Starting phenix.real_space_refine on Thu Feb 5 01:39:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lna_63230/02_2026/9lna_63230.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lna_63230/02_2026/9lna_63230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lna_63230/02_2026/9lna_63230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lna_63230/02_2026/9lna_63230.map" model { file = "/net/cci-nas-00/data/ceres_data/9lna_63230/02_2026/9lna_63230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lna_63230/02_2026/9lna_63230.cif" } resolution = 3.6 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= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 8910 2.51 5 N 2427 2.21 5 O 2658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s 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: 14079 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4693 Classifications: {'peptide': 601} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 572} Restraints were copied for chains: B, C Time building chain proxies: 2.88, per 1000 atoms: 0.20 Number of scatterers: 14079 At special positions: 0 Unit cell: (104.16, 104.16, 119.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2658 8.00 N 2427 7.00 C 8910 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 383 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 383 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 383 " 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: 0.81 Conformation dependent library (CDL) restraints added in 569.7 milliseconds 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3252 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 16 sheets defined 21.9% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 232 through 240 Processing helix chain 'A' and resid 241 through 261 Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 363 through 382 removed outlier: 3.575A pdb=" N GLY A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 417 removed outlier: 3.564A pdb=" N HIS A 404 " --> pdb=" O PRO A 400 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG A 408 " --> pdb=" O HIS A 404 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 removed outlier: 3.599A pdb=" N VAL A 435 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 460 Processing helix chain 'A' and resid 558 through 562 Processing helix chain 'A' and resid 629 through 633 Processing helix chain 'A' and resid 686 through 690 removed outlier: 3.934A pdb=" N CYS A 690 " --> pdb=" O GLY A 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 240 Processing helix chain 'B' and resid 241 through 261 Processing helix chain 'B' and resid 273 through 277 Processing helix chain 'B' and resid 300 through 313 Processing helix chain 'B' and resid 328 through 334 Processing helix chain 'B' and resid 363 through 382 removed outlier: 3.575A pdb=" N GLY B 382 " --> pdb=" O TYR B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 417 removed outlier: 3.563A pdb=" N HIS B 404 " --> pdb=" O PRO B 400 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG B 408 " --> pdb=" O HIS B 404 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 435 removed outlier: 3.599A pdb=" N VAL B 435 " --> pdb=" O TYR B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 460 Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 629 through 633 Processing helix chain 'B' and resid 686 through 690 removed outlier: 3.934A pdb=" N CYS B 690 " --> pdb=" O GLY B 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 240 Processing helix chain 'C' and resid 241 through 261 Processing helix chain 'C' and resid 273 through 277 Processing helix chain 'C' and resid 300 through 313 Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 363 through 382 removed outlier: 3.575A pdb=" N GLY C 382 " --> pdb=" O TYR C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 417 removed outlier: 3.563A pdb=" N HIS C 404 " --> pdb=" O PRO C 400 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG C 408 " --> pdb=" O HIS C 404 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET C 411 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR C 416 " --> pdb=" O VAL C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 removed outlier: 3.599A pdb=" N VAL C 435 " --> pdb=" O TYR C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 460 Processing helix chain 'C' and resid 558 through 562 Processing helix chain 'C' and resid 629 through 633 Processing helix chain 'C' and resid 686 through 690 removed outlier: 3.934A pdb=" N CYS C 690 " --> pdb=" O GLY C 687 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 316 through 321 removed outlier: 3.656A pdb=" N PHE A 348 " --> pdb=" O CYS A 268 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 350 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL A 347 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLN A 388 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE A 349 " --> pdb=" O GLN A 388 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N PHE A 421 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL A 387 " --> pdb=" O PHE A 421 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 285 through 286 Processing sheet with id=AA3, first strand: chain 'A' and resid 474 through 476 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 474 through 476 current: chain 'A' and resid 591 through 597 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 486 through 489 Processing sheet with id=AA5, first strand: chain 'A' and resid 643 through 653 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 643 through 653 current: chain 'A' and resid 713 through 720 removed outlier: 3.904A pdb=" N LYS A 734 " --> pdb=" O GLU A 715 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU A 717 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL A 732 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N TYR A 719 " --> pdb=" O GLY A 730 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLY A 730 " --> pdb=" O TYR A 719 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU A 745 " --> pdb=" O GLY A 730 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 779 through 781 current: chain 'B' and resid 713 through 720 removed outlier: 3.904A pdb=" N LYS B 734 " --> pdb=" O GLU B 715 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU B 717 " --> pdb=" O VAL B 732 