Starting phenix.real_space_refine on Sun Jul 5 23:35:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwt_47264/07_2026/9dwt_47264.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwt_47264/07_2026/9dwt_47264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dwt_47264/07_2026/9dwt_47264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwt_47264/07_2026/9dwt_47264.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dwt_47264/07_2026/9dwt_47264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwt_47264/07_2026/9dwt_47264.map" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 76 5.16 5 C 10040 2.51 5 N 2384 2.21 5 O 2696 1.98 5 H 15032 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30229 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 7557 Classifications: {'peptide': 461} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 450} Chain breaks: 2 Chain: "B" Number of atoms: 7557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 7557 Classifications: {'peptide': 461} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 450} Chain breaks: 2 Chain: "C" Number of atoms: 7557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 7557 Classifications: {'peptide': 461} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 450} Chain breaks: 2 Chain: "D" Number of atoms: 7557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 7557 Classifications: {'peptide': 461} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 450} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 5.34, per 1000 atoms: 0.18 Number of scatterers: 30229 At special positions: 0 Unit cell: (114.838, 114.189, 101.862, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 76 16.00 O 2696 8.00 N 2384 7.00 C 10040 6.00 H 15032 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 344 " distance=2.03 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: 2.58 Conformation dependent library (CDL) restraints added in 797.6 milliseconds 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3536 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 8 sheets defined 61.6% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 214 through 241 removed outlier: 3.961A pdb=" N MET A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 258 removed outlier: 4.042A pdb=" N TYR A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.826A pdb=" N ILE A 367 " --> pdb=" O THR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 412 removed outlier: 3.711A pdb=" N ALA A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 493 Processing helix chain 'A' and resid 505 through 532 Processing helix chain 'A' and resid 532 through 541 removed outlier: 3.800A pdb=" N LEU A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP A 541 " --> pdb=" O GLN A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 572 Processing helix chain 'A' and resid 573 through 577 Processing helix chain 'A' and resid 580 through 620 removed outlier: 4.746A pdb=" N LYS A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ASP A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 628 through 642 removed outlier: 3.617A pdb=" N ALA A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 653 removed outlier: 3.629A pdb=" N ILE A 649 " --> pdb=" O ASN A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 670 removed outlier: 3.535A pdb=" N ILE A 659 " --> pdb=" O VAL A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 692 removed outlier: 4.413A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 242 removed outlier: 3.598A pdb=" N MET B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 258 removed outlier: 3.592A pdb=" N TYR B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 285 Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 363 through 367 removed outlier: 3.782A pdb=" N ILE B 367 " --> pdb=" O THR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 467 through 493 Processing helix chain 'B' and resid 505 through 532 removed outlier: 3.506A pdb=" N SER B 530 " --> pdb=" O ILE B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 removed outlier: 3.871A pdb=" N LEU B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 572 Processing helix chain 'B' and resid 573 through 577 removed outlier: 3.526A pdb=" N ILE B 577 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 620 removed outlier: 4.761A pdb=" N LYS B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASP B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 627 Processing helix chain 'B' and resid 628 through 642 Processing helix chain 'B' and resid 645 through 653 removed outlier: 3.605A pdb=" N ILE B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 670 removed outlier: 3.532A pdb=" N ILE B 659 " --> pdb=" O VAL B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 693 removed outlier: 4.433A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 241 removed outlier: 3.845A pdb=" N MET C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 258 removed outlier: 3.931A pdb=" N TYR C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 285 Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 363 through 367 removed outlier: 3.795A pdb=" N ILE C 367 " --> pdb=" O THR C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 375 Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 467 through 493 removed outlier: 3.565A pdb=" N VAL C 489 " --> pdb=" O PHE C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 532 Processing helix chain 'C' and resid 532 through 541 removed