Starting phenix.real_space_refine on Wed Aug 5 23:23:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vuq_65369/08_2026/9vuq_65369.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vuq_65369/08_2026/9vuq_65369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vuq_65369/08_2026/9vuq_65369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vuq_65369/08_2026/9vuq_65369.map" model { file = "/net/cci-nas-00/data/ceres_data/9vuq_65369/08_2026/9vuq_65369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vuq_65369/08_2026/9vuq_65369.cif" } resolution = 2.79 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= 0.004 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 24 5.16 5 C 7594 2.51 5 N 2098 2.21 5 O 2136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11860 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 5807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5807 Classifications: {'peptide': 733} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 36, 'TRANS': 696} Chain breaks: 3 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 5807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5807 Classifications: {'peptide': 733} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 36, 'TRANS': 696} Chain breaks: 3 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 113 Unusual residues: {'MX7': 1, 'PKZ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 113 Unusual residues: {'MX7': 1, 'PKZ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 2.27, per 1000 atoms: 0.19 Number of scatterers: 11860 At special positions: 0 Unit cell: (188.24, 130, 98.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 8 15.00 O 2136 8.00 N 2098 7.00 C 7594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 530.2 milliseconds 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2732 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 59.0% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 197 through 202 Processing helix chain 'E' and resid 210 through 220 Processing helix chain 'E' and resid 247 through 265 removed outlier: 3.586A pdb=" N LEU E 251 " --> pdb=" O THR E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 283 Processing helix chain 'E' and resid 284 through 299 Processing helix chain 'E' and resid 301 through 317 removed outlier: 3.731A pdb=" N ALA E 305 " --> pdb=" O LYS E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 339 removed outlier: 3.751A pdb=" N ALA E 331 " --> pdb=" O SER E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 355 removed outlier: 3.608A pdb=" N PHE E 351 " --> pdb=" O HIS E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 382 removed outlier: 4.476A pdb=" N LEU E 373 " --> pdb=" O HIS E 369 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER E 376 " --> pdb=" O TYR E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 396 No H-bonds generated for 'chain 'E' and resid 394 through 396' Processing helix chain 'E' and resid 399 through 407 Processing helix chain 'E' and resid 419 through 437 Processing helix chain 'E' and resid 460 through 472 Processing helix chain 'E' and resid 495 through 500 Processing helix chain 'E' and resid 508 through 515 Processing helix chain 'E' and resid 515 through 521 Processing helix chain 'E' and resid 537 through 545 Processing helix chain 'E' and resid 559 through 580 Processing helix chain 'E' and resid 584 through 594 Processing helix chain 'E' and resid 595 through 598 removed outlier: 7.854A pdb=" N LYS E 598 " --> pdb=" O SER E 595 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 595 through 598' Processing helix chain 'E' and resid 603 through 620 Processing helix chain 'E' and resid 632 through 644 Processing helix chain 'E' and resid 661 through 673 removed outlier: 3.765A pdb=" N VAL E 665 " --> pdb=" O GLY E 661 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR E 669 " --> pdb=" O VAL E 665 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE E 670 " --> pdb=" O LEU E 666 " (cutoff:3.500A) Processing helix chain 'E' and resid 674 through 677 Processing helix chain 'E' and resid 678 through 688 removed outlier: 3.714A pdb=" N PHE E 688 " --> pdb=" O ILE E 684 " (cutoff:3.500A) Processing helix chain 'E' and resid 696 through 715 Proline residue: E 708 - end of helix Processing helix chain 'E' and resid 719 through 737 Processing helix chain 'E' and resid 758 through 769 Processing helix chain 'E' and resid 771 through 789 Processing helix chain 'E' and resid 794 through 813 Processing helix chain 'E' and resid 817 through 821 Processing helix chain 'E' and resid 822 through 837 removed outlier: 3.739A pdb=" N LEU E 836 " --> pdb=" O LYS E 832 " (cutoff:3.500A) Processing helix chain 'E' and resid 850 through 860 removed outlier: 3.570A pdb=" N LYS E 854 " --> pdb=" O ASP E 850 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 863 No H-bonds generated for 'chain 'E' and resid 861 through 863' Processing helix chain 'E' and resid 865 through 874 Processing helix chain 'C' and resid 103 through 112 Processing helix chain 'C' and resid 197 through 202 Processing helix chain 'C' and resid 210 through 220 Processing helix chain 'C' and resid 247 through 265 removed outlier: 3.586A pdb=" N LEU C 251 " --> pdb=" O THR C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 283 Processing helix chain 'C' and resid 284 through 299 Processing helix chain 'C' and resid 301 through 317 removed outlier: 3.731A pdb=" N ALA C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 339 removed outlier: 3.751A pdb=" N ALA C 331 " --> pdb=" O SER C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 355 removed outlier: 3.608A pdb=" N PHE C 351 " --> pdb=" O HIS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 382 removed outlier: 3.908A pdb=" N SER C 376 " --> pdb=" O TYR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 