Starting phenix.real_space_refine on Sat Feb 7 06:28:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwt_47264/02_2026/9dwt_47264.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwt_47264/02_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_47264/02_2026/9dwt_47264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwt_47264/02_2026/9dwt_47264.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dwt_47264/02_2026/9dwt_47264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwt_47264/02_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-2.0-5952/lib/python3.9/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.39, 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: 2.43 Conformation dependent library (CDL) restraints added in 695.6 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: 0.76 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: 6.74 Time building geometry restraints manager: 3.52 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: 4.120 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: 0.190 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.410 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 covalent geometry : bond 0.00412 (15592) covalent geometry : angle 0.53904 (21156) SS BOND : bond 0.00086 ( 4) SS BOND : angle 0.68166 ( 8) hydrogen bonds : bond 0.14534 ( 936) hydrogen bonds : angle 5.80177 ( 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 : 0.796 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: 0.2508 time to fit residues: 80.0906 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 : 0.824 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.146776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.113432 restraints weight = 52349.257| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.19 r_work: 0.3056 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 0.026 15596 Z= 0.170 Angle : 0.479 8.473 21164 Z= 0.263 Chirality : 0.038 0.144 2372 Planarity : 0.004 0.032 2628 Dihedral : 6.370 59.569 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 : 11.54 % Favored : 85.76 % 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 D 338 TYR 0.016 0.002 TYR A 227 PHE 0.015 0.001 PHE A 604 TRP 0.007 0.001 TRP B 570 HIS 0.002 0.001 HIS D 550 Details of bonding type rmsd covalent geometry : bond 0.00396 (15592) covalent geometry : angle 0.47904 (21156) SS BOND : bond 0.00058 ( 4) SS BOND : angle 0.57547 ( 8) hydrogen bonds : bond 0.04859 ( 936) hydrogen bonds : angle 4.63200 ( 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 216 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 0.752 Fit side-chains REVERT: A 241 MET cc_start: 0.6669 (mmt) cc_final: 0.6268 (mmm) REVERT: A 266 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7257 (mm-30) REVERT: A 342 LYS cc_start: 0.7730 (pttt) cc_final: 0.7384 (ptpp) REVERT: A 372 LYS cc_start: 0.8672 (tttt) cc_final: 0.8466 (mmtt) REVERT: A 396 SER cc_start: 0.8586 (OUTLIER) cc_final: 0.8218 (p) REVERT: A 456 GLN cc_start: 0.8559 (tt0) cc_final: 0.8199 (tt0) REVERT: B 342 LYS cc_start: 0.7764 (mttt) cc_final: 0.7225 (mmmt) REVERT: B 372 LYS cc_start: 0.8637 (tttt) cc_final: 0.8411 (mmtt) REVERT: B 396 SER cc_start: 0.8507 (m) cc_final: 0.8247 (p) REVERT: C 251 ARG cc_start: 0.8139 (ttt180) cc_final: 0.7753 (ttp-170) REVERT: C 342 LYS cc_start: 0.7784 (pttt) cc_final: 0.7459 (ptpp) REVERT: C 396 SER cc_start: 0.8579 (t) cc_final: 0.8220 (p) REVERT: C 456 GLN cc_start: 0.8573 (tt0) cc_final: 0.8247 (tt0) REVERT: C 543 ASN cc_start: 0.7802 (m-40) cc_final: 0.7381 (t0) REVERT: D 241 MET cc_start: 0.6631 (mtp) cc_final: 0.6076 (mmp) REVERT: D 242 MET cc_start: 0.6168 (OUTLIER) cc_final: 0.5455 (ttm) REVERT: D 396 SER cc_start: 0.8805 (OUTLIER) cc_final: 0.8280 (p) REVERT: D 456 GLN cc_start: 0.8561 (tt0) cc_final: 0.8188 (tt0) REVERT: D 579 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: D 648 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8063 (mt-10) outliers start: 45 outliers final: 28 residues processed: 210 average time/residue: 0.2634 time to fit residues: 84.2239 Evaluate side-chains 200 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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: 2.9990 chunk 131 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.145879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.112249 restraints weight = 52444.602| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.23 r_work: 0.3126 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15596 Z= 0.224 Angle : 0.515 9.840 21164 Z= 0.281 Chirality : 0.039 0.146 2372 Planarity : 0.004 0.038 2628 Dihedral : 5.595 59.916 2043 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.49 % Allowed : 12.08 % Favored : 84.44 % 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: 1.31 (0.20), residues: 1820 helix: 2.10 (0.15), residues: 1044 sheet: -0.24 (0.41), residues: 200 loop : -1.06 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 322 TYR 0.017 0.002 TYR A 227 PHE 0.017 0.001 PHE A 604 TRP 0.006 0.001 TRP B 570 HIS 0.003 0.001 HIS D 550 Details of bonding type rmsd covalent geometry : bond 0.00540 (15592) covalent geometry : angle 0.51534 (21156) SS BOND : bond 0.00102 ( 4) SS BOND : angle 0.63077 ( 8) hydrogen bonds : bond 0.04936 ( 936) hydrogen bonds : angle 4.53697 ( 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 226 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 168 time to evaluate : 0.879 Fit side-chains REVERT: A 342 LYS cc_start: 0.7683 (pttt) cc_final: 0.7324 (ptpp) REVERT: A 372 LYS cc_start: 0.8683 (tttt) cc_final: 0.8446 (mmtt) REVERT: A 396 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8265 (p) REVERT: A 456 GLN cc_start: 0.8577 (tt0) cc_final: 0.8156 (tt0) REVERT: A 579 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.7388 (m-80) REVERT: B 342 LYS cc_start: 0.7770 (mttt) cc_final: 0.7227 (mmmt) REVERT: B 372 LYS cc_start: 0.8612 (tttt) cc_final: 0.8345 (mmtt) REVERT: B 396 SER cc_start: 0.8734 (m) cc_final: 0.8360 (p) REVERT: B 543 ASN cc_start: 0.7794 (OUTLIER) cc_final: 0.7570 (t0) REVERT: B 579 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.7375 (m-80) REVERT: C 251 ARG cc_start: 0.8080 (ttt180) cc_final: 0.7693 (ttp-170) REVERT: C 342 LYS cc_start: 0.7750 (pttt) cc_final: 0.7416 (ptpp) REVERT: C 396 SER cc_start: 0.8694 (t) cc_final: 0.8189 (p) REVERT: C 456 GLN cc_start: 0.8526 (tt0) cc_final: 0.8127 (tt0) REVERT: C 543 ASN cc_start: 0.7795 (OUTLIER) cc_final: 0.7282 (t0) REVERT: D 241 MET cc_start: 0.6631 (mtp) cc_final: 0.6092 (mmp) REVERT: D 242 MET cc_start: 0.6273 (OUTLIER) cc_final: 0.5608 (ttm) REVERT: D 396 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8177 (p) REVERT: D 456 GLN cc_start: 0.8570 (tt0) cc_final: 0.8136 (tt0) REVERT: D 543 ASN cc_start: 0.7765 (OUTLIER) cc_final: 0.7546 (t0) REVERT: D 579 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7469 (m-80) REVERT: D 648 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7969 (mt-10) outliers start: 58 outliers final: 39 residues processed: 215 average time/residue: 0.2521 time to fit residues: 83.6507 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 : 0.535 ------------------------------------------------------------------------------- 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 451 VAL Chi-restraints excluded: chain A residue 579 PHE 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 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: 0.8980 chunk 21 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.146731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.113140 restraints weight = 52097.067| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.22 r_work: 0.3041 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15596 Z= 0.170 Angle : 0.475 9.151 21164 Z= 0.259 Chirality : 0.038 0.145 2372 Planarity : 0.004 0.036 2628 Dihedral : 5.453 58.283 2042 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.03 % Allowed : 12.26 % Favored : 83.71 % 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: 1.42 (0.20), residues: 1820 helix: 2.20 (0.15), residues: 1040 sheet: -0.09 (0.40), residues: 200 loop : -1.06 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 338 TYR 0.016 0.002 TYR A 227 PHE 0.015 0.001 PHE A 600 TRP 0.005 0.001 TRP B 570 HIS 0.002 0.001 HIS D 550 Details of bonding type rmsd covalent geometry : bond 0.00401 (15592) covalent geometry : angle 0.47474 (21156) SS BOND : bond 0.00078 ( 4) SS BOND : angle 0.57109 ( 8) hydrogen bonds : bond 0.04487 ( 936) hydrogen bonds : angle 4.38402 ( 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 236 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 169 time to evaluate : 0.831 Fit side-chains REVERT: A 342 