8q7y_18244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q7y_18244/04_2025/8q7y_18244.map" model { file = "/net/cci-nas-00/data/ceres_data/8q7y_18244/04_2025/8q7y_18244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q7y_18244/04_2025/8q7y_18244.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 6412 2.51 5 N 1824 2.21 5 O 1736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10032 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2508 Classifications: {'peptide': 303} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 284} Chain breaks: 11 Restraints were copied for chains: C, B, D Time building chain proxies: 6.07, per 1000 atoms: 0.61 Number of scatterers: 10032 At special positions: 0 Unit cell: (126.99, 87.15, 80.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1736 8.00 N 1824 7.00 C 6412 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: 2.30 Conformation dependent library (CDL) restraints added in 1.0 seconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 20 sheets defined 34.7% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 192 through 196 removed outlier: 3.549A pdb=" N TYR A 196 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 368 through 382 removed outlier: 3.603A pdb=" N MET A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 406 removed outlier: 3.909A pdb=" N TYR A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 426 removed outlier: 3.942A pdb=" N LEU A 426 " --> pdb=" O MET A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 448 removed outlier: 3.701A pdb=" N ARG A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 479 removed outlier: 3.575A pdb=" N LEU A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 548 through 559 Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.550A pdb=" N TYR B 196 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 368 through 382 removed outlier: 3.602A pdb=" N MET B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 406 removed outlier: 3.909A pdb=" N TYR B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 removed outlier: 3.942A pdb=" N LEU B 426 " --> pdb=" O MET B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 448 removed outlier: 3.701A pdb=" N ARG B 442 " --> pdb=" O GLU B 438 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 479 removed outlier: 3.575A pdb=" N LEU B 471 " --> pdb=" O ASN B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 548 through 559 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 192 through 196 removed outlier: 3.550A pdb=" N TYR C 196 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 368 through 382 removed outlier: 3.603A pdb=" N MET C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 406 removed outlier: 3.908A pdb=" N TYR C 399 " --> pdb=" O HIS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 426 removed outlier: 3.943A pdb=" N LEU C 426 " --> pdb=" O MET C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 448 removed outlier: 3.701A pdb=" N ARG C 442 " --> pdb=" O GLU C 438 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 479 removed outlier: 3.576A pdb=" N LEU C 471 " --> pdb=" O ASN C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 548 through 559 Processing helix chain 'C' and resid 618 through 624 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 192 through 196 removed outlier: 3.549A pdb=" N TYR D 196 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 341 Processing helix chain 'D' and resid 368 through 382 removed outlier: 3.602A pdb=" N MET D 372 " --> pdb=" O ASP D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 406 removed outlier: 3.908A pdb=" N TYR D 399 " --> pdb=" O HIS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 426 removed outlier: 3.943A pdb=" N LEU D 426 " --> pdb=" O MET D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 448 removed outlier: 3.702A pdb=" N ARG D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 479 removed outlier: 3.575A pdb=" N LEU D 471 " --> pdb=" O ASN D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 548 through 559 Processing helix chain 'D' and resid 618 through 624 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 89 removed outlier: 3.796A pdb=" N ILE A 208 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 199 Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 336 Processing sheet with id=AA5, first strand: chain 'A' and resid 351 through 356 removed outlier: 3.647A pdb=" N ALA A 386 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU A 412 " --> pdb=" O CYS A 389 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL A 409 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N SER A 457 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP A 411 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLN A 485 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TRP A 456 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 498 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE A 499 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N CYS A 536 " --> pdb=" O ILE A 499 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU A 533 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N PHE A 566 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU A 535 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AA7, first strand: chain 'B' and resid 88 through 89 removed outlier: 3.794A pdb=" N ILE B 208 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 198 through 199 Processing sheet with id=AA9, first strand: chain 'B' and resid 335 through 336 Processing sheet with id=AB1, first strand: chain 'B' and resid 351 through 356 removed outlier: 3.647A pdb=" N ALA B 386 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU B 412 " --> pdb=" O CYS B 389 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL B 409 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N SER B 457 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASP B 411 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N GLN B 485 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TRP B 456 " --> pdb=" O GLN B 485 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 498 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE B 499 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N CYS B 536 " --> pdb=" O ILE B 499 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU B 533 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N PHE B 566 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU B 535 " --> pdb=" O PHE B 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 23 through 24 Processing sheet with id=AB3, first strand: chain 'C' and resid 88 through 89 removed outlier: 3.795A pdb=" N ILE C 208 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 198 through 199 Processing sheet with id=AB5, first strand: chain 'C' and resid 335 through 336 Processing sheet with id=AB6, first strand: chain 'C' and resid 351 through 356 removed outlier: 3.645A pdb=" N ALA C 386 " --> pdb=" O ARG C 352 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU C 412 " --> pdb=" O CYS C 389 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL C 409 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N SER C 457 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP C 411 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N GLN C 485 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TRP C 456 " --> pdb=" O GLN C 485 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 498 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE C 499 " --> pdb=" O ILE C 534 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N CYS C 536 " --> pdb=" O ILE C 499 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU C 533 " --> pdb=" O GLY C 564 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N PHE C 566 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU C 535 " --> pdb=" O PHE C 566 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 23 through 24 Processing sheet with id=AB8, first strand: chain 'D' and resid 88 through 89 removed outlier: 3.795A pdb=" N ILE D 208 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 198 through 199 Processing sheet with id=AC1, first strand: chain 'D' and resid 335 through 336 Processing sheet with id=AC2, first strand: chain 'D' and resid 351 through 356 removed outlier: 3.646A pdb=" N ALA D 386 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU D 412 " --> pdb=" O CYS D 389 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL D 409 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N SER D 457 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP D 411 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLN D 485 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TRP D 456 " --> pdb=" O GLN D 485 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 498 " --> pdb=" O VAL D 484 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE D 499 " --> pdb=" O ILE D 534 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N CYS D 536 " --> pdb=" O ILE D 499 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU D 533 " --> pdb=" O GLY D 564 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N PHE D 566 " --> pdb=" O LEU D 533 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU D 535 " --> pdb=" O PHE D 566 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 780 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: 2.96 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3279 1.34 - 1.46: 2431 1.46 - 1.58: 4502 1.58 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 10316 Sorted by residual: bond pdb=" CB ARG C 473 " pdb=" CG ARG C 473 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.88e+00 bond pdb=" CB ARG B 473 " pdb=" CG ARG B 473 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.84e+00 bond pdb=" CB ARG A 473 " pdb=" CG ARG A 473 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.78e+00 bond pdb=" CB ARG D 473 " pdb=" CG ARG D 473 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.71e+00 bond pdb=" CD ARG D 473 " pdb=" NE ARG D 473 " ideal model delta sigma weight residual 1.458 1.443 0.015 1.40e-02 5.10e+03 1.09e+00 ... (remaining 10311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 13717 2.19 - 4.38: 193 4.38 - 6.58: 30 6.58 - 8.77: 16 8.77 - 10.96: 4 Bond angle restraints: 13960 Sorted by residual: angle pdb=" C TYR A 472 " pdb=" N ARG A 473 " pdb=" CA ARG A 473 " ideal model delta sigma weight residual 122.38 113.87 8.51 1.81e+00 3.05e-01 2.21e+01 angle pdb=" C TYR C 472 " pdb=" N ARG C 473 " pdb=" CA ARG C 473 " ideal model delta sigma weight residual 122.38 113.93 8.45 1.81e+00 3.05e-01 2.18e+01 angle pdb=" C TYR B 472 " pdb=" N ARG B 473 " pdb=" CA ARG B 473 " ideal model delta sigma weight residual 122.38 113.96 8.42 1.81e+00 3.05e-01 2.17e+01 angle pdb=" C TYR D 472 " pdb=" N ARG D 473 " pdb=" CA ARG D 473 " ideal model delta sigma weight residual 122.38 113.96 8.42 1.81e+00 3.05e-01 2.16e+01 angle pdb=" N PRO C 480 " pdb=" CD PRO C 480 " pdb=" CG PRO C 480 " ideal model delta sigma weight residual 103.20 96.74 6.46 1.50e+00 4.44e-01 1.85e+01 ... (remaining 13955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4943 17.72 - 35.43: 689 35.43 - 53.15: 246 53.15 - 70.87: 74 70.87 - 88.58: 16 Dihedral angle restraints: 5968 sinusoidal: 2492 harmonic: 3476 Sorted by residual: dihedral pdb=" CA ARG C 473 " pdb=" C ARG C 473 " pdb=" N TRP C 474 " pdb=" CA TRP C 474 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ARG D 473 " pdb=" C ARG D 473 " pdb=" N TRP D 474 " pdb=" CA TRP D 474 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ARG A 473 " pdb=" C ARG A 473 " pdb=" N TRP A 474 " pdb=" CA TRP A 474 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 5965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 781 0.026 - 0.051: 327 0.051 - 0.077: 142 