Starting phenix.real_space_refine on Sat Aug 23 06:24:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sie_40507/08_2025/8sie_40507.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sie_40507/08_2025/8sie_40507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sie_40507/08_2025/8sie_40507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sie_40507/08_2025/8sie_40507.map" model { file = "/net/cci-nas-00/data/ceres_data/8sie_40507/08_2025/8sie_40507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sie_40507/08_2025/8sie_40507.cif" } resolution = 2.7 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= 0.007 sd= 0.148 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 6 5.49 5 S 36 5.16 5 C 7008 2.51 5 N 1542 2.21 5 O 1806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10398 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4755 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 24, 'TRANS': 588} Chain breaks: 3 Chain: "C" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4755 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 24, 'TRANS': 588} Chain breaks: 3 Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 444 Unusual residues: {'AV0': 1, 'BCT': 2, 'CLR': 6, 'DMU': 1, 'LBN': 9} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 284 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'LBN:plan-1': 7, 'LBN:plan-3': 7, 'LBN:plan-2': 6} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 444 Unusual residues: {'AV0': 1, 'BCT': 2, 'CLR': 6, 'DMU': 1, 'LBN': 9} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 284 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'LBN:plan-1': 7, 'LBN:plan-3': 7, 'LBN:plan-2': 6} Unresolved non-hydrogen planarities: 72 Time building chain proxies: 2.08, per 1000 atoms: 0.20 Number of scatterers: 10398 At special positions: 0 Unit cell: (90.688, 122.304, 107.328, 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 36 16.00 P 6 15.00 O 1806 8.00 N 1542 7.00 C 7008 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 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!! Possible link ignored !!! !!! HETATM10300 C18 DMU C 818 45.138 61.404 32.360 1.00 58.03 C !!! !!! HETATM 9856 C18 DMU D 818 44.791 59.955 32.316 1.00 58.05 C !!! !!! N-linked glycan : False !!! !!! O-linked glycan : False !!! !!! Glycan-glycan : True !!! !!! No oxygen atom found !!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 353.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 5 sheets defined 72.3% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'D' and resid 28 through 36 Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.507A pdb=" N ASP D 73 " --> pdb=" O PRO D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 109 removed outlier: 3.892A pdb=" N LEU D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU D 85 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU D 107 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 109 " --> pdb=" O TYR D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 131 removed outlier: 3.775A pdb=" N TYR D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) Proline residue: D 123 - end of helix removed outlier: 4.288A pdb=" N ILE D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE D 130 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 156 Processing helix chain 'D' and resid 157 through 162 Processing helix chain 'D' and resid 177 through 207 Processing helix chain 'D' and resid 209 through 215 removed outlier: 4.056A pdb=" N VAL D 212 " --> pdb=" O GLY D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 240 Processing helix chain 'D' and resid 251 through 263 Processing helix chain 'D' and resid 264 through 267 removed outlier: 3.514A pdb=" N THR D 267 " --> pdb=" O ILE D 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 264 through 267' Processing helix chain 'D' and resid 268 through 292 Processing helix chain 'D' and resid 301 through 318 Processing helix chain 'D' and resid 318 through 323 removed outlier: 3.784A pdb=" N ASN D 322 " --> pdb=" O ASN D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 348 removed outlier: 3.518A pdb=" N LEU D 345 " --> pdb=" O PRO D 342 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 376 removed outlier: 3.933A pdb=" N SER D 355 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 397 Processing helix chain 'D' and resid 406 through 416 removed outlier: 3.524A pdb=" N THR D 416 " --> pdb=" O VAL D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 437 Processing helix chain 'D' and resid 439 through 443 removed outlier: 3.612A pdb=" N LEU D 442 " --> pdb=" O GLY D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 458 removed outlier: 4.063A pdb=" N LEU D 450 " --> pdb=" O GLN D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 463 Processing helix chain 'D' and resid 467 through 475 Processing helix chain 'D' and resid 475 through 492 removed outlier: 3.680A pdb=" N ILE D 490 " --> pdb=" O CYS D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 515 removed