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL B 732 " --> pdb=" O LEU B 717 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TYR B 719 " --> pdb=" O GLY B 730 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLY B 730 " --> pdb=" O TYR B 719 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU B 745 " --> pdb=" O GLY B 730 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 779 through 781 current: chain 'C' and resid 713 through 720 removed outlier: 3.903A pdb=" N LYS C 734 " --> pdb=" O GLU C 715 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU C 717 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL C 732 " --> pdb=" O LEU C 717 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TYR C 719 " --> pdb=" O GLY C 730 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLY C 730 " --> pdb=" O TYR C 719 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU C 745 " --> pdb=" O GLY C 730 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 755 through 758 removed outlier: 6.927A pdb=" N ILE A 772 " --> pdb=" O VAL A 757 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 316 through 321 removed outlier: 3.656A pdb=" N PHE B 348 " --> pdb=" O CYS B 268 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET B 350 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL B 347 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N GLN B 388 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE B 349 " --> pdb=" O GLN B 388 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N PHE B 421 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL B 387 " --> pdb=" O PHE B 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 285 through 286 Processing sheet with id=AA9, first strand: chain 'B' and resid 474 through 476 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 474 through 476 current: chain 'B' and resid 591 through 597 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 486 through 489 Processing sheet with id=AB2, first strand: chain 'B' and resid 755 through 758 removed outlier: 6.928A pdb=" N ILE B 772 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 316 through 321 removed outlier: 3.656A pdb=" N PHE C 348 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET C 350 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL C 347 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N GLN C 388 " --> pdb=" O VAL C 347 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE C 349 " --> pdb=" O GLN C 388 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N PHE C 421 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL C 387 " --> pdb=" O PHE C 421 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AB5, first strand: chain 'C' and resid 474 through 476 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 474 through 476 current: chain 'C' and resid 591 through 597 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 486 through 489 Processing sheet with id=AB7, first strand: chain 'C' and resid 755 through 758 removed outlier: 6.927A pdb=" N ILE C 772 " --> pdb=" O VAL C 757 " (cutoff:3.500A) 349 hydrogen bonds defined for protein. 912 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4584 1.34 - 1.46: 3778 1.46 - 1.58: 5960 1.58 - 1.70: 0 1.70 - 1.82: 147 Bond restraints: 14469 Sorted by residual: bond pdb=" C THR C 693 " pdb=" N PRO C 694 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.25e+00 bond pdb=" C THR B 693 " pdb=" N PRO B 694 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.25e+00 bond pdb=" C THR A 693 " pdb=" N PRO A 694 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.22e+00 bond pdb=" CB ASP B 708 " pdb=" CG ASP B 708 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.04e+00 bond pdb=" CB ASP C 708 " pdb=" CG ASP C 708 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.02e+00 ... (remaining 14464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 19166 1.46 - 2.93: 420 2.93 - 4.39: 60 4.39 - 5.85: 22 5.85 - 7.31: 6 Bond angle restraints: 19674 Sorted by residual: angle pdb=" N ASP C 240 " pdb=" CA ASP C 240 " pdb=" C ASP C 240 " ideal model delta sigma weight residual 109.39 113.67 -4.28 1.59e+00 3.96e-01 7.25e+00 angle pdb=" N ASP B 240 " pdb=" CA ASP B 240 " pdb=" C ASP B 240 " ideal model delta sigma weight residual 109.39 113.59 -4.20 1.59e+00 3.96e-01 6.97e+00 angle pdb=" N ASP A 240 " pdb=" CA ASP A 240 " pdb=" C ASP A 240 " ideal model delta sigma weight residual 109.39 113.57 -4.18 1.59e+00 3.96e-01 6.92e+00 angle pdb=" C ASP C 708 " pdb=" CA ASP C 708 " pdb=" CB ASP C 708 " ideal model delta sigma weight residual 110.42 115.28 -4.86 1.99e+00 2.53e-01 5.95e+00 angle pdb=" C ASP A 708 " pdb=" CA ASP A 708 " pdb=" CB ASP A 708 " ideal model delta sigma weight residual 110.42 115.25 -4.83 1.99e+00 2.53e-01 5.89e+00 ... (remaining 19669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 7224 16.46 - 32.92: 828 32.92 - 49.38: 238 49.38 - 65.84: 80 65.84 - 82.30: 21 Dihedral angle restraints: 8391 sinusoidal: 3249 harmonic: 5142 Sorted by residual: dihedral pdb=" CA GLN C 640 " pdb=" C GLN C 640 " pdb=" N ASP C 641 " pdb=" CA ASP C 641 " ideal model delta harmonic sigma weight residual 180.00 153.56 26.44 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA GLN A 640 " pdb=" C GLN A 640 " pdb=" N ASP A 641 " pdb=" CA ASP A 641 " ideal model delta harmonic sigma weight residual 180.00 153.56 26.44 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA GLN B 640 " pdb=" C GLN B 640 " pdb=" N ASP B 641 " pdb=" CA ASP B 641 " ideal model delta harmonic sigma weight residual 180.00 153.58 26.42 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 8388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1294 0.029 - 0.058: 491 0.058 - 0.087: 152 0.087 - 0.116: 94 0.116 - 0.145: 33 Chirality restraints: 2064 Sorted by residual: chirality pdb=" CA ILE C 286 " pdb=" N ILE C 286 " pdb=" C ILE C 286 " pdb=" CB ILE C 286 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA ILE A 286 " pdb=" N ILE A 286 " pdb=" C ILE A 286 " pdb=" CB ILE A 286 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA ILE B 286 " pdb=" N ILE B 286 " pdb=" C ILE B 286 " pdb=" CB ILE B 286 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 2061 not shown) Planarity restraints: 2553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 697 " -0.015 2.00e-02 2.50e+03 1.61e-02 5.17e+00 pdb=" CG TYR A 697 