0.077 - 0.103: 106 0.103 - 0.128: 56 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA ILE C 415 " pdb=" N ILE C 415 " pdb=" C ILE C 415 " pdb=" CB ILE C 415 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA ILE B 415 " pdb=" N ILE B 415 " pdb=" C ILE B 415 " pdb=" CB ILE B 415 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE A 415 " pdb=" N ILE A 415 " pdb=" C ILE A 415 " pdb=" CB ILE A 415 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 1409 not shown) Planarity restraints: 1780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 63 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO C 64 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 63 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO D 64 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 64 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 64 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 63 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO A 64 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " -0.018 5.00e-02 4.00e+02 ... (remaining 1777 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 164 2.64 - 3.21: 8427 3.21 - 3.77: 16021 3.77 - 4.34: 23289 4.34 - 4.90: 36076 Nonbonded interactions: 83977 Sorted by model distance: nonbonded pdb=" NH2 ARG C 473 " pdb=" O ASP D 469 " model vdw 2.081 3.120 nonbonded pdb=" O ASP C 469 " pdb=" NH2 ARG D 473 " model vdw 2.085 3.120 nonbonded pdb=" NH2 ARG A 473 " pdb=" O ASP B 469 " model vdw 2.096 3.120 nonbonded pdb=" O ASP A 469 " pdb=" NH2 ARG B 473 " model vdw 2.099 3.120 nonbonded pdb=" OD2 ASP D 368 " pdb=" OG1 THR D 371 " model vdw 2.137 3.040 ... (remaining 83972 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.800 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10316 Z= 0.133 Angle : 0.685 10.959 13960 Z= 0.371 Chirality : 0.044 0.128 1412 Planarity : 0.005 0.033 1780 Dihedral : 19.409 88.583 3712 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.87 % Allowed : 27.64 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.23), residues: 1116 helix: 0.19 (0.28), residues: 316 sheet: -0.19 (0.58), residues: 64 loop : -1.26 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 568 HIS 0.003 0.001 HIS C 357 PHE 0.003 0.001 PHE B 566 TYR 0.021 0.001 TYR B 472 ARG 0.007 0.001 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.21109 ( 296) hydrogen bonds : angle 8.38449 ( 780) covalent geometry : bond 0.00308 (10316) covalent geometry : angle 0.68507 (13960) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 1.146 Fit side-chains outliers start: 41 outliers final: 28 residues processed: 236 average time/residue: 1.5128 time to fit residues: 377.6931 Evaluate side-chains 214 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 500 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN C 381 GLN ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.211580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.188530 restraints weight = 8532.795| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 0.98 r_work: 0.3510 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 10316 Z= 0.219 Angle : 0.774 12.292 13960 Z= 0.400 Chirality : 0.052 0.252 1412 Planarity : 0.007 0.077 1780 Dihedral : 8.510 58.228 1364 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 7.83 % Allowed : 25.47 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.23), residues: 1116 helix: 0.35 (0.28), residues: 316 sheet: -0.05 (0.60), residues: 64 loop : -1.09 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 553 HIS 0.006 0.002 HIS D 395 PHE 0.008 0.001 PHE C 566 TYR 0.015 0.002 TYR B 559 ARG 0.005 0.001 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.06087 ( 296) hydrogen bonds : angle 6.14743 ( 780) covalent geometry : bond 0.00506 (10316) covalent geometry : angle 0.77426 (13960) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 187 time to evaluate : 1.280 Fit side-chains REVERT: A 17 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.5454 (mt-10) REVERT: A 418 HIS cc_start: 0.5845 (OUTLIER) cc_final: 0.5511 (p-80) REVERT: A 439 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8729 (mtt-85) REVERT: B 17 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.5477 (mt-10) REVERT: B 418 HIS cc_start: 0.5807 (OUTLIER) cc_final: 0.5529 (p-80) REVERT: B 439 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8751 (mtt-85) REVERT: C 17 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.5470 (mt-10) REVERT: C 333 ARG cc_start: 0.5600 (OUTLIER) cc_final: 0.5078 (ptp-170) REVERT: C 418 HIS cc_start: 0.5797 (OUTLIER) cc_final: 0.5546 (p-80) REVERT: C 439 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8739 (mtt-85) REVERT: D 17 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.5453 (mt-10) REVERT: D 418 HIS cc_start: 0.5830 (OUTLIER) cc_final: 0.5538 (p-80) REVERT: D 439 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8735 (mtt-85) REVERT: D 551 LYS cc_start: 0.6934 (mtpp) cc_final: 0.6492 (mttp) outliers start: 83 outliers final: 32 residues processed: 248 average time/residue: 1.6627 time to fit residues: 436.4543 Evaluate side-chains 219 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 520 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 0.0870 chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 381 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN ** D 563 GLN ** 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 = 0.4251 r_free = 0.4251 target = 0.213969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.188893 restraints weight = 8589.052| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.21 r_work: 0.3534 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10316 Z= 0.143 Angle : 0.657 7.560 13960 Z= 0.335 Chirality : 0.047 0.129 1412 Planarity : 0.005 0.048 1780 Dihedral : 6.421 57.560 1332 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 7.64 % Allowed : 24.34 