396 No H-bonds generated for 'chain 'C' and resid 394 through 396' Processing helix chain 'C' and resid 399 through 407 Processing helix chain 'C' and resid 419 through 437 Processing helix chain 'C' and resid 460 through 472 Processing helix chain 'C' and resid 495 through 500 Processing helix chain 'C' and resid 508 through 515 Processing helix chain 'C' and resid 515 through 521 Processing helix chain 'C' and resid 537 through 545 Processing helix chain 'C' and resid 559 through 580 Processing helix chain 'C' and resid 584 through 594 Processing helix chain 'C' and resid 595 through 598 removed outlier: 7.854A pdb=" N LYS C 598 " --> pdb=" O SER C 595 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 595 through 598' Processing helix chain 'C' and resid 603 through 620 Processing helix chain 'C' and resid 632 through 644 Processing helix chain 'C' and resid 661 through 673 removed outlier: 3.765A pdb=" N VAL C 665 " --> pdb=" O GLY C 661 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE C 670 " --> pdb=" O LEU C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 677 Processing helix chain 'C' and resid 678 through 688 removed outlier: 3.714A pdb=" N PHE C 688 " --> pdb=" O ILE C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 715 Proline residue: C 708 - end of helix Processing helix chain 'C' and resid 719 through 737 Processing helix chain 'C' and resid 758 through 769 Processing helix chain 'C' and resid 771 through 789 Processing helix chain 'C' and resid 794 through 813 Processing helix chain 'C' and resid 817 through 821 Processing helix chain 'C' and resid 822 through 837 removed outlier: 3.740A pdb=" N LEU C 836 " --> pdb=" O LYS C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 860 removed outlier: 3.571A pdb=" N LYS C 854 " --> pdb=" O ASP C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 863 No H-bonds generated for 'chain 'C' and resid 861 through 863' Processing helix chain 'C' and resid 865 through 874 Processing sheet with id=AA1, first strand: chain 'E' and resid 182 through 184 removed outlier: 3.558A pdb=" N SER E 183 " --> pdb=" O LEU E 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 343 through 346 removed outlier: 6.220A pdb=" N LEU E 344 " --> pdb=" O VAL E 529 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE E 531 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N HIS E 346 " --> pdb=" O PHE E 531 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL E 482 " --> pdb=" O VAL E 363 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 343 through 346 removed outlier: 6.220A pdb=" N LEU E 344 " --> pdb=" O VAL E 529 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE E 531 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N HIS E 346 " --> pdb=" O PHE E 531 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 582 through 583 Processing sheet with id=AA5, first strand: chain 'E' and resid 600 through 602 Processing sheet with id=AA6, first strand: chain 'E' and resid 693 through 695 removed outlier: 3.810A pdb=" N SER E 744 " --> pdb=" O ILE E 750 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLN E 752 " --> pdb=" O GLN E 742 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLN E 742 " --> pdb=" O GLN E 752 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 182 through 184 removed outlier: 3.558A pdb=" N SER C 183 " --> pdb=" O LEU C 225 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 343 through 346 removed outlier: 6.220A pdb=" N LEU C 344 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE C 531 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N HIS C 346 " --> pdb=" O PHE C 531 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 482 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 343 through 346 removed outlier: 6.220A pdb=" N LEU C 344 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE C 531 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N HIS C 346 " --> pdb=" O PHE C 531 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 582 through 583 Processing sheet with id=AB2, first strand: chain 'C' and resid 600 through 602 Processing sheet with id=AB3, first strand: chain 'C' and resid 693 through 695 removed outlier: 3.810A pdb=" N SER C 744 " --> pdb=" O ILE C 750 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLN C 752 " --> pdb=" O GLN C 742 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLN C 742 " --> pdb=" O GLN C 752 " (cutoff:3.500A) 622 hydrogen bonds defined for protein. 1794 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: 1.75 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2111 1.32 - 1.45: 3080 1.45 - 1.57: 6861 1.57 - 1.69: 12 1.69 - 1.81: 40 Bond restraints: 12104 Sorted by residual: bond pdb=" O11 MX7 C1001 " pdb=" P MX7 C1001 " ideal model delta sigma weight residual 1.707 1.607 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" O11 MX7 E1001 " pdb=" P MX7 E1001 " ideal model delta sigma weight residual 1.707 1.607 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" O3B PKZ E1002 " pdb=" P3B PKZ E1002 " ideal model delta sigma weight residual 1.714 1.625 0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" O3B PKZ C1002 " pdb=" P3B PKZ C1002 " ideal model delta sigma weight residual 1.714 1.625 0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" C1 MX7 E1001 " pdb=" O11 MX7 E1001 " ideal model delta sigma weight residual 1.389 1.452 -0.063 2.00e-02 2.50e+03 9.88e+00 ... (remaining 12099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 16348 3.48 - 6.97: 54 6.97 - 10.45: 6 10.45 - 13.94: 0 13.94 - 17.42: 2 Bond angle restraints: 16410 Sorted by residual: angle pdb=" C1 PKZ C1002 " pdb=" S1P PKZ C1002 " pdb=" C2P PKZ C1002 " ideal model delta sigma weight residual 101.96 119.38 -17.42 3.00e+00 1.11e-01 3.37e+01 angle pdb=" C1 