outlier: 3.806A pdb=" N LEU C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU C 540 " --> pdb=" O LEU C 536 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP C 541 " --> pdb=" O GLN C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 572 Processing helix chain 'C' and resid 573 through 577 Processing helix chain 'C' and resid 580 through 620 removed outlier: 3.572A pdb=" N ALA C 594 " --> pdb=" O MET C 590 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASP C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 627 Processing helix chain 'C' and resid 628 through 642 Processing helix chain 'C' and resid 645 through 653 removed outlier: 3.620A pdb=" N ILE C 649 " --> pdb=" O ASN C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 670 removed outlier: 3.544A pdb=" N ILE C 659 " --> pdb=" O VAL C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 692 removed outlier: 4.508A pdb=" N PHE C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 241 Processing helix chain 'D' and resid 245 through 259 removed outlier: 3.573A pdb=" N PHE D 257 " --> pdb=" O MET D 253 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP D 259 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 285 through 292 Processing helix chain 'D' and resid 363 through 367 removed outlier: 3.831A pdb=" N ILE D 367 " --> pdb=" O THR D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 412 removed outlier: 3.683A pdb=" N ALA D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 493 Processing helix chain 'D' and resid 505 through 532 removed outlier: 3.524A pdb=" N SER D 530 " --> pdb=" O ILE D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 539 removed outlier: 3.780A pdb=" N LEU D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 572 Processing helix chain 'D' and resid 573 through 577 Processing helix chain 'D' and resid 580 through 620 removed outlier: 3.542A pdb=" N ALA D 594 " --> pdb=" O MET D 590 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASP D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET D 603 " --> pdb=" O GLY D 599 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 627 Processing helix chain 'D' and resid 628 through 642 Processing helix chain 'D' and resid 645 through 653 removed outlier: 3.599A pdb=" N ILE D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 670 removed outlier: 3.530A pdb=" N ILE D 659 " --> pdb=" O VAL D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 692 removed outlier: 4.350A pdb=" N PHE D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 391 through 394 removed outlier: 6.681A pdb=" N LEU A 316 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N TYR A 429 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL A 318 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N SER A 427 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 421 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA3, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.691A pdb=" N LEU B 316 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR B 429 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL B 318 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N SER B 427 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 421 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 379 through 380 Processing sheet with id=AA5, first strand: chain 'C' and resid 391 through 394 removed outlier: 6.680A pdb=" N LEU C 316 " --> pdb=" O TYR C 429 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N TYR C 429 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL C 318 " --> pdb=" O SER C 427 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N SER C 427 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 421 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 379 through 380 Processing sheet with id=AA7, first strand: chain 'D' and resid 391 through 394 removed outlier: 6.683A pdb=" N LEU D 316 " --> pdb=" O TYR D 429 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N TYR D 429 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL D 318 " --> pdb=" O SER D 427 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N SER D 427 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D 421 " --> pdb=" O LEU D 324 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 379 through 380 936 hydrogen bonds defined for protein. 2697 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: 6.84 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15004 1.03 - 1.23: 54 1.23 - 1.42: 6898 1.42 - 1.62: 8552 1.62 - 1.81: 116 Bond restraints: 30624 Sorted by residual: bond pdb=" N GLU C 214 " pdb=" H1 GLU C 214 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" N GLU B 214 " pdb=" H1 GLU B 214 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N GLU A 214 " pdb=" H1 GLU A 214 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N GLU D 214 " pdb=" H1 GLU D 214 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C ARG B 355 " pdb=" N ALA B 356 " ideal model delta sigma weight residual 1.327 1.307 0.019 1.39e-02 5.18e+03 1.96e+00 ... (remaining 30619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 53529 1.32 - 2.64: 1356 2.64 - 3.96: 100 3.96 - 5.28: 10 5.28 - 6.60: 9 Bond angle restraints: 55004 Sorted by residual: angle pdb=" N VAL B 466 " pdb=" CA VAL B 466 " pdb=" C VAL B 466 " ideal model delta sigma weight residual 113.71 110.22 3.49 9.50e-01 1.11e+00 1.35e+01 angle pdb=" CA VAL D 318 " pdb=" C VAL D 318 " pdb=" N PRO D 319 " ideal model delta