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 697 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 697 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 697 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 697 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 697 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 697 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 697 " 0.014 2.00e-02 2.50e+03 1.59e-02 5.08e+00 pdb=" CG TYR C 697 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR C 697 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 697 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR C 697 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR C 697 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 697 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 697 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 697 " 0.014 2.00e-02 2.50e+03 1.58e-02 5.02e+00 pdb=" CG TYR B 697 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR B 697 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 697 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR B 697 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 697 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 697 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 697 " -0.001 2.00e-02 2.50e+03 ... (remaining 2550 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3320 2.79 - 3.32: 11749 3.32 - 3.84: 22177 3.84 - 4.37: 24219 4.37 - 4.90: 44966 Nonbonded interactions: 106431 Sorted by model distance: nonbonded pdb=" OH TYR B 429 " pdb=" OE1 GLU B 529 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR A 429 " pdb=" OE1 GLU A 529 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR C 429 " pdb=" OE1 GLU C 529 " model vdw 2.261 3.040 nonbonded pdb=" OE1 GLN B 312 " pdb=" OG1 THR B 605 " model vdw 2.284 3.040 nonbonded pdb=" OE1 GLN A 312 " pdb=" OG1 THR A 605 " model vdw 2.285 3.040 ... (remaining 106426 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 group one per residue 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.550 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 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 : 0.002 0.035 14472 Z= 0.120 Angle : 0.565 7.315 19680 Z= 0.318 Chirality : 0.041 0.145 2064 Planarity : 0.004 0.051 2553 Dihedral : 16.509 82.297 5130 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.34 % Favored : 95.33 % Rotamer: Outliers : 3.85 % Allowed : 23.89 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.20), residues: 1797 helix: 1.42 (0.31), residues: 369 sheet: -0.08 (0.25), residues: 471 loop : -1.71 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 408 TYR 0.040 0.001 TYR A 697 PHE 0.007 0.001 PHE A 305 TRP 0.014 0.001 TRP B 821 HIS 0.003 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00232 (14469) covalent geometry : angle 0.56457 (19674) SS BOND : bond 0.00168 ( 3) SS BOND : angle 1.00162 ( 6) hydrogen bonds : bond 0.14258 ( 349) hydrogen bonds : angle 4.64898 ( 912) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 198 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6816 (mtt) REVERT: A 308 TYR cc_start: 0.7612 (t80) cc_final: 0.7244 (t80) REVERT: A 427 MET cc_start: 0.6816 (mmt) cc_final: 0.6035 (mmt) REVERT: A 432 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.6953 (t80) REVERT: A 477 TRP cc_start: 0.7346 (OUTLIER) cc_final: 0.6478 (p90) REVERT: B 308 TYR cc_start: 0.7527 (t80) cc_final: 0.7320 (t80) REVERT: B 427 MET cc_start: 0.6695 (mmt) cc_final: 0.5893 (mmt) REVERT: B 432 TYR cc_start: 0.7294 (OUTLIER) cc_final: 0.6606 (t80) REVERT: B 477 TRP cc_start: 0.7376 (OUTLIER) cc_final: 0.6590 (p90) REVERT: B 499 SER cc_start: 0.8483 (t) cc_final: 0.8025 (p) REVERT: B 500 ASP cc_start: 0.8142 (p0) cc_final: 0.7240 (t0) REVERT: B 581 ASN cc_start: 0.8086 (t0) cc_final: 0.7791 (t0) REVERT: B 641 ASP cc_start: 0.7196 (t0) cc_final: 0.6659 (p0) REVERT: B 782 GLN cc_start: 0.8042 (tp40) cc_final: 0.7834 (mm-40) REVERT: C 299 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6818 (mtt) REVERT: C 308 TYR cc_start: 0.7485 (t80) cc_final: 0.6925 (t80) REVERT: C 427 MET cc_start: 0.6919 (mmt) cc_final: 0.6075 (mmt) REVERT: C 432 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.6680 (t80) REVERT: C 477 TRP cc_start: 0.7434 (OUTLIER) cc_final: 0.6085 (p90) REVERT: C 480 MET cc_start: 0.8551 (mtt) cc_final: 0.7788 (mtt) REVERT: C 550 TRP cc_start: 0.8453 (m-10) cc_final: 0.8068 (m-10) REVERT: C 581 ASN cc_start: 0.8225 (t0) cc_final: 0.8011 (t0) REVERT: C 641 ASP cc_start: 0.6957 (t0) cc_final: 0.6373 (p0) REVERT: C 797 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.7203 (t80) outliers start: 57 outliers final: 35 residues processed: 233 average time/residue: 0.0918 time to fit residues: 33.4509 Evaluate side-chains 235 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 696 PHE Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 477 TRP Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 696 PHE Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 477 TRP Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 696 PHE Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 820 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.0170 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.7422 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.154826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.125267 restraints weight = 18256.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.128867 restraints weight = 10970.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.131301 restraints weight = 7990.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.132861 restraints weight = 6556.