LYS cc_start: 0.7688 (pttt) cc_final: 0.7329 (ptpp) REVERT: A 372 LYS cc_start: 0.8670 (tttt) cc_final: 0.8427 (mmtt) REVERT: A 396 SER cc_start: 0.8783 (OUTLIER) cc_final: 0.8245 (p) REVERT: A 456 GLN cc_start: 0.8576 (tt0) cc_final: 0.8152 (tt0) REVERT: A 579 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.7385 (m-80) REVERT: B 342 LYS cc_start: 0.7754 (mttt) cc_final: 0.7207 (mmmt) REVERT: B 372 LYS cc_start: 0.8614 (tttt) cc_final: 0.8335 (mmtt) REVERT: B 396 SER cc_start: 0.8664 (m) cc_final: 0.8309 (p) REVERT: B 543 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7677 (t0) REVERT: B 579 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.7405 (m-80) REVERT: C 251 ARG cc_start: 0.8056 (ttt180) cc_final: 0.7672 (ttp-170) REVERT: C 342 LYS cc_start: 0.7750 (pttt) cc_final: 0.7395 (ptpp) REVERT: C 456 GLN cc_start: 0.8541 (tt0) cc_final: 0.8139 (tt0) REVERT: C 543 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7308 (t0) REVERT: C 579 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.7340 (m-80) REVERT: D 241 MET cc_start: 0.6586 (mtp) cc_final: 0.6062 (mmp) REVERT: D 242 MET cc_start: 0.6305 (OUTLIER) cc_final: 0.5581 (ttm) REVERT: D 396 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8169 (p) REVERT: D 456 GLN cc_start: 0.8575 (tt0) cc_final: 0.8147 (tt0) REVERT: D 543 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.7598 (t0) REVERT: D 579 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7468 (m-80) REVERT: D 648 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7994 (mt-10) outliers start: 67 outliers final: 46 residues processed: 223 average time/residue: 0.2598 time to fit residues: 88.5558 Evaluate side-chains 220 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 164 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 254 SER 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 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 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: 0.7980 chunk 168 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 141 optimal weight: 0.0870 chunk 159 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.155102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121653 restraints weight = 52025.843| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.23 r_work: 0.3263 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1140 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= 0.098 Angle : 0.420 7.385 21164 Z= 0.230 Chirality : 0.036 0.139 2372 Planarity : 0.003 0.037 2628 Dihedral : 5.143 56.810 2042 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.58 % Allowed : 13.22 % Favored : 84.19 % 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: 1.81 (0.20), residues: 1820 helix: 2.50 (0.15), residues: 1040 sheet: 0.05 (0.40), residues: 200 loop : -0.84 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 440 TYR 0.014 0.001 TYR A 227 PHE 0.014 0.001 PHE A 600 TRP 0.005 0.001 TRP A 455 HIS 0.001 0.000 HIS A 550 Details of bonding type rmsd covalent geometry : bond 0.00209 (15592) covalent geometry : angle 0.41962 (21156) SS BOND : bond 0.00025 ( 4) SS BOND : angle 0.57535 ( 8) hydrogen bonds : bond 0.03872 ( 936) hydrogen bonds : angle 4.10541 ( 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 214 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 266 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7163 (mm-30) REVERT: A 342 LYS cc_start: 0.7707 (pttt) cc_final: 0.7383 (ptpp) REVERT: A 396 SER cc_start: 0.8685 (OUTLIER) cc_final: 0.8328 (p) REVERT: A 456 GLN cc_start: 0.8551 (tt0) cc_final: 0.8205 (tt0) REVERT: A 483 PHE cc_start: 0.7608 (m-80) cc_final: 0.7325 (t80) REVERT: B 342 LYS cc_start: 0.7764 (mttt) cc_final: 0.7237 (mmmt) REVERT: B 396 SER cc_start: 0.8604 (m) cc_final: 0.8381 (p) REVERT: B 483 PHE cc_start: 0.7532 (m-80) cc_final: 0.7288 (t80) REVERT: B 543 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7690 (t0) REVERT: C 229 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7195 (tt) REVERT: C 251 ARG cc_start: 0.8081 (ttt180) cc_final: 0.7698 (ttt-90) REVERT: C 342 LYS cc_start: 0.7760 (pttt) cc_final: 0.7448 (ptpp) REVERT: C 396 SER cc_start: 0.8466 (t) cc_final: 0.8029 (p) REVERT: C 456 GLN cc_start: 0.8523 (tt0) cc_final: 0.8201 (tt0) REVERT: C 543 ASN cc_start: 0.7803 (m-40) cc_final: 0.7474 (t0) REVERT: D 241 MET cc_start: 0.6499 (mtp) cc_final: 0.6108 (mmp) REVERT: D 242 MET cc_start: 0.6222 (OUTLIER) cc_final: 0.5487 (ttm) REVERT: D 456 GLN cc_start: 0.8596 (tt0) cc_final: 0.8241 (tt0) REVERT: D 543 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7694 (t0) REVERT: D 648 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8078 (mt-10) outliers start: 43 outliers final: 30 residues processed: 205 average time/residue: 0.2600 time to fit residues: 80.8423 Evaluate side-chains 204 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 269 ASN Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 593 CYS 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 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 244 SER 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: 3.9990 chunk 162 optimal weight: 5.9990 chunk 147 optimal weight: 0.0050 chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 57 optimal weight: 0.0570 chunk 115 optimal weight: 0.0570 overall best weight: 0.3832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.157692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124715 restraints weight = 51729.790| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.20 r_work: 0.3305 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15596 Z= 0.084 Angle : 0.393 5.950 21164 Z= 0.215 Chirality : 0.036 0.135 2372 Planarity : 0.003 0.037 2628 Dihedral : 4.774 54.597 2037 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.86 % Allowed : 14.30 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.15 (0.20), residues: 1820 helix: 2.75 (0.16), residues: 1040 sheet: 0.06 (0.40), residues: 200 loop : -0.58 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 251 TYR 0.013 0.001 TYR D 527 PHE 0.013 0.001 PHE A 600 TRP 0.007 0.001 TRP A 455 HIS 0.001 0.000 HIS C 550 Details of bonding type rmsd covalent geometry : bond 0.00175 (15592) covalent geometry : angle 0.39320 (21156) SS BOND : bond 0.00056 ( 4) SS BOND : angle 0.61852 ( 8) hydrogen bonds : bond 0.03486 ( 936) hydrogen bonds : angle 3.89056 ( 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 218 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 266 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7132 (mm-30) REVERT: A 342 LYS cc_start: 0.7703 (pttt) cc_final: 0.7378 (ptpp) REVERT: A 396 SER cc_start: 0.8585 (m) cc_final: 0.8277 (p) REVERT: A 456 GLN cc_start: 0.8562 (tt0) cc_final: 0.8265 (tt0) REVERT: A 483 PHE cc_start: 0.7562 (m-80) cc_final: 0.7312 (t80) REVERT: A 605 PHE cc_start: 0.8900 (m-80) cc_final: 0.8695 (m-80) REVERT: B 342 LYS cc_start: 0.7767 (mttt) cc_final: 0.7213 (mmmt) REVERT: B 456 GLN cc_start: 0.8507 (tt0) cc_final: 0.8196 (tt0) REVERT: B 543 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7681 (t0) REVERT: C 229 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7245 (tt) REVERT: C 251 ARG cc_start: 0.8052 (ttt180) cc_final: 0.7737 (ttt-90) REVERT: C 254 SER cc_start: 0.8809 (OUTLIER) cc_final: 0.8561 (m) REVERT: C 342 LYS cc_start: 0.7770 (pttt) cc_final: 0.7443 (ptpp) REVERT: C 456 GLN cc_start: 0.8494 (tt0) cc_final: 0.8151 (tt0) REVERT: D 241 MET cc_start: 0.6450 (mtp) cc_final: 0.6045 (mmp) REVERT: D 456 GLN cc_start: 0.8588 (tt0) cc_final: 0.8273 (tt0) REVERT: D 543 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7672 (t0) REVERT: D 648 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8103 (mt-10) outliers start: 31 outliers final: 20 residues processed: 207 average time/residue: 0.2551 time to fit residues: 80.0997 Evaluate side-chains 196 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 269 ASN 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 254 SER 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: 2.9990 chunk 165 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 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: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.146287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.115434 restraints weight = 52187.393| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.09 r_work: 0.3115 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 15596 Z= 0.201 Angle : 0.476 8.967 21164 Z= 0.259 Chirality : 0.038 0.141 2372 Planarity : 0.004 0.036 2628 Dihedral : 4.961 54.563 2030 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.94 % Allowed : 12.44 % 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: 