sigma weight residual 116.57 119.91 -3.34 9.80e-01 1.04e+00 1.16e+01 angle pdb=" N GLY D 363 " pdb=" CA GLY D 363 " pdb=" C GLY D 363 " ideal model delta sigma weight residual 110.60 115.40 -4.80 1.46e+00 4.69e-01 1.08e+01 angle pdb=" C VAL D 318 " pdb=" CA VAL D 318 " pdb=" CB VAL D 318 " ideal model delta sigma weight residual 109.33 112.55 -3.22 9.80e-01 1.04e+00 1.08e+01 angle pdb=" N PHE A 310 " pdb=" CA PHE A 310 " pdb=" C PHE A 310 " ideal model delta sigma weight residual 109.96 105.29 4.67 1.58e+00 4.01e-01 8.75e+00 ... (remaining 54999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 12977 17.74 - 35.49: 1124 35.49 - 53.23: 289 53.23 - 70.98: 76 70.98 - 88.72: 42 Dihedral angle restraints: 14508 sinusoidal: 7460 harmonic: 7048 Sorted by residual: dihedral pdb=" CB CYS A 331 " pdb=" SG CYS A 331 " pdb=" SG CYS A 344 " pdb=" CB CYS A 344 " ideal model delta sinusoidal sigma weight residual 93.00 161.88 -68.88 1 1.00e+01 1.00e-02 6.14e+01 dihedral pdb=" CB CYS B 331 " pdb=" SG CYS B 331 " pdb=" SG CYS B 344 " pdb=" CB CYS B 344 " ideal model delta sinusoidal sigma weight residual 93.00 161.85 -68.85 1 1.00e+01 1.00e-02 6.14e+01 dihedral pdb=" CB CYS D 331 " pdb=" SG CYS D 331 " pdb=" SG CYS D 344 " pdb=" CB CYS D 344 " ideal model delta sinusoidal sigma weight residual 93.00 160.77 -67.77 1 1.00e+01 1.00e-02 5.97e+01 ... (remaining 14505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1488 0.028 - 0.055: 589 0.055 - 0.083: 197 0.083 - 0.110: 65 0.110 - 0.138: 33 Chirality restraints: 2372 Sorted by residual: chirality pdb=" CA ILE A 333 " pdb=" N ILE A 333 " pdb=" C ILE A 333 " pdb=" CB ILE A 333 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE D 333 " pdb=" N ILE D 333 " pdb=" C ILE D 333 " pdb=" CB ILE D 333 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE B 333 " pdb=" N ILE B 333 " pdb=" C ILE B 333 " pdb=" CB ILE B 333 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 2369 not shown) Planarity restraints: 4420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 318 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO D 319 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO D 319 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 319 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 539 " -0.006 2.00e-02 2.50e+03 1.21e-02 1.46e+00 pdb=" N GLU D 540 " 0.021 2.00e-02 2.50e+03 pdb=" CA GLU D 540 " -0.005 2.00e-02 2.50e+03 pdb=" H GLU D 540 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 359 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO A 360 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 360 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 360 " -0.017 5.00e-02 4.00e+02 ... (remaining 4417 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 183 2.06 - 2.70: 47624 2.70 - 3.33: 88131 3.33 - 3.97: 110893 3.97 - 4.60: 178824 Nonbonded interactions: 425655 Sorted by model distance: nonbonded pdb="HD11 ILE C 309 " pdb="HG23 VAL C 428 " model vdw 1.429 2.440 nonbonded pdb="HD12 ILE B 309 " pdb="HG22 VAL B 428 " model vdw 1.456 2.440 nonbonded pdb="HD13 ILE B 309 " pdb="HG21 VAL B 428 " model vdw 1.637 2.440 nonbonded pdb=" HD2 ARG C 306 " pdb=" OE2 GLU D 340 " model vdw 1.648 2.620 nonbonded pdb=" HB3 ASN B 313 " pdb="HG12 VAL B 428 " model vdw 1.754 2.440 ... (remaining 425650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 214 through 693) selection = chain 'B' selection = chain 'C' 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: 6.370 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: 0.240 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 27.450 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.004 0.031 15596 Z= 0.186 Angle : 0.539 6.605 21164 Z= 0.326 Chirality : 0.037 0.138 2372 Planarity : 0.003 0.037 2628 Dihedral : 16.037 88.722 5468 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.58 % Allowed : 11.06 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.20), residues: 1820 helix: 2.26 (0.16), residues: 1032 sheet: 0.12 (0.41), residues: 184 loop : -0.74 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 322 TYR 0.015 0.002 TYR A 227 PHE 0.018 0.001 PHE A 600 TRP 0.005 0.001 TRP C 293 HIS 0.002 0.001 HIS D 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (15592) covalent geometry : angle 0.53904 / 0.33 (21156) SS BOND : bond 0.00086 / 0.04 ( 4) SS BOND : angle 0.68166 / 0.32 ( 8) hydrogen bonds : bond 0.14534 / 9.59 ( 936) hydrogen bonds : angle 5.80177 / 4.04 ( 2697) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 173 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.6622 (mmt) cc_final: 0.6299 (mmm) REVERT: A 266 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7146 (mm-30) REVERT: A 342 LYS cc_start: 0.7692 (pttt) cc_final: 0.7340 (ptpp) REVERT: A 372 LYS cc_start: 0.8661 (tttt) cc_final: 0.8419 (mmtt) REVERT: A 396 SER cc_start: 0.8564 (m) cc_final: 0.8134 (p) REVERT: A 456 GLN cc_start: 0.8550 (tt0) cc_final: 0.8193 (tt0) REVERT: A 579 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.7334 (m-80) REVERT: A 630 GLN cc_start: 0.7927 (mp10) cc_final: 0.7682 (mp10) REVERT: B 342 LYS cc_start: 0.7702 (mttt) cc_final: 0.7162 (mmmt) REVERT: B 372 LYS cc_start: 0.8622 (tttt) cc_final: 0.8386 (mmtt) REVERT: B 396 SER cc_start: 0.8515 (OUTLIER) cc_final: 0.8080 (p) REVERT: B 456 GLN cc_start: 0.8572 (tt0) cc_final: 0.8188 (tt0) REVERT: C 251 ARG cc_start: 0.8067 (ttt180) cc_final: 0.7651 (ttp-170) REVERT: C 342 LYS cc_start: 0.7723 (pttt) cc_final: 0.7413 (ptpp) REVERT: C 396 SER cc_start: 0.8588 (OUTLIER) cc_final: 0.8102 (p) REVERT: C 456 GLN cc_start: 0.8559 (tt0) cc_final: 0.8223 (tt0) REVERT: C 543 ASN cc_start: 0.7874 (m-40) cc_final: 0.7530 (t0) REVERT: C 648 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8029 (mt-10) REVERT: D 241 MET cc_start: 0.6546 (mtp) cc_final: 0.6029 (mmp) REVERT: D 372 LYS cc_start: 0.8593 (tttt) cc_final: 0.8362 (mmtt) REVERT: D 456 GLN cc_start: 0.8573 (tt0) cc_final: 0.8215 (tt0) REVERT: D 581 ARG cc_start: 0.7501 (ttt180) cc_final: 0.6964 (mtm180) REVERT: D 648 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7928 (mt-10) outliers start: 43 outliers final: 37 residues processed: 209 average time/residue: 0.2594 time to fit residues: 83.4841 Evaluate side-chains 209 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 543 ASN D 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.146772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.113439 restraints weight = 52341.797| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.19 r_work: 0.3075 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.0525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15596 Z= 0.170 Angle : 0.479 8.503 21164 Z= 0.263 Chirality : 0.038 0.145 2372 Planarity : 0.004 0.032 2628 Dihedral : 6.370 59.520 2075 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.70 % Allowed : 11.66 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.20), residues: 1820 helix: 2.28 (0.15), residues: 1044 sheet: -0.07 (0.42), residues: 192 loop : -0.91 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 322 TYR 0.016 0.002 TYR A 227 PHE 0.015 0.001 PHE A 600 TRP 0.007 0.001 TRP B 570 HIS 0.002 0.001 HIS D 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (15592) covalent geometry : angle 0.47910 / 0.26 (21156) SS BOND : bond 0.00063 / 0.03 ( 4) SS BOND : angle 0.57033 / 0.27 ( 8) hydrogen bonds : bond 0.04856 / 3.21 ( 936) hydrogen bonds : angle 4.63220 / 3.19 ( 2697) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 169 time to evaluate : 0.738 Fit side-chains REVERT: A 241 MET cc_start: 0.6681 (mmt) cc_final: 0.6278 (mmm) REVERT: A 266 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7250 (mm-30) REVERT: A 342 LYS cc_start: 0.7736 (pttt) cc_final: 0.7395 (ptpp) REVERT: A 372 LYS cc_start: 0.8672 (tttt) cc_final: 0.8471 (mmtt) REVERT: A 396 SER cc_start: 0.8585 (OUTLIER) cc_final: 0.8225 (p) REVERT: A 456 GLN cc_start: 0.8553 (tt0) cc_final: 0.8197 (tt0) REVERT: B 342 LYS cc_start: 0.7761 (mttt) cc_final: 0.7232 (mmmt) REVERT: B 372 LYS cc_start: 0.8631 (tttt) cc_final: 0.8415 (mmtt) REVERT: B 396 SER cc_start: 0.8508 (m) cc_final: 0.8255 (p) REVERT: C 251 ARG cc_start: 0.8141 (ttt180) cc_final: 0.7759 (ttp-170) REVERT: C 342 LYS cc_start: 0.7784 (pttt) cc_final: 0.7464 (ptpp) REVERT: C 396 SER cc_start: 0.8574 (t) cc_final: 0.8223 (p) REVERT: C 456 GLN cc_start: 0.8566 (tt0) cc_final: 0.8241 (tt0) REVERT: C 543 ASN cc_start: 0.7815 (m-40) cc_final: 0.7395 (t0) REVERT: D 241 MET cc_start: 0.6636 (mtp) cc_final: 0.6080 (mmp) REVERT: D 242 MET cc_start: 0.6144 (OUTLIER) cc_final: 0.5433 (ttm) REVERT: D 396 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8285 (p) REVERT: D 456 GLN cc_start: 0.8559 (tt0) cc_final: 0.8187 (tt0) REVERT: D 579 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7404 (m-80) REVERT: D 648 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8060 (mt-10) outliers start: 45 outliers final: 28 residues processed: 208 average time/residue: 0.2486 time to fit residues: 79.1375 Evaluate side-chains 198 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 640 ILE Chi-restraints excluded: chain D residue 677 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 166 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.145510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.111986 restraints weight = 52522.022| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.24 r_work: 0.3107 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15596 Z= 0.220 Angle : 0.509 9.699 21164 Z= 0.278 Chirality : 0.039 0.146 2372 Planarity : 0.004 0.037 2628 Dihedral : 5.576 59.857 2043 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.43 % Allowed : 12.02 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.20), residues: 1820 helix: 2.11 (0.15), residues: 1044 sheet: -0.23 (0.41), residues: 200 loop : -1.03 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 306 TYR 0.017 0.002 TYR A 227 PHE 0.016 0.001 PHE A 604 TRP 0.005 0.001 TRP B 570 HIS 0.003 0.001 HIS D 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.22 (15592) covalent geometry : angle 0.50911 / 0.28 (21156) SS BOND : bond 0.00132 / 0.07 ( 4) SS BOND : angle 0.64721 / 0.31 ( 8) hydrogen bonds : bond 0.04897 / 3.24 ( 936) hydrogen bonds : angle 4.53919 / 3.13 ( 2697) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 168 time to evaluate : 0.698 Fit side-chains REVERT: A 338 ARG cc_start: 0.6650 (mmt180) cc_final: 0.6385 (mtt90) REVERT: A 342 LYS cc_start: 0.7681 (pttt) cc_final: 0.7319 (ptpp) REVERT: A 372 LYS cc_start: 0.8693 (tttt) cc_final: 0.8445 (mmtt) REVERT: A 396 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8249 (p) REVERT: A 456 GLN cc_start: 0.8588 (tt0) cc_final: 0.8163 (tt0) REVERT: A 579 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.7386 (m-80) REVERT: B 342 LYS cc_start: 0.7758 (mttt) cc_final: 0.7204 (mmmt) REVERT: B 372 LYS cc_start: 0.8620 (tttt) cc_final: 0.8341 (mmtt) REVERT: B 396 SER cc_start: 0.8721 (m) cc_final: 0.8347 (p) REVERT: B 543 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7579 (t0) REVERT: B 579 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.7379 (m-80) REVERT: C 251 ARG cc_start: 0.8072 (ttt180) cc_final: 0.7677 (ttp-170) REVERT: C 342 LYS cc_start: 0.7751 (pttt) cc_final: 0.7412 (ptpp) REVERT: C 396 SER cc_start: 0.8694 (t) cc_final: 0.8191 (p) REVERT: C 456 GLN cc_start: 0.8547 (tt0) cc_final: 0.8149 (tt0) REVERT: C 543 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7291 (t0) REVERT: D 241 MET cc_start: 0.6630 (mtp) cc_final: 0.6074 (mmp) REVERT: D 242 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.5618 (ttm) REVERT: D 396 SER cc_start: 0.8780 (OUTLIER) cc_final: 0.8155 (p) REVERT: D 456 GLN cc_start: 0.8573 (tt0) cc_final: 0.8135 (tt0) REVERT: D 543 ASN cc_start: 0.7757 (OUTLIER) cc_final: 0.7537 (t0) REVERT: D 579 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7503 (m-80) REVERT: D 648 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7978 (mt-10) outliers start: 57 outliers final: 39 residues processed: 215 average time/residue: 0.2447 time to fit residues: 82.1134 Evaluate side-chains 214 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 166 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 579 PHE Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 640 ILE Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 677 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 75 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.146152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.112716 restraints weight = 52136.806| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.21 r_work: 0.3101 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15596 Z= 0.181 Angle : 0.482 9.317 21164 Z= 0.263 Chirality : 0.038 0.146 2372 Planarity : 0.004 0.037 2628 Dihedral : 5.506 58.480 2043 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.03 % Allowed : 12.02 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.20), residues: 1820 helix: 2.15 (0.15), residues: 1044 sheet: -0.10 (0.41), residues: 200 loop : -1.01 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 322 TYR 0.016 0.002 TYR A 227 PHE 0.015 0.001 PHE A 604 TRP 0.005 0.001 TRP B 570 HIS 0.002 0.001 HIS B 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (15592) covalent geometry : angle 0.48160 / 0.26 (21156) SS BOND : bond 0.00085 / 0.04 ( 4) SS BOND : angle 0.57954 / 0.28 ( 8) hydrogen bonds : bond 0.04542 / 3.00 ( 936) hydrogen bonds : angle 4.40801 / 3.04 ( 2697) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 167 time to evaluate : 0.815 Fit side-chains REVERT: A 338 ARG cc_start: 0.6675 (mmt180) cc_final: 0.6459 (mtt90) REVERT: A 342 LYS cc_start: 0.7684 (pttt) cc_final: 0.7319 (ptpp) REVERT: A 372 LYS cc_start: 0.8666 (tttt) cc_final: 0.8415 (mmtt) REVERT: A 396 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8223 (p) REVERT: A 456 GLN cc_start: 0.8564 (tt0) cc_final: 0.8135 (tt0) REVERT: A 579 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.7390 (m-80) REVERT: B 342 LYS cc_start: 0.7752 (mttt) cc_final: 0.7204 (mmmt) REVERT: B 372 LYS cc_start: 0.8616 (tttt) cc_final: 0.8344 (mmtt) REVERT: B 396 SER cc_start: 0.8682 (m) cc_final: 0.8317 (p) REVERT: B 543 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7684 (t0) REVERT: B 579 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: C 251 ARG cc_start: 0.8048 (ttt180) cc_final: 0.7650 (ttp-170) REVERT: C 342 LYS cc_start: 0.7726 (pttt) cc_final: 0.7370 (ptpp) REVERT: C 456 GLN cc_start: 0.8535 (tt0) cc_final: 0.8119 (tt0) REVERT: C 543 ASN cc_start: 0.7794 (OUTLIER) cc_final: 0.7290 (t0) REVERT: C 579 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.7356 (m-80) REVERT: D 241 MET cc_start: 0.6595 (mtp) cc_final: 0.6036 (mmp) REVERT: D 242 MET cc_start: 0.6327 (OUTLIER) cc_final: 0.5596 (ttm) REVERT: D 396 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8178 (p) REVERT: D 456 GLN cc_start: 0.8564 (tt0) cc_final: 0.8127 (tt0) REVERT: D 543 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7624 (t0) REVERT: D 579 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7484 (m-80) REVERT: D 648 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7961 (mt-10) outliers start: 67 outliers final: 47 residues processed: 223 average time/residue: 0.2377 time to fit residues: 82.2206 Evaluate side-chains 223 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 166 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 579 PHE Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 640 ILE Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 677 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 90 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 168 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.154743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121291 restraints weight = 52070.766| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.23 r_work: 0.3227 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15596 Z= 0.105 Angle : 0.424 7.601 21164 Z= 0.232 Chirality : 0.036 0.143 2372 Planarity : 0.003 0.037 2628 Dihedral : 5.196 56.854 2043 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.70 % Allowed : 13.22 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.20), residues: 1820 helix: 2.47 (0.16), residues: 1040 sheet: 0.02 (0.40), residues: 200 loop : -0.85 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 338 TYR 0.014 0.001 TYR D 527 PHE 0.014 0.001 PHE A 