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133755 restraints weight = 5773.366| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14472 Z= 0.129 Angle : 0.508 7.123 19680 Z= 0.268 Chirality : 0.042 0.146 2064 Planarity : 0.004 0.056 2553 Dihedral : 7.648 86.879 2059 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.12 % Favored : 94.55 % Rotamer: Outliers : 5.80 % Allowed : 21.32 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.20), residues: 1797 helix: 1.34 (0.30), residues: 372 sheet: -0.08 (0.25), residues: 471 loop : -1.79 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 408 TYR 0.017 0.001 TYR C 301 PHE 0.009 0.001 PHE C 305 TRP 0.010 0.001 TRP C 821 HIS 0.002 0.001 HIS C 602 Details of bonding type rmsd covalent geometry : bond 0.00301 (14469) covalent geometry : angle 0.50729 (19674) SS BOND : bond 0.00346 ( 3) SS BOND : angle 1.39476 ( 6) hydrogen bonds : bond 0.04138 ( 349) hydrogen bonds : angle 4.11087 ( 912) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 201 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 427 MET cc_start: 0.7062 (mmt) cc_final: 0.6397 (mmt) REVERT: A 432 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.7992 (t80) REVERT: A 477 TRP cc_start: 0.7118 (OUTLIER) cc_final: 0.6858 (p90) REVERT: A 782 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8350 (mm-40) REVERT: B 427 MET cc_start: 0.6917 (mmt) cc_final: 0.6238 (mmt) REVERT: B 432 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.7865 (t80) REVERT: B 477 TRP cc_start: 0.7295 (OUTLIER) cc_final: 0.6617 (p90) REVERT: B 500 ASP cc_start: 0.7975 (p0) cc_final: 0.7750 (t0) REVERT: B 540 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8084 (mttt) REVERT: B 581 ASN cc_start: 0.8532 (t0) cc_final: 0.8255 (t0) REVERT: B 610 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8298 (pp) REVERT: C 372 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6939 (tt0) REVERT: C 410 GLN cc_start: 0.7621 (mt0) cc_final: 0.7329 (tt0) REVERT: C 427 MET cc_start: 0.7043 (mmt) cc_final: 0.6377 (mmt) REVERT: C 432 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.7962 (t80) REVERT: C 477 TRP cc_start: 0.7252 (OUTLIER) cc_final: 0.6524 (p90) REVERT: C 499 SER cc_start: 0.8505 (t) cc_final: 0.8264 (p) REVERT: C 500 ASP cc_start: 0.7931 (p0) cc_final: 0.7631 (t0) REVERT: C 581 ASN cc_start: 0.8519 (t0) cc_final: 0.8241 (t0) outliers start: 86 outliers final: 48 residues processed: 255 average time/residue: 0.0997 time to fit residues: 39.1963 Evaluate side-chains 241 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 183 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 696 PHE Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 477 TRP Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 696 PHE Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 477 TRP Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 696 PHE Chi-restraints excluded: chain C residue 789 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 8 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 129 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 771 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.142165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.112730 restraints weight = 18784.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.115858 restraints weight = 11779.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.117961 restraints weight = 8859.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.119250 restraints weight = 7425.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.119988 restraints weight = 6658.694| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14472 Z= 0.257 Angle : 0.619 7.969 19680 Z= 0.331 Chirality : 0.046 0.167 2064 Planarity : 0.005 0.061 2553 Dihedral : 7.627 89.755 2035 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.40 % Favored : 93.27 % Rotamer: Outliers : 8.70 % Allowed : 19.91 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.30 (0.20), residues: 1797 helix: 1.33 (0.31), residues: 369 sheet: -0.41 (0.24), residues: 477 loop : -2.08 (0.18), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 408 TYR 0.023 0.002 TYR B 301 PHE 0.016 0.002 PHE B 583 TRP 0.021 0.002 TRP C 550 HIS 0.004 0.001 HIS C 602 Details of bonding type rmsd covalent geometry : bond 0.00628 (14469) covalent geometry : angle 0.61787 (19674) SS BOND : bond 0.00414 ( 3) SS BOND : angle 1.78775 ( 6) hydrogen bonds : bond 0.06364 ( 349) hydrogen bonds : angle 4.36497 ( 912) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 183 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.7174 (mmt) cc_final: 0.6437 (mmt) REVERT: A 432 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.8155 (t80) REVERT: A 445 MET cc_start: 0.8766 (tpt) cc_final: 0.8505 (tpt) REVERT: A 500 ASP cc_start: 0.8073 (p0) cc_final: 0.7706 (t0) REVERT: A 642 GLU cc_start: 0.7219 (mp0) cc_final: 0.6947 (mp0) REVERT: B 427 MET cc_start: 0.7031 (mmt) cc_final: 0.6404 (mmt) REVERT: B 432 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.8030 (t80) REVERT: B 459 MET cc_start: 0.7582 (mtp) cc_final: 0.7070 (mtp) REVERT: B 491 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7238 (mpp) REVERT: B 500 ASP cc_start: 0.8032 (p0) cc_final: 0.7735 (t0) REVERT: B 581 ASN cc_start: 0.8556 (t0) cc_final: 0.8266 (t0) REVERT: B 610 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8452 (pp) REVERT: B 820 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7959 (m-30) REVERT: C 372 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7087 (tt0) REVERT: C 410 GLN cc_start: 0.7594 (mt0) cc_final: 0.7321 (tt0) REVERT: C 427 MET cc_start: 0.7186 (mmt) cc_final: 0.6642 (mmt) REVERT: C 432 TYR cc_start: 0.8857 (OUTLIER) cc_final: 0.8006 (t80) REVERT: C 500 ASP cc_start: 0.7969 (p0) cc_final: 0.7653 (t0) REVERT: C 797 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8731 (t80) outliers start: 129 outliers final: 83 residues processed: 269 average time/residue: 0.0894 time to fit residues: 37.7327 Evaluate side-chains 266 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 175 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 696 PHE Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 696 PHE Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 350 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 696 PHE Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 797 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 114 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 771 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.148747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118584 restraints weight = 18643.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.122059 restraints weight = 11358.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.124326 restraints weight = 8388.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.125794 restraints weight = 6957.