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.23), residues: 1116 helix: 0.49 (0.28), residues: 320 sheet: 0.01 (0.60), residues: 64 loop : -1.08 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 553 HIS 0.004 0.001 HIS B 395 PHE 0.005 0.001 PHE A 150 TYR 0.013 0.001 TYR B 559 ARG 0.008 0.001 ARG B 473 Details of bonding type rmsd hydrogen bonds : bond 0.04638 ( 296) hydrogen bonds : angle 5.59004 ( 780) covalent geometry : bond 0.00331 (10316) covalent geometry : angle 0.65668 (13960) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 205 time to evaluate : 1.098 Fit side-chains REVERT: A 17 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.5437 (mt-10) REVERT: A 336 ARG cc_start: 0.6641 (mmt-90) cc_final: 0.5956 (mmm160) REVERT: A 365 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.6911 (mt0) REVERT: A 418 HIS cc_start: 0.5573 (OUTLIER) cc_final: 0.5208 (p-80) REVERT: A 420 MET cc_start: 0.7426 (mmm) cc_final: 0.7013 (mmm) REVERT: A 439 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8768 (mtt-85) REVERT: B 17 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.5433 (mt-10) REVERT: B 336 ARG cc_start: 0.6662 (mmt-90) cc_final: 0.5971 (mmm160) REVERT: B 365 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.6903 (mt0) REVERT: B 418 HIS cc_start: 0.5495 (OUTLIER) cc_final: 0.5135 (p-80) REVERT: B 420 MET cc_start: 0.7432 (mmm) cc_final: 0.7037 (mmm) REVERT: B 439 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8771 (mtt-85) REVERT: C 333 ARG cc_start: 0.5448 (OUTLIER) cc_final: 0.5007 (ptp-170) REVERT: C 336 ARG cc_start: 0.6654 (mmt-90) cc_final: 0.5971 (mmm160) REVERT: C 365 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.6915 (mt0) REVERT: C 418 HIS cc_start: 0.5556 (OUTLIER) cc_final: 0.5227 (p-80) REVERT: C 420 MET cc_start: 0.7393 (mmm) cc_final: 0.6957 (mmm) REVERT: C 439 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8765 (mtt-85) REVERT: D 336 ARG cc_start: 0.6651 (mmt-90) cc_final: 0.5975 (mmm160) REVERT: D 365 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.6935 (mt0) REVERT: D 418 HIS cc_start: 0.5609 (OUTLIER) cc_final: 0.5234 (p-80) REVERT: D 420 MET cc_start: 0.7418 (mmm) cc_final: 0.6985 (mmm) REVERT: D 439 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8767 (mtt-85) outliers start: 81 outliers final: 28 residues processed: 264 average time/residue: 1.4205 time to fit residues: 397.9982 Evaluate side-chains 239 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 520 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 3 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.212023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.198339 restraints weight = 8425.712| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 0.50 r_work: 0.3812 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10316 Z= 0.163 Angle : 0.647 6.650 13960 Z= 0.332 Chirality : 0.047 0.144 1412 Planarity : 0.005 0.033 1780 Dihedral : 5.642 44.361 1328 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 7.36 % Allowed : 26.04 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.23), residues: 1116 helix: 0.43 (0.27), residues: 320 sheet: -0.28 (0.58), residues: 64 loop : -1.13 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 553 HIS 0.005 0.001 HIS A 395 PHE 0.006 0.001 PHE C 566 TYR 0.011 0.002 TYR B 559 ARG 0.006 0.001 ARG B 473 Details of bonding type rmsd hydrogen bonds : bond 0.04773 ( 296) hydrogen bonds : angle 5.35395 ( 780) covalent geometry : bond 0.00381 (10316) covalent geometry : angle 0.64737 (13960) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 195 time to evaluate : 1.196 Fit side-chains REVERT: A 17 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.5379 (mt-10) REVERT: A 336 ARG cc_start: 0.6896 (mmt-90) cc_final: 0.6638 (mmm160) REVERT: A 365 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7070 (mt0) REVERT: A 418 HIS cc_start: 0.6033 (OUTLIER) cc_final: 0.5813 (p-80) REVERT: A 420 MET cc_start: 0.7624 (mmm) cc_final: 0.7270 (mmm) REVERT: A 439 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8693 (mtt-85) REVERT: A 497 ASP cc_start: 0.8176 (m-30) cc_final: 0.7943 (m-30) REVERT: A 537 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: B 17 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.5371 (mt-10) REVERT: B 365 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7081 (mt0) REVERT: B 418 HIS cc_start: 0.6015 (OUTLIER) cc_final: 0.5785 (p-80) REVERT: B 420 MET cc_start: 0.7651 (mmm) cc_final: 0.7306 (mmm) REVERT: B 439 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8691 (mtt-85) REVERT: B 537 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: C 17 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.5374 (mt-10) REVERT: C 333 ARG cc_start: 0.5557 (OUTLIER) cc_final: 0.5154 (ptp-170) REVERT: C 336 ARG cc_start: 0.6857 (mmt-90) cc_final: 0.6639 (mmm160) REVERT: C 365 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7079 (mt0) REVERT: C 418 HIS cc_start: 0.6016 (OUTLIER) cc_final: 0.5773 (p-80) REVERT: C 420 MET cc_start: 0.7615 (mmm) cc_final: 0.7232 (mmm) REVERT: C 439 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8690 (mtt-85) REVERT: C 537 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8171 (mp0) REVERT: D 17 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.5384 (mt-10) REVERT: D 336 ARG cc_start: 0.6864 (mmt-90) cc_final: 0.6628 (mmm160) REVERT: D 365 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7086 (mt0) REVERT: D 418 HIS cc_start: 0.6024 (OUTLIER) cc_final: 0.5819 (p-80) REVERT: D 420 MET cc_start: 0.7647 (mmm) cc_final: 0.7294 (mmm) REVERT: D 439 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8694 (mtt-85) REVERT: D 497 ASP cc_start: 0.8186 (m-30) cc_final: 0.7977 (m-30) REVERT: D 537 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8154 (mp0) outliers start: 78 outliers final: 34 residues processed: 249 average time/residue: 1.4700 time to fit residues: 