600 TRP 0.005 0.001 TRP A 455 HIS 0.001 0.000 HIS C 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (15592) covalent geometry : angle 0.42345 / 0.23 (21156) SS BOND : bond 0.00010 / 0.00 ( 4) SS BOND : angle 0.56647 / 0.28 ( 8) hydrogen bonds : bond 0.03930 / 2.58 ( 936) hydrogen bonds : angle 4.17724 / 2.88 ( 2697) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 0.820 Fit side-chains REVERT: A 266 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7252 (mm-30) REVERT: A 342 LYS cc_start: 0.7712 (pttt) cc_final: 0.7383 (ptpp) REVERT: A 396 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.8378 (p) REVERT: A 456 GLN cc_start: 0.8557 (tt0) cc_final: 0.8209 (tt0) REVERT: A 483 PHE cc_start: 0.7625 (m-80) cc_final: 0.7342 (t80) REVERT: B 342 LYS cc_start: 0.7755 (mttt) cc_final: 0.7230 (mmmt) REVERT: B 396 SER cc_start: 0.8606 (m) cc_final: 0.8376 (p) REVERT: B 483 PHE cc_start: 0.7533 (m-80) cc_final: 0.7288 (t80) REVERT: B 543 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7713 (t0) REVERT: C 229 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7220 (tt) REVERT: C 251 ARG cc_start: 0.8077 (ttt180) cc_final: 0.7702 (ttt-90) REVERT: C 342 LYS cc_start: 0.7751 (pttt) cc_final: 0.7453 (ptpp) REVERT: C 396 SER cc_start: 0.8495 (t) cc_final: 0.8056 (p) REVERT: C 456 GLN cc_start: 0.8534 (tt0) cc_final: 0.8208 (tt0) REVERT: C 543 ASN cc_start: 0.7817 (m-40) cc_final: 0.7490 (t0) REVERT: D 241 MET cc_start: 0.6559 (mtp) cc_final: 0.6129 (mmp) REVERT: D 242 MET cc_start: 0.6231 (OUTLIER) cc_final: 0.5491 (ttm) REVERT: D 456 GLN cc_start: 0.8586 (tt0) cc_final: 0.8230 (tt0) REVERT: D 543 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7715 (t0) REVERT: D 648 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8099 (mt-10) outliers start: 45 outliers final: 30 residues processed: 208 average time/residue: 0.2636 time to fit residues: 83.4687 Evaluate side-chains 199 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 640 ILE Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 677 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 56 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 80 optimal weight: 0.0470 chunk 57 optimal weight: 0.7980 chunk 115 optimal weight: 0.0010 overall best weight: 0.4684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.157265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124145 restraints weight = 51715.168| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.21 r_work: 0.3296 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 15596 Z= 0.087 Angle : 0.397 6.237 21164 Z= 0.217 Chirality : 0.036 0.137 2372 Planarity : 0.003 0.037 2628 Dihedral : 4.846 54.749 2038 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.04 % Allowed : 14.06 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.20), residues: 1820 helix: 2.71 (0.15), residues: 1040 sheet: 0.06 (0.39), residues: 200 loop : -0.59 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 325 TYR 0.013 0.001 TYR D 527 PHE 0.014 0.001 PHE A 600 TRP 0.006 0.001 TRP D 455 HIS 0.001 0.000 HIS C 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00184 / 0.09 (15592) covalent geometry : angle 0.39713 / 0.22 (21156) SS BOND : bond 0.00052 / 0.03 ( 4) SS BOND : angle 0.63048 / 0.30 ( 8) hydrogen bonds : bond 0.03550 / 2.33 ( 936) hydrogen bonds : angle 3.95823 / 2.75 ( 2697) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 266 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7161 (mm-30) REVERT: A 342 LYS cc_start: 0.7710 (pttt) cc_final: 0.7383 (ptpp) REVERT: A 396 SER cc_start: 0.8603 (m) cc_final: 0.8289 (p) REVERT: A 456 GLN cc_start: 0.8559 (tt0) cc_final: 0.8264 (tt0) REVERT: A 483 PHE cc_start: 0.7590 (m-80) cc_final: 0.7349 (t80) REVERT: B 342 LYS cc_start: 0.7766 (mttt) cc_final: 0.7212 (mmmt) REVERT: B 456 GLN cc_start: 0.8517 (tt0) cc_final: 0.8200 (tt0) REVERT: B 543 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.7723 (t0) REVERT: C 229 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7265 (tt) REVERT: C 251 ARG cc_start: 0.8049 (ttt180) cc_final: 0.7680 (ttt-90) REVERT: C 342 LYS cc_start: 0.7757 (pttt) cc_final: 0.7435 (ptpp) REVERT: C 396 SER cc_start: 0.8396 (t) cc_final: 0.8034 (p) REVERT: C 456 GLN cc_start: 0.8521 (tt0) cc_final: 0.8160 (tt0) REVERT: D 241 MET cc_start: 0.6464 (mtp) cc_final: 0.6055 (mmp) REVERT: D 456 GLN cc_start: 0.8577 (tt0) cc_final: 0.8261 (tt0) REVERT: D 543 ASN cc_start: 0.7926 (OUTLIER) cc_final: 0.7685 (t0) outliers start: 34 outliers final: 23 residues processed: 205 average time/residue: 0.2752 time to fit residues: 85.4946 Evaluate side-chains 194 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 677 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 83 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 138 optimal weight: 10.9990 chunk 181 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.144351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.110676 restraints weight = 52710.612| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.21 r_work: 0.3041 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 15596 Z= 0.230 Angle : 0.498 9.687 21164 Z= 0.271 Chirality : 0.039 0.142 2372 Planarity : 0.004 0.037 2628 Dihedral : 5.096 54.796 2031 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.25 % Allowed : 12.38 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.20), residues: 1820 helix: 2.35 (0.15), residues: 1040 sheet: 0.04 (0.40), residues: 200 loop : -0.94 