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.126409 restraints weight = 6180.592| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14472 Z= 0.168 Angle : 0.536 7.091 19680 Z= 0.286 Chirality : 0.043 0.181 2064 Planarity : 0.005 0.060 2553 Dihedral : 7.112 83.874 2027 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.73 % Favored : 93.93 % Rotamer: Outliers : 6.88 % Allowed : 22.13 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.36 (0.20), residues: 1797 helix: 1.30 (0.30), residues: 369 sheet: -0.48 (0.24), residues: 471 loop : -2.11 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 408 TYR 0.022 0.001 TYR A 301 PHE 0.012 0.001 PHE A 305 TRP 0.020 0.001 TRP C 550 HIS 0.002 0.001 HIS A 602 Details of bonding type rmsd covalent geometry : bond 0.00402 (14469) covalent geometry : angle 0.53520 (19674) SS BOND : bond 0.00298 ( 3) SS BOND : angle 1.55171 ( 6) hydrogen bonds : bond 0.04914 ( 349) hydrogen bonds : angle 4.17750 ( 912) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 178 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.7156 (mmt) cc_final: 0.6443 (mmt) REVERT: A 432 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8118 (t80) REVERT: A 445 MET cc_start: 0.8672 (tpt) cc_final: 0.8416 (tpt) REVERT: A 477 TRP cc_start: 0.7373 (OUTLIER) cc_final: 0.6968 (p90) REVERT: A 500 ASP cc_start: 0.8088 (p0) cc_final: 0.7679 (t0) REVERT: A 782 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8389 (mm-40) REVERT: B 427 MET cc_start: 0.7039 (mmt) cc_final: 0.6343 (mmt) REVERT: B 432 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.8054 (t80) REVERT: B 491 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7340 (tpp) REVERT: B 500 ASP cc_start: 0.8051 (p0) cc_final: 0.7724 (t0) REVERT: B 540 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8122 (mttt) REVERT: B 581 ASN cc_start: 0.8558 (t0) cc_final: 0.8275 (t0) REVERT: B 610 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8450 (pp) REVERT: C 372 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7090 (tt0) REVERT: C 410 GLN cc_start: 0.7580 (tt0) cc_final: 0.7333 (tt0) REVERT: C 427 MET cc_start: 0.7211 (mmt) cc_final: 0.6593 (mmt) REVERT: C 432 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.8040 (t80) REVERT: C 477 TRP cc_start: 0.7227 (OUTLIER) cc_final: 0.6980 (p90) REVERT: C 500 ASP cc_start: 0.8008 (p0) cc_final: 0.7600 (t0) REVERT: C 797 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8702 (t80) REVERT: C 820 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7789 (m-30) outliers start: 102 outliers final: 68 residues processed: 248 average time/residue: 0.0954 time to fit residues: 37.5582 Evaluate side-chains 251 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 171 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 696 PHE Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 696 PHE Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 477 TRP Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 696 PHE Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 820 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 59 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 143 optimal weight: 0.0050 chunk 179 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 ASN ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.149792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.119674 restraints weight = 18547.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.123172 restraints weight = 11287.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.125425 restraints weight = 8330.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.126889 restraints weight = 6907.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127725 restraints weight = 6140.080| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14472 Z= 0.141 Angle : 0.518 7.163 19680 Z= 0.274 Chirality : 0.043 0.158 2064 Planarity : 0.004 0.056 2553 Dihedral : 6.955 82.713 2025 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.18 % Favored : 93.49 % Rotamer: Outliers : 7.15 % Allowed : 22.67 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.29 (0.20), residues: 1797 helix: 1.40 (0.30), residues: 366 sheet: -0.48 (0.25), residues: 471 loop : -2.03 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 408 TYR 0.021 0.001 TYR C 301 PHE 0.011 0.001 PHE A 305 TRP 0.013 0.001 TRP C 550 HIS 0.002 0.000 HIS A 602 Details of bonding type rmsd covalent geometry : bond 0.00335 (14469) covalent geometry : angle 0.51728 (19674) SS BOND : bond 0.00272 ( 3) SS BOND : angle 1.46515 ( 6) hydrogen bonds : bond 0.04485 ( 349) hydrogen bonds : angle 4.08254 ( 912) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 174 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 427 MET cc_start: 0.7149 (mmt) cc_final: 0.6376 (mmt) REVERT: A 432 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.8249 (t80) REVERT: A 445 MET cc_start: 0.8630 (tpt) cc_final: 0.8364 (tpt) REVERT: A 477 TRP cc_start: 0.7235 (OUTLIER) cc_final: 0.6636 (p90) REVERT: A 500 ASP cc_start: 0.8088 (p0) cc_final: 0.7697 (t0) REVERT: A 820 ASP cc_start: 0.8191 (m-30) cc_final: 0.7903 (m-30) REVERT: B 427 MET cc_start: 0.7044 (mmt) cc_final: 0.6323 (mmt) REVERT: B 432 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.8042 (t80) REVERT: B 491 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7320 (tpp) REVERT: B 500 ASP cc_start: 0.8059 (p0) cc_final: 0.7713 (t0) REVERT: B 540 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8120 (mttt) REVERT: B 581 ASN cc_start: 0.8545 (t0) cc_final: 0.8257 (t0) REVERT: C 372 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7091 (tt0) REVERT: C 414 ARG cc_start: 0.8328 (tpp80) cc_final: 0.8091 (tpp-160) REVERT: C 427 MET cc_start: 0.7144 (mmt) cc_final: 0.6495 (mmt) REVERT: C 432 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8084 (t80) REVERT: C 500 ASP cc_start: 0.8007 (p0) cc_final: 0.7603 (t0) outliers start: 106 outliers final: 74 residues processed: 249 average time/residue: 0.0959 time to fit residues: 37.6808 Evaluate side-chains 246 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 165 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 696 PHE Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 565 GLN Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain B residue 696 PHE Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 696 PHE Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 789 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 63 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 GLN B 660 GLN ** C 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.147788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.117733 restraints weight = 18489.