PKZ E1002 " pdb=" S1P PKZ E1002 " pdb=" C2P PKZ E1002 " ideal model delta sigma weight residual 101.96 118.95 -16.99 3.00e+00 1.11e-01 3.21e+01 angle pdb=" N HIS C 369 " pdb=" CA HIS C 369 " pdb=" C HIS C 369 " ideal model delta sigma weight residual 113.18 107.44 5.74 1.21e+00 6.83e-01 2.25e+01 angle pdb=" N HIS E 369 " pdb=" CA HIS E 369 " pdb=" C HIS E 369 " ideal model delta sigma weight residual 112.54 107.09 5.45 1.22e+00 6.72e-01 1.99e+01 angle pdb=" N PRO C 841 " pdb=" CA PRO C 841 " pdb=" C PRO C 841 " ideal model delta sigma weight residual 114.92 110.60 4.32 1.19e+00 7.06e-01 1.32e+01 ... (remaining 16405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.05: 7026 28.05 - 56.09: 148 56.09 - 84.14: 26 84.14 - 112.19: 6 112.19 - 140.24: 8 Dihedral angle restraints: 7214 sinusoidal: 2978 harmonic: 4236 Sorted by residual: dihedral pdb=" C3B MX7 C1001 " pdb=" C3C MX7 C1001 " pdb=" C3D MX7 C1001 " pdb=" C3E MX7 C1001 " ideal model delta sinusoidal sigma weight residual 183.24 43.00 140.24 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" C3B MX7 E1001 " pdb=" C3C MX7 E1001 " pdb=" C3D MX7 E1001 " pdb=" C3E MX7 E1001 " ideal model delta sinusoidal sigma weight residual 183.24 43.13 140.11 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" C2B MX7 C1001 " pdb=" C2C MX7 C1001 " pdb=" C2D MX7 C1001 " pdb=" C2E MX7 C1001 " ideal model delta sinusoidal sigma weight residual -179.74 -43.51 -136.23 1 3.00e+01 1.11e-03 1.84e+01 ... (remaining 7211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1392 0.043 - 0.085: 316 0.085 - 0.128: 91 0.128 - 0.170: 5 0.170 - 0.213: 2 Chirality restraints: 1806 Sorted by residual: chirality pdb=" CA ARG C 367 " pdb=" N ARG C 367 " pdb=" C ARG C 367 " pdb=" CB ARG C 367 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ARG E 367 " pdb=" N ARG E 367 " pdb=" C ARG E 367 " pdb=" CB ARG E 367 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C3B PKZ C1002 " pdb=" C2B PKZ C1002 " pdb=" C4B PKZ C1002 " pdb=" O3B PKZ C1002 " both_signs ideal model delta sigma weight residual False -2.66 -2.51 -0.15 2.00e-01 2.50e+01 5.35e-01 ... (remaining 1803 not shown) Planarity restraints: 2102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P PKZ E1002 " 0.336 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C5P PKZ E1002 " -0.076 2.00e-02 2.50e+03 pdb=" C6P PKZ E1002 " 0.113 2.00e-02 2.50e+03 pdb=" N4P PKZ E1002 " -0.519 2.00e-02 2.50e+03 pdb=" O5P PKZ E1002 " 0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P PKZ C1002 " -0.335 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C5P PKZ C1002 " 0.075 2.00e-02 2.50e+03 pdb=" C6P PKZ C1002 " -0.110 2.00e-02 2.50e+03 pdb=" N4P PKZ C1002 " 0.518 2.00e-02 2.50e+03 pdb=" O5P PKZ C1002 " -0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 MX7 E1001 " 0.077 2.00e-02 2.50e+03 1.52e-01 2.32e+02 pdb=" C39 MX7 E1001 " -0.202 2.00e-02 2.50e+03 pdb=" C3A MX7 E1001 " 0.201 2.00e-02 2.50e+03 pdb=" C3B MX7 E1001 " -0.076 2.00e-02 2.50e+03 ... (remaining 2099 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 6573 3.01 - 3.48: 12251 3.48 - 3.96: 20292 3.96 - 4.43: 23932 4.43 - 4.90: 37112 Nonbonded interactions: 100160 Sorted by model distance: nonbonded pdb=" CCP PKZ C1002 " pdb=" OAP PKZ C1002 " model vdw 2.539 2.752 nonbonded pdb=" O2B PKZ C1002 " pdb=" O7A PKZ C1002 " model vdw 2.543 3.040 nonbonded pdb=" O2B PKZ E1002 " pdb=" O7A PKZ E1002 " model vdw 2.543 3.040 nonbonded pdb=" CCP PKZ E1002 " pdb=" OAP PKZ E1002 " model vdw 2.544 2.752 nonbonded pdb=" C23 MX7 E1001 " pdb=" O21 MX7 E1001 " model vdw 2.590 2.752 ... (remaining 100155 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 'E' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.690 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 : 0.005 0.100 12104 Z= 0.223 Angle : 0.618 17.421 16410 Z= 0.300 Chirality : 0.039 0.213 1806 Planarity : 0.012 0.290 2102 Dihedral : 13.533 140.237 4482 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.33 % Allowed : 4.32 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.23), residues: 1450 helix: 1.63 (0.19), residues: 790 sheet: -1.60 (0.51), residues: 114 loop : -1.23 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 753 TYR 0.012 0.001 TYR E 622 PHE 0.010 0.001 PHE E 670 TRP 0.012 0.001 TRP E 683 HIS 0.005 0.001 HIS E 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.22 (12104) covalent geometry : angle 0.61783 / 0.30 (16410) hydrogen bonds : bond 0.13917 / 9.15 ( 614) hydrogen bonds : angle 5.95425 / 4.17 ( 1794) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: E 203 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6421 (mm-30) REVERT: E 204 ASN cc_start: 0.7794 (p0) cc_final: 0.7501 (p0) REVERT: E 220 ASN cc_start: 0.5301 (m110) cc_final: 0.4978 (m-40) REVERT: E 294 GLN cc_start: 0.7477 (tp40) cc_final: 0.7182 (tp-100) REVERT: E 307 GLU cc_start: 0.7566 (mm-30) cc_final: 0.6599 (pp20) REVERT: E 349 ASP cc_start: 0.7686 (m-30) cc_final: 0.7177 (t70) REVERT: E 721 GLU cc_start: 0.7959 (tt0) cc_final: 0.7684 (mp0) REVERT: E 732 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8061 (mm-30) REVERT: E 741 GLU cc_start: 0.8533 (tt0) cc_final: 0.8207 (tt0) REVERT: E 827 ARG cc_start: 0.7623 (ttm110) cc_final: 0.7382 (ttp-110) REVERT: E 861 ARG cc_start: 0.8004 (mtm180) cc_final: 0.7639 (mtp-110) REVERT: C 183 SER cc_start: 0.8385 (p) cc_final: 0.8059 (p) REVERT: C 203 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6687 (mm-30) REVERT: C 204 ASN cc_start: 0.8182 (p0) cc_final: 0.7945 (p0) REVERT: C 307 GLU cc_start: 0.7662 (mm-30) cc_final: 0.6768 (pp20) REVERT: C 349 ASP cc_start: 0.7653 (m-30) cc_final: 0.6736 (t70) REVERT: C 353 GLN cc_start: 0.7724 (mt0) cc_final: 0.7195 (mp10) REVERT: C 417 LYS cc_start: 0.7113 (mttt) cc_final: 0.6838 (mtmm) REVERT: C 520 LEU cc_start: 0.7788 (mp) cc_final: 