outlier: 3.653A pdb=" N LEU D 499 " --> pdb=" O ASP D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 537 removed outlier: 4.388A pdb=" N LYS D 537 " --> pdb=" O THR D 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 533 through 537' Processing helix chain 'D' and resid 555 through 571 Processing helix chain 'D' and resid 573 through 585 removed outlier: 3.559A pdb=" N VAL D 577 " --> pdb=" O ASP D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 686 removed outlier: 3.760A pdb=" N ILE D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 706 Processing helix chain 'D' and resid 723 through 732 removed outlier: 3.603A pdb=" N GLN D 732 " --> pdb=" O HIS D 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.507A pdb=" N ASP C 73 " --> pdb=" O PRO C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 109 removed outlier: 3.896A pdb=" N LEU C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU C 85 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU C 107 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU C 108 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 131 removed outlier: 3.773A pdb=" N TYR C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Proline residue: C 123 - end of helix removed outlier: 4.271A pdb=" N ILE C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE C 130 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 156 Processing helix chain 'C' and resid 157 through 162 Processing helix chain 'C' and resid 177 through 207 Processing helix chain 'C' and resid 209 through 215 removed outlier: 4.055A pdb=" N VAL C 212 " --> pdb=" O GLY C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 240 Processing helix chain 'C' and resid 251 through 263 Processing helix chain 'C' and resid 264 through 267 removed outlier: 3.521A pdb=" N THR C 267 " --> pdb=" O ILE C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 267' Processing helix chain 'C' and resid 268 through 292 Processing helix chain 'C' and resid 301 through 318 Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.757A pdb=" N ASN C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 348 removed outlier: 3.518A pdb=" N LEU C 345 " --> pdb=" O PRO C 342 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 376 removed outlier: 3.944A pdb=" N SER C 355 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 397 Processing helix chain 'C' and resid 406 through 416 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 439 through 443 removed outlier: 3.605A pdb=" N LEU C 442 " --> pdb=" O GLY C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 458 removed outlier: 4.066A pdb=" N LEU C 450 " --> pdb=" O GLN C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 463 Processing helix chain 'C' and resid 467 through 475 Processing helix chain 'C' and resid 475 through 492 Processing helix chain 'C' and resid 493 through 515 removed outlier: 3.523A pdb=" N LEU C 499 " --> pdb=" O ASP C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 537 removed outlier: 4.392A pdb=" N LYS C 537 " --> pdb=" O THR C 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 533 through 537' Processing helix chain 'C' and resid 555 through 571 Processing helix chain 'C' and resid 573 through 585 removed outlier: 3.559A pdb=" N VAL C 577 " --> pdb=" O ASP C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 686 removed outlier: 3.760A pdb=" N ILE C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 706 Processing helix chain 'C' and resid 723 through 732 removed outlier: 3.603A pdb=" N GLN C 732 " --> pdb=" O HIS C 728 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 19 through 25 removed outlier: 3.748A pdb=" N VAL D 22 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL C 22 " --> pdb=" O VAL D 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 138 through 139 Processing sheet with id=AA3, first strand: chain 'D' and resid 530 through 532 removed outlier: 4.305A pdb=" N ILE D 547 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N SER D 523 " --> pdb=" O VAL D 545 " (cutoff:3.500A) removed outlier: 12.844A pdb=" N VAL D 545 " --> pdb=" O SER D 523 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS D 546 " --> pdb=" O VAL D 659 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ASP D 661 " --> pdb=" O LYS D 546 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU D 548 " --> pdb=" O ASP D 661 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N PHE D 719 " --> pdb=" O VAL D 690 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE D 692 " --> pdb=" O PHE D 719 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 138 through 139 Processing sheet with id=AA5, first strand: chain 'C' and resid 530 through 532 removed outlier: 4.300A pdb=" N ILE C 547 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N SER C 523 " --> pdb=" O VAL C 545 " (cutoff:3.500A) removed outlier: 12.844A pdb=" N VAL C 545 " --> pdb=" O SER C 523 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS C 546 " --> pdb=" O VAL C 659 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ASP C 661 " --> pdb=" O LYS C 546 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU C 548 " --> pdb=" O ASP C 661 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N PHE C 719 " --> pdb=" O VAL C 690 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE C 692 " --> pdb=" O PHE C 719 " (cutoff:3.500A) 617 hydrogen bonds defined for protein. 