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 338 TYR 0.015 0.002 TYR A 227 PHE 0.021 0.002 PHE A 604 TRP 0.006 0.001 TRP C 570 HIS 0.002 0.001 HIS D 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.23 (15592) covalent geometry : angle 0.49776 / 0.27 (21156) SS BOND : bond 0.00068 / 0.03 ( 4) SS BOND : angle 0.75318 / 0.36 ( 8) hydrogen bonds : bond 0.04442 / 2.93 ( 936) hydrogen bonds : angle 4.20920 / 2.91 ( 2697) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 0.719 Fit side-chains REVERT: A 342 LYS cc_start: 0.7715 (pttt) cc_final: 0.7365 (ptpp) REVERT: A 396 SER cc_start: 0.8766 (OUTLIER) cc_final: 0.8352 (p) REVERT: A 456 GLN cc_start: 0.8572 (tt0) cc_final: 0.8185 (tt0) REVERT: A 483 PHE cc_start: 0.7591 (m-80) cc_final: 0.7305 (t80) REVERT: B 342 LYS cc_start: 0.7761 (mttt) cc_final: 0.7237 (mmmt) REVERT: B 396 SER cc_start: 0.8717 (m) cc_final: 0.8430 (p) REVERT: C 229 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7159 (tt) REVERT: C 251 ARG cc_start: 0.8154 (ttt180) cc_final: 0.7713 (ttt-90) REVERT: C 342 LYS cc_start: 0.7737 (pttt) cc_final: 0.7410 (ptpp) REVERT: C 396 SER cc_start: 0.8596 (t) cc_final: 0.8125 (p) REVERT: C 456 GLN cc_start: 0.8560 (tt0) cc_final: 0.8196 (tt0) REVERT: C 543 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7280 (t0) REVERT: D 241 MET cc_start: 0.6591 (mtp) cc_final: 0.6075 (mmp) REVERT: D 242 MET cc_start: 0.6276 (OUTLIER) cc_final: 0.5514 (ttm) REVERT: D 396 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8272 (p) REVERT: D 456 GLN cc_start: 0.8576 (tt0) cc_final: 0.8187 (tt0) REVERT: D 543 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7717 (t0) outliers start: 54 outliers final: 39 residues processed: 210 average time/residue: 0.2301 time to fit residues: 74.8542 Evaluate side-chains 209 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 640 ILE Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 16 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 58 optimal weight: 0.0020 chunk 155 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 116 optimal weight: 0.0870 chunk 82 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.7570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.148486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.117332 restraints weight = 51741.429| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.11 r_work: 0.3153 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 15596 Z= 0.095 Angle : 0.415 7.188 21164 Z= 0.227 Chirality : 0.036 0.146 2372 Planarity : 0.004 0.038 2628 Dihedral : 4.683 54.310 2028 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.10 % Allowed : 13.28 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.20), residues: 1820 helix: 2.58 (0.15), residues: 1044 sheet: 0.22 (0.41), residues: 200 loop : -0.68 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 338 TYR 0.015 0.001 TYR B 227 PHE 0.014 0.001 PHE A 600 TRP 0.005 0.001 TRP A 455 HIS 0.001 0.000 HIS C 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (15592) covalent geometry : angle 0.41486 / 0.23 (21156) SS BOND : bond 0.00014 / 0.01 ( 4) SS BOND : angle 0.54579 / 0.27 ( 8) hydrogen bonds : bond 0.03717 / 2.45 ( 936) hydrogen bonds : angle 3.97855 / 2.76 ( 2697) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7101 (mm-30) REVERT: A 342 LYS cc_start: 0.7681 (pttt) cc_final: 0.7322 (ptpp) REVERT: A 396 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8225 (p) REVERT: A 456 GLN cc_start: 0.8509 (tt0) cc_final: 0.8101 (tt0) REVERT: A 483 PHE cc_start: 0.7523 (m-80) cc_final: 0.7265 (t80) REVERT: B 342 LYS cc_start: 0.7712 (mttt) cc_final: 0.7130 (mmmt) REVERT: B 396 SER cc_start: 0.8588 (m) cc_final: 0.8246 (p) REVERT: C 229 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7019 (tt) REVERT: C 251 ARG cc_start: 0.7922 (ttt180) cc_final: 0.7410 (ttt-90) REVERT: C 342 LYS cc_start: 0.7714 (pttt) cc_final: 0.7362 (ptpp) REVERT: C 396 SER cc_start: 0.8593 (t) cc_final: 0.8098 (p) REVERT: C 456 GLN cc_start: 0.8510 (tt0) cc_final: 0.8104 (tt0) REVERT: C 543 ASN cc_start: 0.7725 (OUTLIER) cc_final: 0.7361 (t0) REVERT: D 241 MET cc_start: 0.6433 (mtp) cc_final: 0.5974 (mmp) REVERT: D 325 ARG cc_start: 0.8184 (mmm-85) cc_final: 0.7947 (mtp85) REVERT: D 456 GLN cc_start: 0.8528 (tt0) cc_final: 0.8115 (tt0) REVERT: D 543 ASN cc_start: 0.7888 (OUTLIER) cc_final: 0.7665 (t0) outliers start: 35 outliers final: 27 residues processed: 192 average time/residue: 0.2530 time to fit residues: 74.5746 Evaluate side-chains 197 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 45 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 chunk 119 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.149721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.118669 restraints weight = 51708.966| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.11 r_work: 0.3167 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15596 Z= 0.094 Angle : 0.399 6.144 21164 Z= 0.218 Chirality : 0.036 0.135 2372 Planarity : 0.003 0.037 2628 Dihedral : 4.491 54.610 2028 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.04 % Allowed : 13.28 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.20), residues: 1820 helix: 2.76 (0.15), residues: 1040 sheet: 0.24 (0.41), residues: 200 loop : -0.55 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 338 TYR 0.011 0.001 TYR B 227 PHE 0.015 0.001 PHE A 600 TRP 0.006 0.001 TRP D 455 HIS 0.001 0.000 HIS D 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (15592) covalent geometry : angle 0.39895 / 0.22 (21156) SS BOND : bond 0.00055 / 0.03 ( 4) SS BOND : angle 0.55298 / 0.27 ( 8) hydrogen bonds : bond 0.03509 / 2.31 ( 936) hydrogen bonds : angle 3.86126 / 2.68 ( 2697) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7115 (mm-30) REVERT: A 342 LYS cc_start: 0.7691 (pttt) cc_final: 0.7318 (ptpp) REVERT: A 396 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.8165 (p) REVERT: A 456 GLN cc_start: 0.8488 (tt0) cc_final: 0.8112 (tt0) REVERT: A 483 PHE cc_start: 0.7514 (m-80) cc_final: 0.7270 (t80) REVERT: B 251 ARG cc_start: 0.7965 (ttp-170) cc_final: 0.7760 (ttt-90) REVERT: B 338 ARG cc_start: 0.6676 (mtt90) cc_final: 0.6274 (mmt180) REVERT: B 342 LYS cc_start: 0.7744 (mttt) cc_final: 0.7144 (mmmt) REVERT: B 456 GLN cc_start: 0.8506 (tt0) cc_final: 0.8122 (tt0) REVERT: C 229 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7077 (tt) REVERT: C 251 ARG cc_start: 0.7913 (ttt180) cc_final: 0.7409 (ttt-90) REVERT: C 342 LYS cc_start: 0.7696 (pttt) cc_final: 0.7329 (ptpp) REVERT: C 396 SER cc_start: 0.8620 (t) cc_final: 0.8225 (p) REVERT: C 456 GLN cc_start: 0.8493 (tt0) cc_final: 0.8124 (tt0) REVERT: C 543 ASN cc_start: 0.7679 (OUTLIER) cc_final: 0.7341 (t0) REVERT: D 241 MET cc_start: 0.6407 (mtp) cc_final: 0.5975 (mmp) REVERT: D 325 ARG cc_start: 0.8203 (mmm-85) cc_final: 0.7947 (mtp85) REVERT: D 396 SER cc_start: 0.8605 (m) cc_final: 0.8100 (p) REVERT: D 456 GLN cc_start: 0.8533 (tt0) cc_final: 0.8148 (tt0) REVERT: D 543 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7665 (t0) outliers start: 34 outliers final: 26 residues processed: 202 average time/residue: 0.2646 time to fit residues: 80.6348 Evaluate side-chains 200 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 102 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.148726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.117586 restraints weight = 51670.145| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.11 r_work: 0.3121 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15596 Z= 0.110 Angle : 0.414 6.746 21164 Z= 0.225 Chirality : 0.036 0.138 2372 Planarity : 0.003 0.036 2628 Dihedral : 4.530 54.654 2028 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.98 % Allowed : 13.34 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.20), residues: 1820 helix: 2.73 (0.15), residues: 1040 sheet: 0.25 (0.41), residues: 200 loop : -0.59 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 338 TYR 0.013 0.001 TYR A 227 PHE 0.015 0.001 PHE A 600 TRP 0.004 0.001 TRP C 570 HIS 0.001 0.000 HIS D 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (15592) covalent geometry : angle 0.41391 / 0.23 (21156) SS BOND : bond 0.00018 / 0.01 ( 4) SS BOND : angle 0.56424 / 0.27 ( 8) hydrogen bonds : bond 0.03617 / 2.39 ( 936) hydrogen bonds : angle 3.88920 / 2.70 ( 2697) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7120 (mm-30) REVERT: A 342 LYS cc_start: 0.7697 (pttt) cc_final: 0.7338 (ptpp) REVERT: A 396 SER cc_start: 0.8611 (OUTLIER) cc_final: 0.8203 (p) REVERT: A 456 GLN cc_start: 0.8489 (tt0) cc_final: 0.8099 (tt0) REVERT: A 483 PHE cc_start: 0.7505 (m-80) cc_final: 0.7277 (t80) REVERT: B 251 ARG cc_start: 0.7979 (ttp-170) cc_final: 0.7771 (ttt-90) REVERT: B 342 LYS cc_start: 0.7684 (mttt) cc_final: 0.7159 (pttt) REVERT: B 456 GLN cc_start: 0.8483 (tt0) cc_final: 0.8096 (tt0) REVERT: C 229 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7060 (tt) REVERT: C 251 ARG cc_start: 0.7915 (ttt180) cc_final: 0.7416 (ttt-90) REVERT: C 342 LYS cc_start: 0.7691 (pttt) cc_final: 0.7318 (ptpp) REVERT: C 396 SER cc_start: 0.8634 (t) cc_final: 0.8245 (p) REVERT: C 456 GLN cc_start: 0.8497 (tt0) cc_final: 0.8132 (tt0) REVERT: C 543 ASN cc_start: 0.7687 (OUTLIER) cc_final: 0.7358 (t0) REVERT: D 241 MET cc_start: 0.6392 (mtp) cc_final: 0.5986 (mmp) REVERT: D 325 ARG cc_start: 0.8205 (mmm-85) cc_final: 0.7967 (mtp85) REVERT: D 396 SER cc_start: 0.8615 (m) cc_final: 0.8109 (p) REVERT: D 456 GLN cc_start: 0.8549 (tt0) cc_final: 0.8170 (tt0) REVERT: D 543 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7617 (t0) outliers start: 33 outliers final: 26 residues processed: 195 average time/residue: 0.2568 time to fit residues: 77.2292 Evaluate side-chains 199 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 164 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.148151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.117063 restraints weight = 51995.397| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.11 r_work: 0.3089 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15596 Z= 0.121 Angle : 0.421 7.209 21164 Z= 0.229 Chirality : 0.036 0.138 2372 Planarity : 0.003 0.036 2628 Dihedral : 4.586 54.970 2028 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.10 % Allowed : 13.10 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.20), residues: 1820 helix: 2.70 (0.15), residues: 1040 sheet: 0.24 (0.41), residues: 200 loop : -0.63 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 338 TYR 0.013 0.001 TYR A 227 PHE 0.015 0.001 PHE A 600 TRP 0.005 0.001 TRP D 570 HIS 0.001 0.001 HIS D 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (15592) covalent geometry : angle 0.42118 / 0.23 (21156) SS BOND : bond 0.00010 / 0.00 ( 4) SS BOND : angle 0.53805 / 0.25 ( 8) hydrogen bonds : bond 0.03713 / 2.45 ( 936) hydrogen bonds : angle 3.92253 / 2.72 ( 2697) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6926.35 seconds wall clock time: 118 minutes 2.53 seconds (7082.53 seconds total)