0.7537 (mt) REVERT: C 721 GLU cc_start: 0.7922 (tt0) cc_final: 0.7714 (mp0) REVERT: C 827 ARG cc_start: 0.7638 (ttm110) cc_final: 0.7371 (ttp-170) REVERT: C 861 ARG cc_start: 0.8032 (mtm180) cc_final: 0.7672 (mtp-110) outliers start: 16 outliers final: 5 residues processed: 179 average time/residue: 0.5713 time to fit residues: 109.8315 Evaluate side-chains 114 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 366 HIS Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 686 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 188 GLN E 353 GLN E 711 GLN E 742 GLN E 752 GLN E 803 GLN E 870 HIS C 188 GLN C 220 ASN C 689 GLN C 711 GLN C 742 GLN C 752 GLN C 803 GLN C 870 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.162576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.120997 restraints weight = 14339.407| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.70 r_work: 0.3237 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12104 Z= 0.147 Angle : 0.524 6.430 16410 Z= 0.266 Chirality : 0.039 0.157 1806 Planarity : 0.005 0.040 2102 Dihedral : 12.702 139.474 1746 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.41 % Allowed : 8.97 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.23), residues: 1450 helix: 1.53 (0.18), residues: 810 sheet: -1.61 (0.48), residues: 120 loop : -1.05 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 450 TYR 0.013 0.002 TYR E 622 PHE 0.009 0.001 PHE C 670 TRP 0.008 0.001 TRP C 76 HIS 0.002 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (12104) covalent geometry : angle 0.52421 / 0.27 (16410) hydrogen bonds : bond 0.04533 / 3.00 ( 614) hydrogen bonds : angle 4.82072 / 3.36 ( 1794) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 203 GLU cc_start: 0.6764 (mm-30) cc_final: 0.6194 (mm-30) REVERT: E 204 ASN cc_start: 0.7931 (p0) cc_final: 0.7630 (p0) REVERT: E 220 ASN cc_start: 0.5237 (m110) cc_final: 0.4913 (m-40) REVERT: E 307 GLU cc_start: 0.7750 (mm-30) cc_final: 0.6678 (pp20) REVERT: E 349 ASP cc_start: 0.7747 (m-30) cc_final: 0.7286 (t70) REVERT: E 694 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8607 (ttt) REVERT: E 827 ARG cc_start: 0.7647 (ttm110) cc_final: 0.7417 (ttp-170) REVERT: E 861 ARG cc_start: 0.8010 (mtm180) cc_final: 0.7745 (mtp180) REVERT: C 203 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6715 (mm-30) REVERT: C 204 ASN cc_start: 0.8215 (p0) cc_final: 0.7928 (p0) REVERT: C 307 GLU cc_start: 0.7757 (mm-30) cc_final: 0.6872 (pp20) REVERT: C 341 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8309 (mmt90) REVERT: C 349 ASP cc_start: 0.7605 (m-30) cc_final: 0.7011 (t70) REVERT: C 417 LYS cc_start: 0.7206 (mttt) cc_final: 0.6867 (mtmm) REVERT: C 520 LEU cc_start: 0.7679 (mp) cc_final: 0.7401 (mt) REVERT: C 827 ARG cc_start: 0.7636 (ttm110) cc_final: 0.7430 (ttp-170) REVERT: C 861 ARG cc_start: 0.8049 (mtm180) cc_final: 0.7557 (mmm-85) outliers start: 29 outliers final: 15 residues processed: 138 average time/residue: 0.4542 time to fit residues: 68.1962 Evaluate side-chains 115 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 366 HIS Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 694 MET Chi-restraints excluded: chain E residue 836 LEU Chi-restraints excluded: chain E residue 844 THR Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 366 HIS Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 844 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 17 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 0.0010 chunk 16 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 353 GLN C 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.162169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.120564 restraints weight = 14391.769| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.69 r_work: 0.3254 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12104 Z= 0.144 Angle : 0.518 6.476 16410 Z= 0.263 Chirality : 0.039 0.141 1806 Planarity : 0.004 0.039 2102 Dihedral : 11.921 140.184 1746 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.91 % Allowed : 9.80 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.23), residues: 1450 helix: 1.55 (0.18), residues: 814 sheet: -1.64 (0.47), residues: 120 loop : -1.12 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 450 TYR 0.012 0.002 TYR E 622 PHE 0.010 0.001 PHE C 670 TRP 0.011 0.001 TRP C 306 HIS 0.002 0.001 HIS C 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (12104) covalent geometry : angle 0.51850 / 0.26 (16410) hydrogen bonds : bond 0.04049 / 2.70 ( 614) hydrogen bonds : angle 4.65285 / 3.25 ( 1794) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: E 203 GLU cc_start: 0.6720 (mm-30) cc_final: 0.6424 (mm-30) REVERT: E 204 ASN cc_start: 0.8032 (p0) cc_final: 0.7768 (p0) REVERT: E 220 ASN cc_start: 0.5276 (m110) cc_final: 0.4913 (m-40) REVERT: E 260 ARG cc_start: 0.6101 (mtp-110) cc_final: 0.5854 (ttm-80) REVERT: E 307 GLU cc_start: 0.7767 (mm-30) cc_final: 0.6685 (pp20) REVERT: E 349 ASP cc_start: 0.7821 (m-30) cc_final: 0.7381 (t70) REVERT: E 380 TYR cc_start: 0.8371 (t80) cc_final: 0.8121 (t80) REVERT: E 557 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6988 (tt0) REVERT: E 694 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8644 (ttt) REVERT: E 861 ARG cc_start: 0.8049 (mtm180) cc_final: 0.7784 (mtp180) REVERT: C 203 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6728 (mm-30) REVERT: C 204 ASN cc_start: 0.8191 (p0) cc_final: 0.7910 (p0) REVERT: C 289 GLU cc_start: 0.7707 (tp30) cc_final: 0.7278 (tp30) REVERT: C 294 GLN cc_start: 0.7289 (tp40) cc_final: 0.7005 (tp40) REVERT: C 307 GLU cc_start: 0.7729 (mm-30) cc_final: 0.6847 (pp20) REVERT: C 341 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8217 (mmt90) REVERT: C 349 ASP cc_start: 0.7714 (m-30) cc_final: 0.7096 (t70) REVERT: C 417 LYS cc_start: 0.7195 (mttt) cc_final: 