387.9171 Evaluate side-chains 245 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 190 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 GLU Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 537 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 82 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 84 optimal weight: 0.0770 chunk 46 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.208665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.196005 restraints weight = 8399.429| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 0.47 r_work: 0.3844 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10316 Z= 0.216 Angle : 0.711 7.050 13960 Z= 0.367 Chirality : 0.050 0.159 1412 Planarity : 0.005 0.038 1780 Dihedral : 5.531 36.509 1321 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 8.30 % Allowed : 24.62 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.23), residues: 1116 helix: 0.24 (0.26), residues: 320 sheet: -0.22 (0.57), residues: 64 loop : -1.17 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 553 HIS 0.006 0.001 HIS A 395 PHE 0.009 0.002 PHE B 566 TYR 0.013 0.002 TYR A 486 ARG 0.006 0.001 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.05510 ( 296) hydrogen bonds : angle 5.45562 ( 780) covalent geometry : bond 0.00508 (10316) covalent geometry : angle 0.71102 (13960) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 191 time to evaluate : 1.201 Fit side-chains REVERT: A 17 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.5414 (mt-10) REVERT: A 336 ARG cc_start: 0.6902 (mmt-90) cc_final: 0.6668 (mmm160) REVERT: A 350 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7691 (tm) REVERT: A 365 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7239 (mt0) REVERT: A 418 HIS cc_start: 0.6162 (OUTLIER) cc_final: 0.5738 (p-80) REVERT: A 420 MET cc_start: 0.7585 (mmm) cc_final: 0.7272 (mmm) REVERT: A 439 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8672 (mtt-85) REVERT: B 17 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.5356 (mt-10) REVERT: B 350 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7661 (tm) REVERT: B 365 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7216 (mt0) REVERT: B 418 HIS cc_start: 0.6176 (OUTLIER) cc_final: 0.5778 (p-80) REVERT: B 420 MET cc_start: 0.7633 (mmm) cc_final: 0.7362 (mmm) REVERT: B 439 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8691 (mtt-85) REVERT: C 17 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.5409 (mt-10) REVERT: C 333 ARG cc_start: 0.5592 (OUTLIER) cc_final: 0.5204 (ptp-170) REVERT: C 350 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7642 (tm) REVERT: C 365 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7239 (mt0) REVERT: C 418 HIS cc_start: 0.6088 (OUTLIER) cc_final: 0.5685 (p-80) REVERT: C 420 MET cc_start: 0.7618 (mmm) cc_final: 0.7307 (mmm) REVERT: C 439 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8657 (mtt-85) REVERT: C 497 ASP cc_start: 0.8199 (m-30) cc_final: 0.7976 (m-30) REVERT: D 17 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.5390 (mt-10) REVERT: D 350 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7668 (tm) REVERT: D 365 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7254 (mt0) REVERT: D 418 HIS cc_start: 0.6138 (OUTLIER) cc_final: 0.5707 (p-80) REVERT: D 420 MET cc_start: 0.7664 (mmm) cc_final: 0.7390 (mmm) REVERT: D 439 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8675 (mtt-85) outliers start: 88 outliers final: 48 residues processed: 256 average time/residue: 1.8950 time to fit residues: 515.5780 Evaluate side-chains 258 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 189 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 520 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 1 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.209620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.196351 restraints weight = 8446.062| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 0.51 r_work: 0.3833 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10316 Z= 0.154 Angle : 0.637 6.494 13960 Z= 0.327 Chirality : 0.047 0.133 1412 Planarity : 0.005 0.035 1780 Dihedral : 5.116 31.603 1320 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 7.36 % Allowed : 26.42 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.23), residues: 1116 helix: 0.44 (0.27), residues: 320 sheet: -0.32 (0.57), residues: 64 loop : -1.12 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 553 HIS 0.004 0.001 HIS B 395 PHE 0.006 0.001 PHE C 566 TYR 0.010 0.002 TYR C 559 ARG 0.006 0.001 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 296) hydrogen bonds : angle 5.24113 ( 780) covalent geometry : bond 0.00362 (10316) covalent geometry : angle 0.63665 (13960) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 180 time to evaluate : 1.127 Fit side-chains REVERT: A 17 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.5211 (mt-10) REVERT: A 365 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7085 (mt0) REVERT: A 418 HIS cc_start: 0.6030 (OUTLIER) cc_final: 0.5664 (p-80) REVERT: A 420 MET cc_start: 0.7444 (mmm) cc_final: 0.7111 (mmm) REVERT: A 439 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8661 (mtt-85) REVERT: A 497 ASP cc_start: 0.8003 (m-30) cc_final: 0.7779 (m-30) REVERT: A 537 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: B 17 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.5254 (mt-10) REVERT: B 365 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7056 (mt0) REVERT: B 418 HIS cc_start: 0.6041 (OUTLIER) cc_final: 0.5669 (p-80) REVERT: B 420 MET cc_start: 0.7410 (mmm) cc_final: 0.7089 (mmm) REVERT: B 439 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8658 (mtt-85) REVERT: B 537 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7922 (mt-10) REVERT: C 17 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.5267 (mt-10) REVERT: C 333 ARG cc_start: 0.5551 (OUTLIER) cc_final: 0.5180 (ptp-170) REVERT: C 365 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7035 (mt0) REVERT: C 418 HIS cc_start: 0.6012 (OUTLIER) cc_final: 0.5625 (p-80) REVERT: C 420 MET cc_start: 0.7426 (mmm) cc_final: 0.7053 (mmm) REVERT: C 439 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8660 (mtt-85) REVERT: C 537 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: D 17 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.5244 (mt-10) REVERT: D 365 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7018 (mt0) REVERT: D 418 HIS cc_start: 0.6010 (OUTLIER) cc_final: 0.5607 (p-80) REVERT: D 420 MET cc_start: 0.7450 (mmm) cc_final: 0.7123 (mmm) REVERT: D 439 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8670 (mtt-85) REVERT: D 497 ASP cc_start: 0.8055 (m-30) cc_final: 0.7801 (m-30) REVERT: D 537 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7965 (mt-10) outliers start: 78 outliers final: 39 residues processed: 235 average time/residue: 1.4558 time to fit residues: 363.4459 Evaluate side-chains 235 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 175 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 GLU Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 537 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 21 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 37 optimal weight: 0.0970 chunk 118 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.208346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.193799 restraints weight = 8508.495| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 0.52 r_work: 0.3803 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10316 Z= 0.174 Angle : 0.666 6.820 13960 Z= 0.341 Chirality : 0.048 0.148 1412 Planarity : 0.005 0.036 1780 Dihedral : 5.165 31.424 1320 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 8.40 % Allowed : 25.19 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.23), residues: 1116 helix: 0.02 (0.26), residues: 344 sheet: -0.36 (0.57), residues: 64 loop : -1.27 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 553 HIS 0.005 0.001 HIS A 395 PHE 0.007 0.001 PHE B 566 TYR 0.010 0.002 TYR C 486 ARG 0.004 0.001 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.04839 ( 296) hydrogen bonds : angle 5.27846 ( 780) covalent geometry : bond 0.00410 (10316) covalent geometry : angle 0.66565 (13960) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 183 time to evaluate : 1.151 Fit side-chains REVERT: A 17 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.5289 (mt-10) REVERT: A 202 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7668 (ptt) REVERT: A 365 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.6991 (mt0) REVERT: A 418 HIS cc_start: 0.6047 (OUTLIER) cc_final: 0.5552 (p-80) REVERT: A 420 MET cc_start: 0.7507 (mmm) cc_final: 0.7176 (mmm) REVERT: A 439 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8664 (mtt-85) REVERT: A 537 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: B 17 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.5285 (mt-10) REVERT: B 202 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7720 (ptt) REVERT: B 365 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.6992 (mt0) REVERT: B 418 HIS cc_start: 0.6045 (OUTLIER) cc_final: 0.5552 (p-80) REVERT: B 420 MET cc_start: 0.7512 (mmm) cc_final: 0.7179 (mmm) REVERT: B 439 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8678 (mtt-85) REVERT: B 537 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: C 17 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.5280 (mt-10) REVERT: C 202 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7608 (ptt) REVERT: C 333 ARG cc_start: 0.5515 (OUTLIER) cc_final: 0.5152 (ptp-170) REVERT: C 365 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7001 (mt0) REVERT: C 418 HIS cc_start: 0.6009 (OUTLIER) cc_final: 0.5528 (p-80) REVERT: C 420 MET cc_start: 0.7514 (mmm) cc_final: 0.7165 (mmm) REVERT: C 439 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8668 (mtt-85) REVERT: C 537 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7983 (mt-10) REVERT: D 17 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.5319 (mt-10) REVERT: D 365 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7121 (mt0) REVERT: D 418 HIS cc_start: 0.6040 (OUTLIER) cc_final: 0.5540 (p-80) REVERT: D 420 MET cc_start: 0.7520 (mmm) cc_final: 0.7204 (mmm) REVERT: D 439 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8670 (mtt-85) REVERT: D 537 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7972 (mt-10) outliers start: 89 outliers final: 48 residues processed: 249 average time/residue: 1.4650 time to fit residues: 387.3439 Evaluate side-chains 246 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 174 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 GLU Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 537 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 77 optimal weight: 0.4980 chunk 115 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 107 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.207622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.192895 restraints weight = 8499.741| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 0.60 r_work: 0.3789 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10316 Z= 0.170 Angle : 0.660 6.994 13960 Z= 0.339 Chirality : 0.048 0.145 1412 Planarity : 0.005 0.036 1780 Dihedral : 5.146 31.071 1320 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 8.02 % Allowed : 25.57 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.23), residues: 1116 helix: 0.09 (0.26), residues: 344 sheet: -0.38 (0.57), residues: 64 loop : -1.27 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 553 HIS 0.005 0.001 HIS A 395 PHE 0.007 0.001 PHE C 566 TYR 0.010 0.002 TYR D 486 ARG 0.004 0.001 ARG D 190 Details of bonding type rmsd hydrogen bonds : bond 0.04768 ( 296) hydrogen bonds : angle 5.26694 ( 780) covalent geometry : bond 0.00402 (10316) covalent geometry : angle 0.65994 (13960) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 176 time to evaluate : 1.288 Fit side-chains REVERT: A 17 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.5286 (mt-10) REVERT: A 193 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7175 (t70) REVERT: A 202 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7891 (ptt) REVERT: A 333 ARG cc_start: 0.5755 (OUTLIER) cc_final: 0.5360 (ptp-170) REVERT: A 365 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7051 (mt0) REVERT: A 418 HIS cc_start: 0.5999 (OUTLIER) cc_final: 0.5465 (p-80) REVERT: A 420 MET cc_start: 0.7597 (mmm) cc_final: 0.7316 (mmm) REVERT: A 439 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8661 (mtt-85) REVERT: A 537 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8085 (mt-10) REVERT: B 17 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.5252 (mt-10) REVERT: B 333 ARG cc_start: 0.5726 (OUTLIER) cc_final: 0.5233 (ptp-170) REVERT: B 365 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7214 (mt0) REVERT: B 418 HIS cc_start: 0.5995 (OUTLIER) cc_final: 0.5443 (p-80) REVERT: B 420 MET cc_start: 0.7636 (mmm) cc_final: 0.7380 (mmm) REVERT: B 439 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8692 (mtt-85) REVERT: B 537 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8061 (mt-10) REVERT: C 17 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.5303 (mt-10) REVERT: C 202 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7889 (ptt) REVERT: C 333 ARG cc_start: 0.5580 (OUTLIER) cc_final: 0.5203 (ptp-170) REVERT: C 365 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7068 (mt0) REVERT: C 418 HIS cc_start: 0.5931 (OUTLIER) cc_final: 0.5383 (p-80) REVERT: C 420 MET cc_start: 0.7640 (mmm) cc_final: 0.7343 (mmm) REVERT: C 439 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8692 (mtt-85) REVERT: C 537 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: D 17 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.5313 (mt-10) REVERT: D 193 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7241 (t70) REVERT: D 333 ARG cc_start: 0.5698 (OUTLIER) cc_final: 0.5297 (ptp-170) REVERT: D 365 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7188 (mt0) REVERT: D 418 HIS cc_start: 0.6017 (OUTLIER) cc_final: 0.5453 (p-80) REVERT: D 420 MET cc_start: 0.7652 (mmm) cc_final: 0.7388 (mmm) REVERT: D 439 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8686 (mtt-85) REVERT: D 537 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8013 (mt-10) REVERT: D 551 LYS cc_start: 0.7168 (mtpp) cc_final: 0.6824 (mttp) outliers start: 85 outliers final: 42 residues processed: 238 average time/residue: 1.6875 time to fit residues: 425.4816 Evaluate side-chains 243 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 173 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 GLU Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 537 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 20 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.206782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.182497 restraints weight = 8452.984| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.17 r_work: 0.3467 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10316 Z= 0.190 Angle : 0.688 6.870 13960 Z= 0.354 Chirality : 0.049 0.152 1412 Planarity : 0.005 0.037 1780 Dihedral : 5.260 32.218 1320 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 7.92 % Allowed : 25.75 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.23), residues: 1116 helix: -0.02 (0.26), residues: 344 sheet: -0.35 (0.56), residues: 64 loop : -1.28 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 553 HIS 0.005 0.001 HIS B 395 PHE 0.008 0.001 PHE C 566 TYR 0.012 0.002 TYR D 486 ARG 0.005 0.001 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.05038 ( 296) hydrogen bonds : angle 5.33328 ( 780) covalent geometry : bond 0.00449 (10316) covalent geometry : angle 0.68831 (13960) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 174 time to evaluate : 1.054 Fit side-chains REVERT: A 17 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.5426 (mt-10) REVERT: A 333 ARG cc_start: 0.5565 (OUTLIER) cc_final: 0.5154 (ptp-170) REVERT: A 350 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7665 (tm) REVERT: A 365 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7072 (mt0) REVERT: A 418 HIS cc_start: 0.5524 (OUTLIER) cc_final: 0.4884 (p-80) REVERT: A 420 MET cc_start: 0.7558 (mmm) cc_final: 0.7235 (mmm) REVERT: A 439 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8741 (mtt-85) REVERT: A 537 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8060 (mt-10) REVERT: B 17 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.5430 (mt-10) REVERT: B 333 ARG cc_start: 0.5592 (OUTLIER) cc_final: 0.5180 (ptp-170) REVERT: B 350 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7663 (tm) REVERT: B 418 HIS cc_start: 0.5548 (OUTLIER) cc_final: 0.4879 (p-80) REVERT: B 420 MET cc_start: 0.7561 (mmm) cc_final: 0.7235 (mmm) REVERT: B 439 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8748 (mtt-85) REVERT: B 537 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8089 (mt-10) REVERT: C 17 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.5399 (mt-10) REVERT: C 333 ARG cc_start: 0.5484 (OUTLIER) cc_final: 0.5061 (ptp-170) REVERT: C 350 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7672 (tm) REVERT: C 365 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7092 (mt0) REVERT: C 418 HIS cc_start: 0.5472 (OUTLIER) cc_final: 0.4774 (p-80) REVERT: C 420 MET cc_start: 0.7584 (mmm) cc_final: 0.7251 (mmm) REVERT: C 439 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8759 (mtt-85) REVERT: C 537 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: C 551 LYS cc_start: 0.7056 (mtpp) cc_final: 0.6552 (mttp) REVERT: D 17 