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.121146 restraints weight = 11322.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.123383 restraints weight = 8390.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.124761 restraints weight = 6978.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.125342 restraints weight = 6216.473| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14472 Z= 0.182 Angle : 0.550 7.037 19680 Z= 0.293 Chirality : 0.044 0.161 2064 Planarity : 0.004 0.056 2553 Dihedral : 7.051 83.741 2024 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.73 % Favored : 92.93 % Rotamer: Outliers : 7.09 % Allowed : 23.62 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.38 (0.20), residues: 1797 helix: 1.38 (0.30), residues: 366 sheet: -0.62 (0.25), residues: 468 loop : -2.08 (0.18), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 408 TYR 0.022 0.001 TYR C 301 PHE 0.013 0.001 PHE A 305 TRP 0.012 0.001 TRP C 550 HIS 0.002 0.001 HIS C 602 Details of bonding type rmsd covalent geometry : bond 0.00438 (14469) covalent geometry : angle 0.54948 (19674) SS BOND : bond 0.00321 ( 3) SS BOND : angle 1.60792 ( 6) hydrogen bonds : bond 0.05077 ( 349) hydrogen bonds : angle 4.13501 ( 912) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 166 time to evaluate : 0.484 Fit side-chains REVERT: A 427 MET cc_start: 0.7186 (mmt) cc_final: 0.6379 (mmt) REVERT: A 432 TYR cc_start: 0.8857 (OUTLIER) cc_final: 0.8258 (t80) REVERT: A 445 MET cc_start: 0.8688 (tpt) cc_final: 0.8462 (tpt) REVERT: A 500 ASP cc_start: 0.8123 (p0) cc_final: 0.7709 (t0) REVERT: A 820 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7917 (m-30) REVERT: B 427 MET cc_start: 0.7053 (mmt) cc_final: 0.6378 (mmt) REVERT: B 432 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.8118 (t80) REVERT: B 491 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7372 (tpp) REVERT: B 500 ASP cc_start: 0.8094 (p0) cc_final: 0.7718 (t0) REVERT: B 540 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8139 (mttt) REVERT: B 581 ASN cc_start: 0.8555 (t0) cc_final: 0.8244 (t0) REVERT: C 274 MET cc_start: 0.7736 (ttt) cc_final: 0.7522 (ttt) REVERT: C 372 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7129 (tt0) REVERT: C 410 GLN cc_start: 0.7651 (tt0) cc_final: 0.7439 (tt0) REVERT: C 414 ARG cc_start: 0.8365 (tpp80) cc_final: 0.8109 (tpp-160) REVERT: C 427 MET cc_start: 0.7123 (mmt) cc_final: 0.6423 (mmt) REVERT: C 432 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.8080 (t80) REVERT: C 500 ASP cc_start: 0.8052 (p0) cc_final: 0.7601 (t0) outliers start: 105 outliers final: 86 residues processed: 239 average time/residue: 0.1002 time to fit residues: 37.3596 Evaluate side-chains 257 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 164 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 696 PHE Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 565 GLN Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 660 GLN Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 696 PHE Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 696 PHE Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 789 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.148407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.118484 restraints weight = 18325.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.121859 restraints weight = 11261.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.124086 restraints weight = 8364.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.125025 restraints weight = 6961.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.126225 restraints weight = 6320.897| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14472 Z= 0.161 Angle : 0.542 7.149 19680 Z= 0.287 Chirality : 0.043 0.167 2064 Planarity : 0.004 0.055 2553 Dihedral : 7.001 82.111 2024 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.95 % Favored : 93.71 % Rotamer: Outliers : 7.49 % Allowed : 23.21 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1797 helix: 1.35 (0.30), residues: 369 sheet: -0.65 (0.25), residues: 468 loop : -2.11 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 408 TYR 0.022 0.001 TYR C 301 PHE 0.012 0.001 PHE A 305 TRP 0.015 0.001 TRP C 293 HIS 0.002 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00387 (14469) covalent geometry : angle 0.54108 (19674) SS BOND : bond 0.00301 ( 3) SS BOND : angle 1.55003 ( 6) hydrogen bonds : bond 0.04818 ( 349) hydrogen bonds : angle 4.09386 ( 912) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 172 time to evaluate : 0.548 Fit side-chains REVERT: A 427 MET cc_start: 0.7164 (mmt) cc_final: 0.6351 (mmt) REVERT: A 432 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.8335 (t80) REVERT: A 445 MET cc_start: 0.8679 (tpt) cc_final: 0.8421 (tpt) REVERT: A 477 TRP cc_start: 0.7550 (OUTLIER) cc_final: 0.6650 (p90) REVERT: A 500 ASP cc_start: 0.8112 (p0) cc_final: 0.7699 (t0) REVERT: A 820 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: B 427 MET cc_start: 0.7006 (mmt) cc_final: 0.6318 (mmt) REVERT: B 432 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.8091 (t80) REVERT: B 445 MET cc_start: 0.8644 (tpt) cc_final: 0.8135 (tpt) REVERT: B 491 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7395 (tpp) REVERT: B 500 ASP cc_start: 0.8083 (p0) cc_final: 0.7716 (t0) REVERT: B 540 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8116 (mttt) REVERT: B 581 ASN cc_start: 0.8538 (t0) cc_final: 0.8232 (t0) REVERT: C 274 MET cc_start: 0.7744 (ttt) cc_final: 0.7532 (ttt) REVERT: C 372 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7138 (tt0) REVERT: C 414 ARG cc_start: 0.8314 (tpp80) cc_final: 0.8086 (tpp-160) REVERT: C 427 MET cc_start: 0.7099 (mmt) cc_final: 0.6397 (mmt) REVERT: C 432 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.8082 (t80) REVERT: C 500 ASP cc_start: 0.8031 (p0) cc_final: 0.7581 (t0) outliers start: 111 outliers final: 89 residues processed: 247 average time/residue: 0.0983 time to fit residues: 37.7705 Evaluate side-chains 263 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 166 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 540 LYS Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 696 PHE Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 565 GLN Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 696 PHE Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 696 PHE Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 789 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 19 optimal weight: 0.0470 chunk 149 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 164 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.151964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.121738 restraints weight = 18258.