0.6853 (mtmm) REVERT: C 520 LEU cc_start: 0.7724 (mp) cc_final: 0.7431 (mt) REVERT: C 732 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8074 (mm-30) REVERT: C 861 ARG cc_start: 0.8097 (mtm180) cc_final: 0.7613 (mmm-85) outliers start: 35 outliers final: 16 residues processed: 138 average time/residue: 0.4495 time to fit residues: 67.9013 Evaluate side-chains 123 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 366 HIS Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 557 GLU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 694 MET Chi-restraints excluded: chain E residue 836 LEU Chi-restraints excluded: chain E residue 844 THR Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 844 THR Chi-restraints excluded: chain C residue 862 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 0.0770 chunk 65 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 353 GLN C 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.162076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120433 restraints weight = 14356.778| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.69 r_work: 0.3224 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12104 Z= 0.147 Angle : 0.514 6.470 16410 Z= 0.261 Chirality : 0.039 0.138 1806 Planarity : 0.004 0.039 2102 Dihedral : 11.616 140.522 1746 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.99 % Allowed : 10.80 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.23), residues: 1450 helix: 1.57 (0.19), residues: 814 sheet: -1.65 (0.47), residues: 120 loop : -1.09 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 450 TYR 0.014 0.002 TYR E 622 PHE 0.010 0.001 PHE C 670 TRP 0.013 0.001 TRP C 306 HIS 0.002 0.001 HIS C 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (12104) covalent geometry : angle 0.51407 / 0.26 (16410) hydrogen bonds : bond 0.03958 / 2.65 ( 614) hydrogen bonds : angle 4.58706 / 3.21 ( 1794) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: E 203 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6168 (mm-30) REVERT: E 204 ASN cc_start: 0.8065 (p0) cc_final: 0.7797 (p0) REVERT: E 260 ARG cc_start: 0.6238 (mtp-110) cc_final: 0.5972 (ttm-80) REVERT: E 307 GLU cc_start: 0.7784 (mm-30) cc_final: 0.6719 (pp20) REVERT: E 349 ASP cc_start: 0.7832 (m-30) cc_final: 0.7359 (t70) REVERT: E 557 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7004 (tt0) REVERT: E 694 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8653 (ttt) REVERT: E 813 TYR cc_start: 0.7620 (m-80) cc_final: 0.7289 (m-80) REVERT: E 861 ARG cc_start: 0.8094 (mtm180) cc_final: 0.7778 (mtp180) REVERT: C 203 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6727 (mm-30) REVERT: C 204 ASN cc_start: 0.8184 (p0) cc_final: 0.7909 (p0) REVERT: C 289 GLU cc_start: 0.7716 (tp30) cc_final: 0.7277 (tp30) REVERT: C 307 GLU cc_start: 0.7744 (mm-30) cc_final: 0.6837 (pp20) REVERT: C 341 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8130 (mmt90) REVERT: C 349 ASP cc_start: 0.7743 (m-30) cc_final: 0.7096 (t70) REVERT: C 417 LYS cc_start: 0.7188 (mttt) cc_final: 0.6824 (mtmm) REVERT: C 520 LEU cc_start: 0.7698 (mp) cc_final: 0.7399 (mt) REVERT: C 557 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6924 (tt0) REVERT: C 732 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8057 (mm-30) REVERT: C 861 ARG cc_start: 0.8131 (mtm180) cc_final: 0.7595 (mmm-85) outliers start: 36 outliers final: 17 residues processed: 130 average time/residue: 0.4399 time to fit residues: 62.4592 Evaluate side-chains 115 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 557 GLU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 694 MET Chi-restraints excluded: chain E residue 836 LEU Chi-restraints excluded: chain E residue 844 THR Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 844 THR Chi-restraints excluded: chain C residue 862 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 40 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 0.1980 chunk 48 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 41 optimal weight: 0.0270 chunk 55 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 220 ASN E 353 GLN C 220 ASN C 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.160208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118137 restraints weight = 14388.673| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.69 r_work: 0.3221 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12104 Z= 0.192 Angle : 0.554 6.496 16410 Z= 0.281 Chirality : 0.040 0.137 1806 Planarity : 0.005 0.041 2102 Dihedral : 11.619 145.042 1744 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.24 % Allowed : 11.05 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.23), residues: 1450 helix: 1.45 (0.18), residues: 814 sheet: -1.68 (0.47), residues: 120 loop : -1.19 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 450 TYR 0.015 0.002 TYR C 779 PHE 0.013 0.002 PHE C 670 TRP 0.016 0.002 TRP C 306 HIS 0.003 0.001 HIS C 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (12104) covalent geometry : angle 0.55433 / 0.28 (16410) hydrogen bonds : bond 0.04293 / 2.90 ( 614) hydrogen bonds : angle 4.68663 / 3.28 ( 1794) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 101 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: E 203 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6220 (mm-30) REVERT: E 204 ASN cc_start: 0.8115 (p0) cc_final: 0.7844 (p0) REVERT: E 289 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7340 (tm-30) REVERT: E 307 GLU cc_start: 0.7841 (mm-30) cc_final: 0.6792 (pp20) REVERT: E 349 ASP cc_start: 0.7842 (m-30) cc_final: 0.7406 (t70) REVERT: E 557 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: E 694 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8663 (ttt) REVERT: E 861 ARG cc_start: 0.8125 (mtm180) cc_final: 0.7812 (mtp180) REVERT: E 867 GLU