1.75 (0.20), residues: 1820 helix: 2.45 (0.15), residues: 1040 sheet: 0.02 (0.40), residues: 200 loop : -0.86 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 338 TYR 0.014 0.002 TYR A 227 PHE 0.019 0.001 PHE A 604 TRP 0.005 0.001 TRP D 570 HIS 0.002 0.001 HIS D 550 Details of bonding type rmsd covalent geometry : bond 0.00484 (15592) covalent geometry : angle 0.47552 (21156) SS BOND : bond 0.00049 ( 4) SS BOND : angle 0.66959 ( 8) hydrogen bonds : bond 0.04256 ( 936) hydrogen bonds : angle 4.11697 ( 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 221 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 0.737 Fit side-chains REVERT: A 266 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7122 (mm-30) REVERT: A 342 LYS cc_start: 0.7692 (pttt) cc_final: 0.7336 (ptpp) REVERT: A 396 SER cc_start: 0.8702 (OUTLIER) cc_final: 0.8296 (p) REVERT: A 456 GLN cc_start: 0.8504 (tt0) cc_final: 0.8107 (tt0) REVERT: A 483 PHE cc_start: 0.7543 (m-80) cc_final: 0.7271 (t80) REVERT: B 338 ARG cc_start: 0.6658 (mtt90) cc_final: 0.6206 (mmt180) REVERT: B 342 LYS cc_start: 0.7739 (mttt) cc_final: 0.7200 (mmmt) REVERT: B 396 SER cc_start: 0.8694 (m) cc_final: 0.8363 (p) REVERT: B 543 ASN cc_start: 0.7925 (OUTLIER) cc_final: 0.7716 (t0) REVERT: C 229 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7057 (tt) REVERT: C 251 ARG cc_start: 0.8043 (ttt180) cc_final: 0.7573 (ttt-90) REVERT: C 342 LYS cc_start: 0.7736 (pttt) cc_final: 0.7385 (ptpp) REVERT: C 396 SER cc_start: 0.8520 (t) cc_final: 0.8053 (p) REVERT: C 456 GLN cc_start: 0.8540 (tt0) cc_final: 0.8158 (tt0) REVERT: C 543 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7270 (t0) REVERT: D 241 MET cc_start: 0.6549 (mtp) cc_final: 0.6036 (mmp) REVERT: D 242 MET cc_start: 0.6204 (OUTLIER) cc_final: 0.5478 (ttm) REVERT: D 396 SER cc_start: 0.8724 (OUTLIER) cc_final: 0.8185 (p) REVERT: D 456 GLN cc_start: 0.8537 (tt0) cc_final: 0.8129 (tt0) REVERT: D 543 ASN cc_start: 0.7919 (OUTLIER) cc_final: 0.7695 (t0) REVERT: D 648 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7970 (mt-10) outliers start: 49 outliers final: 36 residues processed: 209 average time/residue: 0.2626 time to fit residues: 82.9214 Evaluate side-chains 209 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 166 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 603 MET 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 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 543 ASN Chi-restraints excluded: chain B residue 591 SER 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 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 307 SER Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 433 ILE 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: 2.9990 chunk 131 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 105 optimal weight: 0.1980 chunk 116 optimal weight: 0.0470 chunk 82 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.147922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.114531 restraints weight = 52131.478| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.20 r_work: 0.3115 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1417 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= 0.116 Angle : 0.427 7.779 21164 Z= 0.233 Chirality : 0.036 0.139 2372 Planarity : 0.004 0.036 2628 Dihedral : 4.686 54.547 2027 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.10 % Allowed : 13.40 % Favored : 84.50 % 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: 1.92 (0.20), residues: 1820 helix: 2.57 (0.15), residues: 1040 sheet: 0.18 (0.41), residues: 200 loop : -0.78 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 338 TYR 0.014 0.001 TYR A 227 PHE 0.014 0.001 PHE A 600 TRP 0.004 0.001 TRP A 570 HIS 0.001 0.001 HIS D 550 Details of bonding type rmsd covalent geometry : bond 0.00263 (15592) covalent geometry : angle 0.42723 (21156) SS BOND : bond 0.00015 ( 4) SS BOND : angle 0.48928 ( 8) hydrogen bonds : bond 0.03850 ( 936) hydrogen bonds : angle 4.00455 ( 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 204 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7149 (mm-30) REVERT: A 342 LYS cc_start: 0.7703 (pttt) cc_final: 0.7352 (ptpp) REVERT: A 396 SER cc_start: 0.8679 (OUTLIER) cc_final: 0.8297 (p) REVERT: A 456 GLN cc_start: 0.8512 (tt0) cc_final: 0.8117 (tt0) REVERT: A 483 PHE cc_start: 0.7574 (m-80) cc_final: 0.7311 (t80) REVERT: B 338 ARG cc_start: 0.6682 (mtt90) cc_final: 0.6162 (mmt180) REVERT: B 342 LYS cc_start: 0.7735 (mttt) cc_final: 0.7178 (mmmt) REVERT: B 543 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7732 (t0) REVERT: C 229 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7086 (tt) REVERT: C 251 ARG cc_start: 0.8051 (ttt180) cc_final: 0.7629 (ttt-90) REVERT: C 254 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8457 (m) REVERT: C 342 LYS cc_start: 0.7752 (pttt) cc_final: 0.7413 (ptpp) REVERT: C 396 SER cc_start: 0.8636 (t) cc_final: 0.8205 (p) REVERT: C 456 GLN cc_start: 0.8543 (tt0) cc_final: 0.8187 (tt0) REVERT: C 543 ASN cc_start: 0.7770 (OUTLIER) cc_final: 0.7407 (t0) REVERT: D 241 MET cc_start: 0.6459 (mtp) cc_final: 0.6007 (mmp) REVERT: D 396 SER cc_start: 0.8709 (m) cc_final: 0.8206 (p) REVERT: D 456 GLN cc_start: 0.8568 (tt0) cc_final: 0.8186 (tt0) REVERT: D 543 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7660 (t0) REVERT: D 648 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7978 (mt-10) outliers start: 35 outliers final: 25 residues processed: 194 average time/residue: 0.2337 time to fit residues: 70.1452 Evaluate side-chains 199 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 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 323 GLN 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 254 SER 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 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 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: 1.9990 chunk 136 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 50 optimal weight: 0.1980 chunk 119 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.148515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.117375 restraints weight = 51762.839| |-----------------------------------------------------------------------------| 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: 4.05 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1496 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= 0.106 Angle : 0.410 6.753 21164 Z= 0.224 Chirality : 0.036 0.136 2372 Planarity : 0.003 0.036 2628 Dihedral : 4.555 54.460 2027 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.22 % Allowed : 13.22 % 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: 2.07 (0.20), residues: 1820 helix: 2.66 (0.15), residues: 1040 sheet: 0.23 (0.41), residues: 200 loop : -0.66 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 338 TYR 0.012 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 covalent geometry : bond 0.00237 (15592) covalent geometry : angle 0.40950 (21156) SS BOND : bond 0.00017 ( 4) SS BOND : angle 0.50516 ( 8) hydrogen bonds : bond 0.03664 ( 936) hydrogen bonds : angle 3.91724 ( 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 208 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7124 (mm-30) REVERT: A 342 LYS cc_start: 0.7677 (pttt) cc_final: 0.7324 (ptpp) REVERT: A 396 SER cc_start: 0.8613 (m) cc_final: 0.8210 (p) REVERT: A 456 GLN cc_start: 0.8499 (tt0) cc_final: 0.8102 (tt0) REVERT: A 483 PHE cc_start: 0.7524 (m-80) cc_final: 0.7278 (t80) REVERT: B 251 ARG cc_start: 0.7972 (ttp-170) cc_final: 0.7762 (ttt-90) REVERT: B 342 LYS cc_start: 0.7726 (mttt) cc_final: 0.7148 (mmmt) REVERT: B 543 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7682 (t0) REVERT: C 229 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7073 (tt) REVERT: C 251 ARG cc_start: 0.7929 (ttt180) cc_final: 0.7488 (ttt-90) REVERT: C 254 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8397 (m) REVERT: C 342 LYS cc_start: 0.7710 (pttt) cc_final: 0.7335 (ptpp) REVERT: C 396 SER cc_start: 0.8650 (t) cc_final: 0.8252 (p) REVERT: C 456 GLN cc_start: 0.8502 (tt0) cc_final: 0.8133 (tt0) REVERT: D 241 MET cc_start: 0.6404 (mtp) cc_final: 0.5972 (mmp) REVERT: D 396 SER cc_start: 0.8651 (m) cc_final: 0.8108 (p) REVERT: D 456 GLN cc_start: 0.8532 (tt0) cc_final: 0.8129 (tt0) REVERT: D 543 ASN cc_start: 0.7882 (OUTLIER) cc_final: 0.7671 (t0) REVERT: D 648 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7895 (mt-10) outliers start: 37 outliers final: 29 residues processed: 200 average time/residue: 0.2404 time to fit residues: 73.1897 Evaluate side-chains 200 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 593 CYS 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 