1803 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: 1.44 Time building geometry restraints manager: 0.88 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: 1550 1.32 - 1.44: 2631 1.44 - 1.57: 6369 1.57 - 1.69: 12 1.69 - 1.81: 56 Bond restraints: 10618 Sorted by residual: bond pdb=" C BCT D 816 " pdb=" O3 BCT D 816 " ideal model delta sigma weight residual 1.389 1.263 0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" C BCT C 816 " pdb=" O3 BCT C 816 " ideal model delta sigma weight residual 1.389 1.264 0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C BCT C 816 " pdb=" O1 BCT C 816 " ideal model delta sigma weight residual 1.236 1.332 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C BCT D 816 " pdb=" O1 BCT D 816 " ideal model delta sigma weight residual 1.236 1.332 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C BCT D 817 " pdb=" O3 BCT D 817 " ideal model delta sigma weight residual 1.389 1.333 0.056 2.00e-02 2.50e+03 7.87e+00 ... (remaining 10613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 14204 2.41 - 4.82: 170 4.82 - 7.23: 8 7.23 - 9.64: 4 9.64 - 12.05: 8 Bond angle restraints: 14394 Sorted by residual: angle pdb=" N ILE D 490 " pdb=" CA ILE D 490 " pdb=" C ILE D 490 " ideal model delta sigma weight residual 111.81 108.09 3.72 8.60e-01 1.35e+00 1.87e+01 angle pdb=" O1 BCT C 816 " pdb=" C BCT C 816 " pdb=" O2 BCT C 816 " ideal model delta sigma weight residual 129.92 117.87 12.05 3.00e+00 1.11e-01 1.61e+01 angle pdb=" O1 BCT D 816 " pdb=" C BCT D 816 " pdb=" O2 BCT D 816 " ideal model delta sigma weight residual 129.92 117.90 12.02 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O1 LBN D 806 " pdb=" P1 LBN D 806 " pdb=" O2 LBN D 806 " ideal model delta sigma weight residual 93.45 104.03 -10.58 3.00e+00 1.11e-01 1.24e+01 angle pdb=" O1 LBN C 807 " pdb=" P1 LBN C 807 " pdb=" O2 LBN C 807 " ideal model delta sigma weight residual 93.45 104.03 -10.58 3.00e+00 1.11e-01 1.24e+01 ... (remaining 14389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 6800 34.22 - 68.45: 248 68.45 - 102.67: 35 102.67 - 136.89: 57 136.89 - 171.12: 10 Dihedral angle restraints: 7150 sinusoidal: 3600 harmonic: 3550 Sorted by residual: dihedral pdb=" CA VAL C 722 " pdb=" C VAL C 722 " pdb=" N HIS C 723 " pdb=" CA HIS C 723 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA VAL D 722 " pdb=" C VAL D 722 " pdb=" N HIS D 723 " pdb=" CA HIS D 723 " ideal model delta harmonic sigma weight residual 180.00 151.32 28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CBS AV0 D 819 " pdb=" C1 AV0 D 819 " pdb=" O1 AV0 D 819 " pdb=" O5 AV0 D 819 " ideal model delta sinusoidal sigma weight residual 85.89 -85.23 171.12 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 7147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.971: 1756 0.971 - 1.943: 0 1.943 - 2.914: 0 2.914 - 3.885: 0 3.885 - 4.857: 2 Chirality restraints: 1758 Sorted by residual: chirality pdb=" C2 LBN D 815 " pdb=" C1 LBN D 815 " pdb=" C3 LBN D 815 " pdb=" O7 LBN D 815 " both_signs ideal model delta sigma weight residual False -2.36 2.49 -4.86 2.00e-01 2.50e+01 5.90e+02 chirality pdb=" C2 LBN C 801 " pdb=" C1 LBN C 801 " pdb=" C3 LBN C 801 " pdb=" O7 LBN C 801 " both_signs ideal model delta sigma weight residual False -2.36 2.49 -4.85 2.00e-01 2.50e+01 5.89e+02 chirality pdb=" C2 LBN D 807 " pdb=" C1 LBN D 807 " pdb=" C3 LBN D 807 " pdb=" O7 LBN D 807 " both_signs ideal model delta sigma weight residual False -2.36 -2.59 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1755 not shown) Planarity restraints: 1642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN C 801 " -0.101 2.00e-02 2.50e+03 2.46e-01 6.03e+02 pdb=" C42 LBN C 801 " 0.331 2.00e-02 2.50e+03 pdb=" C5 LBN C 801 " -0.333 2.00e-02 2.50e+03 pdb=" C8 LBN C 801 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN D 815 " -0.242 2.00e-02 2.50e+03 2.40e-01 5.75e+02 pdb=" C42 LBN D 815 " 0.247 2.00e-02 2.50e+03 pdb=" C5 LBN D 815 " 0.232 2.00e-02 2.50e+03 pdb=" C8 LBN D 815 " -0.238 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN D 806 " -0.049 2.00e-02 2.50e+03 9.20e-02 8.46e+01 pdb=" C42 LBN D 806 " 0.120 2.00e-02 2.50e+03 pdb=" C5 LBN D 806 " -0.120 2.00e-02 2.50e+03 pdb=" C8 LBN D 806 " 0.049 2.00e-02 2.50e+03 ... (remaining 1639 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 3 2.17 - 2.85: 3361 2.85 - 3.54: 14529 3.54 - 4.22: 23056 4.22 - 4.90: 42242 Nonbonded interactions: 83191 Sorted by model distance: nonbonded pdb=" C18 DMU D 818 " pdb=" C18 DMU C 818 " model vdw 1.491 3.840 nonbonded pdb=" O16 DMU D 818 " pdb=" C18 DMU C 818 " model vdw 2.131 3.440 nonbonded pdb=" OG SER C 90 " pdb=" O GLN C 