cc_start: 0.8087 (mp0) cc_final: 0.7215 (mp0) REVERT: C 203 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6742 (mm-30) REVERT: C 204 ASN cc_start: 0.8256 (p0) cc_final: 0.8051 (p0) REVERT: C 289 GLU cc_start: 0.7825 (tp30) cc_final: 0.7445 (tp30) REVERT: C 307 GLU cc_start: 0.7752 (mm-30) cc_final: 0.6811 (pp20) REVERT: C 341 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8160 (mmt90) REVERT: C 349 ASP cc_start: 0.7820 (m-30) cc_final: 0.7338 (t70) REVERT: C 414 ARG cc_start: 0.7044 (mmm-85) cc_final: 0.6729 (mmm-85) REVERT: C 417 LYS cc_start: 0.7215 (mttt) cc_final: 0.6864 (mtmm) REVERT: C 520 LEU cc_start: 0.7716 (mp) cc_final: 0.7404 (mt) REVERT: C 557 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6907 (tt0) REVERT: C 861 ARG cc_start: 0.8138 (mtm180) cc_final: 0.7587 (mmm-85) outliers start: 39 outliers final: 23 residues processed: 136 average time/residue: 0.4612 time to fit residues: 68.4010 Evaluate side-chains 127 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 557 GLU Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 694 MET Chi-restraints excluded: chain E residue 836 LEU Chi-restraints excluded: chain E residue 844 THR Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 844 THR Chi-restraints excluded: chain C residue 862 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 58 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 139 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 353 GLN C 353 GLN C 870 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.159659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117478 restraints weight = 14325.215| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.70 r_work: 0.3178 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12104 Z= 0.211 Angle : 0.578 6.499 16410 Z= 0.291 Chirality : 0.041 0.143 1806 Planarity : 0.005 0.049 2102 Dihedral : 11.468 149.362 1744 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.99 % Allowed : 11.46 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.23), residues: 1450 helix: 1.32 (0.18), residues: 814 sheet: -1.73 (0.46), residues: 120 loop : -1.25 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 450 TYR 0.016 0.002 TYR E 813 PHE 0.014 0.002 PHE C 670 TRP 0.018 0.002 TRP C 306 HIS 0.003 0.001 HIS C 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (12104) covalent geometry : angle 0.57847 / 0.29 (16410) hydrogen bonds : bond 0.04363 / 2.95 ( 614) hydrogen bonds : angle 4.73917 / 3.31 ( 1794) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: E 203 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6245 (mm-30) REVERT: E 204 ASN cc_start: 0.8178 (p0) cc_final: 0.7893 (p0) REVERT: E 260 ARG cc_start: 0.6096 (mtp-110) cc_final: 0.5752 (ttm-80) REVERT: E 289 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7356 (tm-30) REVERT: E 307 GLU cc_start: 0.7859 (mm-30) cc_final: 0.6780 (pp20) REVERT: E 349 ASP cc_start: 0.7873 (m-30) cc_final: 0.7400 (t70) REVERT: E 694 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8673 (ttt) REVERT: E 861 ARG cc_start: 0.8146 (mtm180) cc_final: 0.7819 (mtp180) REVERT: C 203 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6738 (mm-30) REVERT: C 204 ASN cc_start: 0.8230 (p0) cc_final: 0.8017 (p0) REVERT: C 307 GLU cc_start: 0.7768 (mm-30) cc_final: 0.6857 (pp20) REVERT: C 341 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8213 (mmt90) REVERT: C 349 ASP cc_start: 0.7849 (m-30) cc_final: 0.7377 (t70) REVERT: C 414 ARG cc_start: 0.7038 (mmm-85) cc_final: 0.6737 (mmm-85) REVERT: C 417 LYS cc_start: 0.7221 (mttt) cc_final: 0.6835 (mtmm) REVERT: C 421 LEU cc_start: 0.7736 (tp) cc_final: 0.7367 (tt) REVERT: C 520 LEU cc_start: 0.7750 (mp) cc_final: 0.7440 (mt) REVERT: C 861 ARG cc_start: 0.8148 (mtm180) cc_final: 0.7556 (mmm-85) outliers start: 36 outliers final: 22 residues processed: 131 average time/residue: 0.4602 time to fit residues: 66.0644 Evaluate side-chains 123 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 694 MET Chi-restraints excluded: chain E residue 836 LEU Chi-restraints excluded: chain E residue 844 THR Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 844 THR Chi-restraints excluded: chain C residue 862 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 79 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 19 optimal weight: 0.2980 chunk 96 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 chunk 53 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 220 ASN E 353 GLN E 870 HIS C 353 GLN C 870 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.161319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119255 restraints weight = 14314.939| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.70 r_work: 0.3247 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12104 Z= 0.147 Angle : 0.530 6.459 16410 Z= 0.269 Chirality : 0.039 0.142 1806 Planarity : 0.005 0.041 2102 Dihedral : 10.979 147.424 1744 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.66 % Allowed : 12.04 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.23), residues: 1450 helix: 1.45 (0.18), residues: 814 sheet: -1.66 (0.44), residues: 124 loop : -1.28 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 450 TYR 0.013 0.002 TYR E 622 PHE 0.010 0.001 PHE E 709 TRP 0.019 0.001 TRP C 306 HIS 0.002 0.001 HIS E 870 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (12104) covalent geometry : angle 0.52952 / 0.27 (16410) hydrogen bonds : bond 0.03938 / 2.64 ( 614) hydrogen bonds : angle 4.62119 / 3.23 ( 1794) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: E 203 GLU cc_start: 0.6704 (mm-30) cc_final: 0.6193 (mm-30) REVERT: E 204 ASN cc_start: 0.8098 (p0) cc_final: 0.7826 (p0) REVERT: E 289 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7333 (tm-30) REVERT: E 307 GLU cc_start: 0.7821 (mm-30) cc_final: 0.6766 (pp20) REVERT: E 349 ASP cc_start: 0.7815 (m-30) cc_final: 0.7355 (t70) REVERT: E 450 ARG cc_start: 0.8484 (mtt90) cc_final: 0.8250 (mtt-85) REVERT: E 536 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8206 (mt0) REVERT: E 557 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7050 (tt0) REVERT: E 861 ARG cc_start: 0.8105 (mtm180) cc_final: 0.7779 (mtp180) REVERT: C 203 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6683 (mm-30) REVERT: C 204 ASN cc_start: 0.8185 (p0) cc_final: 0.7932 (p0) REVERT: C 307 GLU cc_start: 0.7726 (mm-30) cc_final: 0.6762 (pp20) REVERT: C 341 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8167 (mmt90) REVERT: C 349 ASP cc_start: 0.7826 (m-30) cc_final: 0.7351 (t70) REVERT: C 417 LYS cc_start: 0.7197 (mttt) cc_final: 0.6804 (mtmm) REVERT: C 421 LEU cc_start: 0.7657 (tp) cc_final: 0.7294 (tt) REVERT: C 520 LEU cc_start: 0.7616 (mp) cc_final: 0.7301 (mt) REVERT: C 813 TYR cc_start: 0.7490 (m-80) cc_final: 0.6936 (m-80) REVERT: C 861 ARG cc_start: 0.8148 (mtm180) cc_final: 0.7598 (mmm-85) REVERT: C 867 GLU cc_start: 0.7452 (mp0) cc_final: 0.6996 (mp0) outliers start: 32 outliers final: 16 residues processed: 129 average time/residue: 0.4681 time to fit residues: 66.5092 Evaluate side-chains 116 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 536 GLN Chi-restraints excluded: chain E residue 557 GLU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 836 LEU Chi-restraints excluded: chain E residue 844 THR Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 844 THR Chi-restraints excluded: chain C residue 862 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 84 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 75 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 120 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 220 ASN E 353 GLN E 870 HIS C 353 GLN C 689 GLN C 870 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.161511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.119573 restraints weight = 14258.267| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.70 r_work: 0.3219 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12104 Z= 0.146 Angle : 0.523 6.469 16410 Z= 0.266 Chirality : 0.039 0.151 1806 Planarity : 0.004 0.041 2102 Dihedral : 10.631 145.530 1744 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.74 % Allowed : 12.21 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.23), residues: 1450 helix: 1.49 (0.18), residues: 814 sheet: -1.66 (0.45), residues: 124 loop : -1.26 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 450 TYR 0.013 0.002 TYR E 622 PHE 0.010 0.001 PHE C 670 TRP 0.025 0.001 TRP C 306 HIS 0.002 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (12104) covalent geometry : angle 0.52291 / 0.27 (16410) hydrogen bonds : bond 0.03900 / 2.62 ( 614) hydrogen bonds : angle 4.58181 / 3.20 ( 1794) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: E 203 GLU cc_start: 0.6748 (mm-30) cc_final: 0.6232 (mm-30) REVERT: E 204 ASN cc_start: 0.8118 (p0) cc_final: 0.7845 (p0) REVERT: E 260 ARG cc_start: 0.6185 (mtp-110) cc_final: 0.5923 (ttm-80) REVERT: E 289 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7357 (tm-30) REVERT: E 307 GLU cc_start: 0.7828 (mm-30) cc_final: 0.6800 (pp20) REVERT: E 349 ASP cc_start: 0.7831 (m-30) cc_final: 0.7392 (t70) REVERT: E 557 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7103 (tt0) REVERT: E 861 ARG cc_start: 0.8115 (mtm180) cc_final: 0.7796 (mtp180) REVERT: C 203 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6710 (mm-30) REVERT: C 204 ASN cc_start: 0.8220 (p0) cc_final: 0.7937 (p0) REVERT: C 307 GLU cc_start: 0.7762 (mm-30) cc_final: 0.6806 (pp20) REVERT: C 341 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8162 (mmt90) REVERT: C 349 ASP cc_start: 0.7819 (m-30) cc_final: 0.7369 (t70) REVERT: C 417 LYS cc_start: 0.7199 (mttt) cc_final: 0.6809 (mtmm) REVERT: C 421 LEU cc_start: 0.7695 (tp) cc_final: 0.7328 (tt) REVERT: C 520 LEU cc_start: 0.7625 (mp) cc_final: 0.7299 (mt) REVERT: C 861 ARG cc_start: 0.8169 (mtm180) cc_final: 0.7619 (mmm-85) outliers start: 33 outliers final: 21 residues processed: 125 average time/residue: 0.4718 time to fit residues: 64.5526 Evaluate side-chains 119 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 557 GLU Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 694 MET Chi-restraints excluded: chain E residue 836 LEU Chi-restraints excluded: chain E residue 844 THR Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 844 THR Chi-restraints excluded: chain C residue 862 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 110 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 220 ASN E 353 GLN E 870 HIS C 353 GLN C 689 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.160268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.118278 restraints weight = 14151.331| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.68 r_work: 0.3181 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12104 Z= 0.187 Angle : 0.559 6.483 16410 Z= 0.283 Chirality : 0.040 0.141 1806 Planarity : 0.005 0.041 2102 Dihedral : 10.631 147.583 1744 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.49 % Allowed : 12.54 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.23), residues: 1450 helix: 1.39 (0.18), residues: 814 sheet: -1.71 (0.45), residues: 124 loop : -1.32 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 450 TYR 0.014 0.002 TYR E 622 PHE 0.013 0.002 PHE C 670 TRP 0.031 0.002 TRP C 306 HIS 0.002 0.001 HIS C 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (12104) covalent geometry : angle 0.55868 / 0.28 (16410) hydrogen bonds : bond 0.04188 / 2.83 ( 614) hydrogen bonds : angle 4.66912 / 3.26 ( 1794) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: E 203 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6217 (mm-30) REVERT: E 204 ASN cc_start: 0.8180 (p0) cc_final: 0.7900 (p0) REVERT: E 260 ARG cc_start: 0.6222 (mtp-110) cc_final: 0.5928 (ttm-80) REVERT: E 289 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: E 307 GLU cc_start: 0.7844 (mm-30) cc_final: 0.6796 (pp20) REVERT: E 349 ASP cc_start: 0.7841 (m-30) cc_final: 0.7348 (t70) REVERT: E 557 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7087 (tt0) REVERT: E 861 ARG cc_start: 0.8148 (mtm180) cc_final: 0.7793 (mtp180) REVERT: C 203 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6701 (mm-30) REVERT: C 204 ASN cc_start: 0.8167 (p0) cc_final: 0.7928 (p0) REVERT: C 307 GLU cc_start: 0.7765 (mm-30) cc_final: 0.6840 (pp20) REVERT: C 341 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8215 (mmt90) REVERT: C 349 ASP cc_start: 0.7849 (m-30) cc_final: 0.7364 (t70) REVERT: C 417 LYS cc_start: 0.7226 (mttt) cc_final: 0.6816 (mtmm) REVERT: C 421 LEU cc_start: 0.7700 (tp) cc_final: 0.7333 (tt) REVERT: C 520 LEU cc_start: 0.7612 (mp) cc_final: 0.7275 (mt) REVERT: C 744 SER cc_start: 0.8613 (t) cc_final: 0.8180 (m) REVERT: C 861 ARG cc_start: 0.8134 (mtm180) cc_final: 0.7525 (mmm-85) outliers start: 30 outliers final: 22 residues processed: 123 average time/residue: 0.5414 time to fit residues: 72.9113 Evaluate side-chains 121 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 557 GLU Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 694 MET Chi-restraints excluded: chain E residue 836 LEU Chi-restraints excluded: chain E residue 844 THR Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 844 THR Chi-restraints excluded: chain C residue 862 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 57 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 220 ASN E 353 GLN C 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.161140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119211 restraints weight = 14401.992| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.71 r_work: 0.3209 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12104 Z= 0.157 Angle : 0.549 14.772 16410 Z= 0.274 Chirality : 0.039 0.141 1806 Planarity : 0.005 0.041 2102 Dihedral : 10.514 146.500 1744 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.33 % Allowed : 12.79 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.23), residues: 1450 helix: 1.42 (0.18), residues: 814 sheet: -1.75 (0.44), residues: 124 loop : -1.29 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 450 TYR 0.013 0.002 TYR E 622 PHE 0.010 0.001 PHE C 670 TRP 0.035 0.002 TRP C 306 HIS 0.002 0.001 HIS C 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (12104) covalent geometry : angle 0.54853 / 0.27 (16410) hydrogen bonds : bond 0.03966 / 2.67 ( 614) hydrogen bonds : angle 4.61812 / 3.23 ( 1794) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: E 203 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6241 (mm-30) REVERT: E 204 ASN cc_start: 0.8136 (p0) cc_final: 0.7861 (p0) REVERT: E 260 ARG cc_start: 0.6246 (mtp-110) cc_final: 0.5949 (ttm-80) REVERT: E 289 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7368 (tm-30) REVERT: E 307 GLU cc_start: 0.7837 (mm-30) cc_final: 0.6820 (pp20) REVERT: E 349 ASP cc_start: 0.7830 (m-30) cc_final: 0.7383 (t70) REVERT: E 557 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7103 (tt0) REVERT: E 861 ARG cc_start: 0.8138 (mtm180) cc_final: 0.7603 (mmm-85) REVERT: C 203 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6684 (mm-30) REVERT: C 204 ASN cc_start: 0.8190 (p0) cc_final: 0.7906 (p0) REVERT: C 307 GLU cc_start: 0.7712 (mm-30) cc_final: 0.6754 (pp20) REVERT: C 341 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8190 (mmt90) REVERT: C 349 ASP cc_start: 0.7847 (m-30) cc_final: 0.7395 (t70) REVERT: C 417 LYS cc_start: 0.7223 (mttt) cc_final: 0.6814 (mtmm) REVERT: C 421 LEU cc_start: 0.7699 (tp) cc_final: 0.7324 (tt) REVERT: C 520 LEU cc_start: 0.7623 (mp) cc_final: 0.7288 (mt) REVERT: C 744 SER cc_start: 0.8627 (t) cc_final: 0.8197 (m) REVERT: C 861 ARG cc_start: 0.8179 (mtm180) cc_final: 0.7607 (mmm-85) outliers start: 28 outliers final: 22 residues processed: 120 average time/residue: 0.4928 time to fit residues: 64.9062 Evaluate side-chains 120 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 557 GLU Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 694 MET Chi-restraints excluded: chain E residue 836 LEU Chi-restraints excluded: chain E residue 844 THR Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 844 THR Chi-restraints excluded: chain C residue 862 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 129 optimal weight: 0.4980 chunk 95 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 220 ASN E 353 GLN C 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.160171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118097 restraints weight = 14289.074| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.69 r_work: 0.3185 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12104 Z= 0.195 Angle : 0.578 13.510 16410 Z= 0.290 Chirality : 0.041 0.144 1806 Planarity : 0.005 0.041 2102 Dihedral : 10.615 149.144 1744 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.49 % Allowed : 12.79 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.23), residues: 1450 helix: 1.35 (0.18), residues: 814 sheet: -1.79 (0.44), residues: 124 loop : -1.33 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 450 TYR 0.016 0.002 TYR E 377 PHE 0.013 0.002 PHE C 670 TRP 0.039 0.002 TRP C 306 HIS 0.002 0.001 HIS E 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (12104) covalent geometry : angle 0.57839 / 0.29 (16410) hydrogen bonds : bond 0.04224 / 2.86 ( 614) hydrogen bonds : angle 4.69105 / 3.28 ( 1794) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3918.82 seconds wall clock time: 67 minutes 18.52 seconds (4038.52 seconds total)