451 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 512 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 102 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.147848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.116748 restraints weight = 51670.343| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.10 r_work: 0.3114 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1476 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= 0.128 Angle : 0.430 7.589 21164 Z= 0.234 Chirality : 0.036 0.139 2372 Planarity : 0.004 0.035 2628 Dihedral : 4.615 54.477 2027 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.22 % Allowed : 13.34 % Favored : 84.44 % 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: 2.61 (0.15), residues: 1040 sheet: 0.22 (0.41), residues: 200 loop : -0.70 (0.25), 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 covalent geometry : bond 0.00295 (15592) covalent geometry : angle 0.43011 (21156) SS BOND : bond 0.00011 ( 4) SS BOND : angle 0.51852 ( 8) hydrogen bonds : bond 0.03807 ( 936) hydrogen bonds : angle 3.96035 ( 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 207 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7140 (mm-30) REVERT: A 342 LYS cc_start: 0.7679 (pttt) cc_final: 0.7321 (ptpp) REVERT: A 396 SER cc_start: 0.8633 (m) cc_final: 0.8229 (p) REVERT: A 456 GLN cc_start: 0.8517 (tt0) cc_final: 0.8106 (tt0) REVERT: A 483 PHE cc_start: 0.7508 (m-80) cc_final: 0.7252 (t80) REVERT: B 251 ARG cc_start: 0.8009 (ttp-170) cc_final: 0.7797 (ttt-90) REVERT: B 342 LYS cc_start: 0.7740 (mttt) cc_final: 0.7166 (mmmt) REVERT: C 229 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7053 (tt) REVERT: C 251 ARG cc_start: 0.7972 (ttt180) cc_final: 0.7512 (ttt-90) REVERT: C 254 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.8400 (m) REVERT: C 342 LYS cc_start: 0.7688 (pttt) cc_final: 0.7313 (ptpp) REVERT: C 396 SER cc_start: 0.8675 (t) cc_final: 0.8284 (p) REVERT: C 456 GLN cc_start: 0.8518 (tt0) cc_final: 0.8143 (tt0) REVERT: C 543 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.7389 (t0) REVERT: D 241 MET cc_start: 0.6449 (mtp) cc_final: 0.6006 (mmp) REVERT: D 396 SER cc_start: 0.8676 (m) cc_final: 0.8143 (p) REVERT: D 456 GLN cc_start: 0.8544 (tt0) cc_final: 0.8139 (tt0) REVERT: D 543 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7657 (t0) REVERT: D 648 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7915 (mt-10) outliers start: 37 outliers final: 31 residues processed: 198 average time/residue: 0.2354 time to fit residues: 72.4636 Evaluate side-chains 203 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 593 CYS 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 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 B residue 640 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 254 SER 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 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 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=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: 3.9990 chunk 48 optimal weight: 2.9990 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: 1.9990 chunk 22 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.147979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.116861 restraints weight = 51914.463| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.11 r_work: 0.3129 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1507 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= 0.120 Angle : 0.422 7.334 21164 Z= 0.230 Chirality : 0.036 0.138 2372 Planarity : 0.003 0.035 2628 Dihedral : 4.591 55.078 2027 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.16 % Allowed : 13.40 % Favored : 84.44 % 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: 2.05 (0.20), residues: 1820 helix: 2.64 (0.15), residues: 1040 sheet: 0.26 (0.41), residues: 200 loop : -0.66 (0.25), 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 455 HIS 0.001 0.001 HIS B 550 Details of bonding type rmsd covalent geometry : bond 0.00274 (15592) covalent geometry : angle 0.42181 (21156) SS BOND : bond 0.00013 ( 4) SS BOND : angle 0.49532 ( 8) hydrogen bonds : bond 0.03750 ( 936) hydrogen bonds : angle 3.94206 ( 2697) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6691.64 seconds wall clock time: 114 minutes 4.71 seconds (6844.71 seconds total)