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.5422 (mt-10) REVERT: D 333 ARG cc_start: 0.5496 (OUTLIER) cc_final: 0.5084 (ptp-170) REVERT: D 350 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7658 (tm) REVERT: D 365 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7127 (mt0) REVERT: D 418 HIS cc_start: 0.5505 (OUTLIER) cc_final: 0.4835 (p-80) REVERT: D 420 MET cc_start: 0.7579 (mmm) cc_final: 0.7258 (mmm) REVERT: D 439 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8742 (mtt-85) REVERT: D 537 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8087 (mt-10) outliers start: 84 outliers final: 46 residues processed: 235 average time/residue: 1.4878 time to fit residues: 370.3512 Evaluate side-chains 247 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 174 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 537 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 14 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.206418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.182061 restraints weight = 8455.637| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.13 r_work: 0.3450 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10316 Z= 0.204 Angle : 0.709 6.937 13960 Z= 0.365 Chirality : 0.050 0.156 1412 Planarity : 0.006 0.038 1780 Dihedral : 5.350 33.252 1320 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 7.17 % Allowed : 26.51 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.23), residues: 1116 helix: -0.11 (0.26), residues: 344 sheet: -0.26 (0.56), residues: 64 loop : -1.29 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 553 HIS 0.005 0.001 HIS D 395 PHE 0.008 0.001 PHE C 566 TYR 0.014 0.002 TYR D 486 ARG 0.006 0.001 ARG D 190 Details of bonding type rmsd hydrogen bonds : bond 0.05176 ( 296) hydrogen bonds : angle 5.38567 ( 780) covalent geometry : bond 0.00482 (10316) covalent geometry : angle 0.70916 (13960) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 177 time to evaluate : 1.371 Fit side-chains REVERT: A 17 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.5489 (mt-10) REVERT: A 193 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7115 (t70) REVERT: A 333 ARG cc_start: 0.5594 (OUTLIER) cc_final: 0.5195 (ptp-170) REVERT: A 350 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7680 (tm) REVERT: A 418 HIS cc_start: 0.5592 (OUTLIER) cc_final: 0.4925 (p-80) REVERT: A 420 MET cc_start: 0.7575 (mmm) cc_final: 0.7260 (mmm) REVERT: A 439 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8757 (mtt-85) REVERT: A 537 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8148 (mt-10) REVERT: B 17 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.5530 (mt-10) REVERT: B 333 ARG cc_start: 0.5594 (OUTLIER) cc_final: 0.5195 (ptp-170) REVERT: B 350 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7670 (tm) REVERT: B 418 HIS cc_start: 0.5648 (OUTLIER) cc_final: 0.4894 (p-80) REVERT: B 420 MET cc_start: 0.7555 (mmm) cc_final: 0.7230 (mmm) REVERT: B 439 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8763 (mtt-85) REVERT: B 537 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8177 (mt-10) REVERT: C 17 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.5463 (mt-10) REVERT: C 193 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7171 (t70) REVERT: C 333 ARG cc_start: 0.5472 (OUTLIER) cc_final: 0.5053 (ptp-170) REVERT: C 350 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7679 (tm) REVERT: C 418 HIS cc_start: 0.5584 (OUTLIER) cc_final: 0.4846 (p-80) REVERT: C 420 MET cc_start: 0.7621 (mmm) cc_final: 0.7321 (mmm) REVERT: C 439 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8758 (mtt-85) REVERT: C 537 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8105 (mt-10) REVERT: D 17 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.5471 (mt-10) REVERT: D 333 ARG cc_start: 0.5503 (OUTLIER) cc_final: 0.5105 (ptp-170) REVERT: D 350 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7683 (tm) REVERT: D 365 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7160 (mt0) REVERT: D 418 HIS cc_start: 0.5607 (OUTLIER) cc_final: 0.4851 (p-80) REVERT: D 420 MET cc_start: 0.7629 (mmm) cc_final: 0.7310 (mmm) REVERT: D 439 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8745 (mtt-85) REVERT: D 537 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8098 (mt-10) REVERT: D 551 LYS cc_start: 0.7074 (mtpp) cc_final: 0.6558 (mttp) outliers start: 76 outliers final: 43 residues processed: 233 average time/residue: 1.5112 time to fit residues: 373.1241 Evaluate side-chains 245 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 175 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 537 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 84 optimal weight: 0.1980 chunk 109 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN B 381 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.207152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.181454 restraints weight = 8380.265| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 1.07 r_work: 0.3431 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10316 Z= 0.185 Angle : 0.689 6.899 13960 Z= 0.355 Chirality : 0.049 0.148 1412 Planarity : 0.005 0.037 1780 Dihedral : 5.274 32.012 1320 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 7.08 % Allowed : 26.60 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.23), residues: 1116 helix: -0.08 (0.26), residues: 344 sheet: -0.25 (0.56), residues: 64 loop : -1.30 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 191 HIS 0.005 0.001 HIS A 395 PHE 0.007 0.001 PHE C 566 TYR 0.012 0.002 TYR D 486 ARG 0.005 0.001 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.04936 ( 296) hydrogen bonds : angle 5.35309 ( 780) covalent geometry : bond 0.00439 (10316) covalent geometry : angle 0.68945 (13960) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8984.31 seconds wall clock time: 157 minutes 5.11 seconds (9425.11 seconds total)