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.125243 restraints weight = 11194.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.127526 restraints weight = 8288.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.128846 restraints weight = 6879.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.129876 restraints weight = 6138.567| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14472 Z= 0.108 Angle : 0.505 6.996 19680 Z= 0.266 Chirality : 0.042 0.171 2064 Planarity : 0.004 0.052 2553 Dihedral : 6.800 79.066 2024 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.56 % Favored : 94.10 % Rotamer: Outliers : 5.87 % Allowed : 25.17 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.32 (0.20), residues: 1797 helix: 1.43 (0.30), residues: 366 sheet: -0.55 (0.25), residues: 465 loop : -2.04 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 408 TYR 0.019 0.001 TYR C 301 PHE 0.010 0.001 PHE C 606 TRP 0.015 0.001 TRP C 293 HIS 0.002 0.000 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00249 (14469) covalent geometry : angle 0.50432 (19674) SS BOND : bond 0.00226 ( 3) SS BOND : angle 1.35310 ( 6) hydrogen bonds : bond 0.03854 ( 349) hydrogen bonds : angle 3.97239 ( 912) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 175 time to evaluate : 0.510 Fit side-chains REVERT: A 270 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8024 (tp) REVERT: A 427 MET cc_start: 0.7131 (mmt) cc_final: 0.6335 (mmt) REVERT: A 432 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.8282 (t80) REVERT: A 445 MET cc_start: 0.8563 (tpt) cc_final: 0.8301 (tpt) REVERT: A 477 TRP cc_start: 0.7490 (OUTLIER) cc_final: 0.6611 (p90) REVERT: A 500 ASP cc_start: 0.8145 (p0) cc_final: 0.7668 (t0) REVERT: A 820 ASP cc_start: 0.8101 (m-30) cc_final: 0.7864 (m-30) REVERT: B 427 MET cc_start: 0.6991 (mmt) cc_final: 0.6327 (mmt) REVERT: B 432 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.8073 (t80) REVERT: B 445 MET cc_start: 0.8557 (tpt) cc_final: 0.8069 (tpt) REVERT: B 491 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7290 (tpp) REVERT: B 500 ASP cc_start: 0.8084 (p0) cc_final: 0.7712 (t0) REVERT: B 540 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8091 (mttt) REVERT: B 581 ASN cc_start: 0.8523 (t0) cc_final: 0.8246 (t0) REVERT: C 274 MET cc_start: 0.7691 (ttt) cc_final: 0.7489 (ttt) REVERT: C 372 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7147 (tt0) REVERT: C 414 ARG cc_start: 0.8303 (tpp80) cc_final: 0.8100 (tpp-160) REVERT: C 427 MET cc_start: 0.6996 (mmt) cc_final: 0.6328 (mmt) REVERT: C 432 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.8131 (t80) REVERT: C 477 TRP cc_start: 0.7195 (OUTLIER) cc_final: 0.6448 (p90) REVERT: C 500 ASP cc_start: 0.7963 (p0) cc_final: 0.7514 (t0) outliers start: 87 outliers final: 70 residues processed: 233 average time/residue: 0.1029 time to fit residues: 37.6489 Evaluate side-chains 250 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 171 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 540 LYS Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 696 PHE Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 565 GLN Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 696 PHE Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 477 TRP Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 696 PHE Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 789 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 172 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 75 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN A 660 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.143562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.114021 restraints weight = 18528.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.116874 restraints weight = 11696.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.119140 restraints weight = 8913.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.120502 restraints weight = 7469.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.121360 restraints weight = 6668.840| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14472 Z= 0.187 Angle : 0.556 7.111 19680 Z= 0.296 Chirality : 0.044 0.202 2064 Planarity : 0.004 0.053 2553 Dihedral : 6.919 83.072 2021 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.73 % Favored : 92.93 % Rotamer: Outliers : 6.34 % Allowed : 24.97 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.50 (0.20), residues: 1797 helix: 1.41 (0.30), residues: 366 sheet: -0.77 (0.26), residues: 429 loop : -2.12 (0.17), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 408 TYR 0.022 0.001 TYR C 301 PHE 0.012 0.002 PHE B 305 TRP 0.021 0.001 TRP C 550 HIS 0.003 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00451 (14469) covalent geometry : angle 0.55524 (19674) SS BOND : bond 0.00345 ( 3) SS BOND : angle 1.64303 ( 6) hydrogen bonds : bond 0.05109 ( 349) hydrogen bonds : angle 4.09539 ( 912) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 171 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 427 MET cc_start: 0.7194 (mmt) cc_final: 0.6407 (mmt) REVERT: A 432 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.8337 (t80) REVERT: A 445 MET cc_start: 0.8706 (tpt) cc_final: 0.8502 (tpt) REVERT: A 477 TRP cc_start: 0.7526 (OUTLIER) cc_final: 0.6679 (p90) REVERT: A 500 ASP cc_start: 0.8055 (p0) cc_final: 0.7668 (t0) REVERT: A 820 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: B 427 MET cc_start: 0.7036 (mmt) cc_final: 0.6345 (mmt) REVERT: B 432 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.8184 (t80) REVERT: B 445 MET cc_start: 0.8662 (tpt) cc_final: 0.8202 (tpt) REVERT: B 491 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7310 (tpp) REVERT: B 500 ASP cc_start: 0.8048 (p0) cc_final: 0.7698 (t0) REVERT: B 540 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8117 (mttt) REVERT: B 581 ASN cc_start: 0.8526 (t0) cc_final: 0.8246 (t0) REVERT: C 274 MET cc_start: 0.7778 (ttt) cc_final: 0.7562 (ttt) REVERT: C 372 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7155 (tt0) REVERT: C 427 MET cc_start: 0.7092 (mmt) cc_final: 0.6383 (mmt) REVERT: C 432 TYR cc_start: 0.8842 (OUTLIER) cc_final: 0.8179 (t80) REVERT: C 477 TRP cc_start: 0.7289 (OUTLIER) cc_final: 0.6570 (p90) REVERT: C 500 ASP cc_start: 0.7930 (p0) cc_final: 0.7484 (t0) outliers start: 94 outliers final: 78 residues processed: 234 average time/residue: 0.1013 time to fit residues: 37.3565 Evaluate side-chains 255 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 168 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 696 PHE Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 565 GLN Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 696 PHE Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 477 TRP Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 696 PHE Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 789 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 176 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 117 optimal weight: 0.0070 chunk 43 optimal weight: 4.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN A 660 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.150775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.120809 restraints weight = 18323.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.124270 restraints weight = 11201.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.126533 restraints weight = 8260.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.128007 restraints weight = 6859.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.128802 restraints weight = 6085.332| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14472 Z= 0.124 Angle : 0.521 6.942 19680 Z= 0.277 Chirality : 0.043 0.212 2064 Planarity : 0.004 0.050 2553 Dihedral : 6.749 79.720 2021 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.40 % Favored : 94.27 % Rotamer: Outliers : 6.07 % Allowed : 25.30 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.36 (0.20), residues: 1797 helix: 1.44 (0.30), residues: 366 sheet: -0.64 (0.25), residues: 465 loop : -2.06 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 408 TYR 0.020 0.001 TYR C 301 PHE 0.010 0.001 PHE A 305 TRP 0.023 0.001 TRP C 550 HIS 0.002 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00289 (14469) covalent geometry : angle 0.52096 (19674) SS BOND : bond 0.00253 ( 3) SS BOND : angle 1.40728 ( 6) hydrogen bonds : bond 0.04240 ( 349) hydrogen bonds : angle 4.01014 ( 912) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 167 time to evaluate : 0.532 Fit side-chains REVERT: A 270 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8083 (tp) REVERT: A 427 MET cc_start: 0.7157 (mmt) cc_final: 0.6347 (mmt) REVERT: A 432 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.8280 (t80) REVERT: A 445 MET cc_start: 0.8623 (tpt) cc_final: 0.8368 (tpt) REVERT: A 477 TRP cc_start: 0.7457 (OUTLIER) cc_final: 0.6627 (p90) REVERT: A 500 ASP cc_start: 0.8068 (p0) cc_final: 0.7647 (t0) REVERT: A 820 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7899 (m-30) REVERT: B 427 MET cc_start: 0.6990 (mmt) cc_final: 0.6286 (mmt) REVERT: B 432 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.8071 (t80) REVERT: B 445 MET cc_start: 0.8575 (tpt) cc_final: 0.8102 (tpt) REVERT: B 491 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7292 (tpp) REVERT: B 500 ASP cc_start: 0.8057 (p0) cc_final: 0.7679 (t0) REVERT: B 540 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8107 (mttt) REVERT: B 581 ASN cc_start: 0.8533 (t0) cc_final: 0.8252 (t0) REVERT: C 274 MET cc_start: 0.7704 (ttt) cc_final: 0.7484 (ttt) REVERT: C 372 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7147 (tt0) REVERT: C 427 MET cc_start: 0.7060 (mmt) cc_final: 0.6323 (mmt) REVERT: C 432 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8134 (t80) REVERT: C 477 TRP cc_start: 0.7185 (OUTLIER) cc_final: 0.6347 (p90) REVERT: C 500 ASP cc_start: 0.7954 (p0) cc_final: 0.7458 (t0) outliers start: 90 outliers final: 78 residues processed: 229 average time/residue: 0.0992 time to fit residues: 35.5784 Evaluate side-chains 254 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 166 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 540 LYS Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 696 PHE Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 565 GLN Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 696 PHE Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 477 TRP Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 696 PHE Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 789 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 139 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.141306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.111666 restraints weight = 18636.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.114683 restraints weight = 11860.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.116693 restraints weight = 8973.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.117977 restraints weight = 7582.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118741 restraints weight = 6811.115| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14472 Z= 0.250 Angle : 0.617 7.536 19680 Z= 0.329 Chirality : 0.046 0.193 2064 Planarity : 0.005 0.051 2553 Dihedral : 7.127 83.937 2021 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.24 % Favored : 91.43 % Rotamer: Outliers : 6.55 % Allowed : 24.90 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.66 (0.19), residues: 1797 helix: 1.38 (0.30), residues: 366 sheet: -0.84 (0.25), residues: 444 loop : -2.31 (0.17), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 505 TYR 0.025 0.002 TYR C 301 PHE 0.014 0.002 PHE B 305 TRP 0.024 0.002 TRP C 550 HIS 0.004 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00608 (14469) covalent geometry : angle 0.61621 (19674) SS BOND : bond 0.00411 ( 3) SS BOND : angle 1.83828 ( 6) hydrogen bonds : bond 0.06004 ( 349) hydrogen bonds : angle 4.24027 ( 912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2089.40 seconds wall clock time: 36 minutes 55.54 seconds (2215.54 seconds total)