413 " model vdw 2.171 3.040 nonbonded pdb=" O PRO C 553 " pdb=" ND2 ASN C 558 " model vdw 2.175 3.120 nonbonded pdb=" O PRO D 553 " pdb=" ND2 ASN D 558 " model vdw 2.176 3.120 ... (remaining 83186 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 'C' and (resid 17 through 732 or resid 802 through 805 or (resid 807 and \ (name C1 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 \ or name C40 or name O1 or name O2 or name O3 or name O4 or name O7 or name O8 o \ r name P1 )) or (resid 810 through 811 and (name C10 or name C31 or name C32 or \ name C33 or name C4 or name C7 )) or (resid 812 through 813 and (name C10 or nam \ e C29 or name C30 or name C31 or name C32 or name C33 or name C4 or name C7 )) o \ r resid 814 through 819)) selection = (chain 'D' and (resid 17 through 732 or resid 802 through 805 or (resid 807 and \ (name C1 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 \ or name C40 or name O1 or name O2 or name O3 or name O4 or name O7 or name O8 o \ r name P1 )) or (resid 810 through 811 and (name C10 or name C31 or name C32 or \ name C33 or name C4 or name C7 )) or (resid 812 through 813 and (name C10 or nam \ e C29 or name C30 or name C31 or name C32 or name C33 or name C4 or name C7 )) o \ r (resid 814 through 815 and (name C10 or name C25 or name C26 or name C27 or na \ me C28 or name C29 or name C30 or name C31 or name C32 or name C33 or name C4 or \ name C7 )) or resid 816 through 819)) } 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.190 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:8.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 0.126 10618 Z= 0.236 Angle : 0.672 12.052 14394 Z= 0.322 Chirality : 0.170 4.857 1758 Planarity : 0.010 0.246 1642 Dihedral : 21.892 171.116 4862 Min Nonbonded Distance : 1.491 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.19 % Allowed : 0.10 % Favored : 99.71 % 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 aren not related in a simple way. whole: 1.29 (0.25), residues: 1210 helix: 2.02 (0.19), residues: 802 sheet: 1.16 (0.61), residues: 54 loop : -2.08 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 730 TYR 0.012 0.001 TYR D 323 PHE 0.029 0.001 PHE D 385 TRP 0.009 0.001 TRP C 482 HIS 0.002 0.001 HIS C 728 Details of bonding type rmsd covalent geometry : bond 0.00475 (10618) covalent geometry : angle 0.67187 (14394) hydrogen bonds : bond 0.13372 ( 617) hydrogen bonds : angle 5.23381 ( 1803) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 0.282 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 128 average time/residue: 0.5803 time to fit residues: 79.4275 Evaluate side-chains 103 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN D 684 GLN C 246 ASN C 684 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.161272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.125739 restraints weight = 11974.187| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.74 r_work: 0.3279 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10618 Z= 0.139 Angle : 0.619 11.278 14394 Z= 0.296 Chirality : 0.044 0.212 1758 Planarity : 0.004 0.030 1642 Dihedral : 19.676 158.731 2714 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.43 % Allowed : 5.64 % Favored : 92.93 % 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 aren not related in a simple way. whole: 1.36 (0.24), residues: 1210 helix: 2.11 (0.19), residues: 794 sheet: 1.43 (0.59), residues: 50 loop : -2.04 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 79 TYR 0.012 0.001 TYR D 556 PHE 0.015 0.001 PHE C 385 TRP 0.007 0.001 TRP D 482 HIS 0.003 0.001 HIS D 728 Details of bonding type rmsd covalent geometry : bond 0.00298 (10618) covalent geometry : angle 0.61946 (14394) hydrogen bonds : bond 0.05674 ( 617) hydrogen bonds : angle 4.13821 ( 1803) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.288 Fit side-chains REVERT: D 37 GLU cc_start: 0.6837 (mp0) cc_final: 0.6545 (pt0) REVERT: D 576 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.5529 (mpt90) REVERT: C 37 GLU cc_start: 0.6858 (mp0) cc_final: 0.6575 (pt0) REVERT: C 315 TYR cc_start: 0.7413 (t80) cc_final: 0.7067 (t80) REVERT: C 503 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7386 (mmt) REVERT: C 576 ARG cc_start: 0.6732 (OUTLIER) cc_final: 0.5456 (mpt90) outliers start: 15 outliers final: 4 residues processed: 107 average time/residue: 0.5303 time to fit residues: 60.9065 Evaluate side-chains 103 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 576 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 63 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 88 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN D 464 GLN D 684 GLN C 246 ASN C 464 GLN C 684 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.162935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.127503 restraints weight = 12055.009| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.77 r_work: 0.3311 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10618 Z= 0.117 Angle : 0.515 7.497 14394 Z= 0.260 Chirality : 0.044 0.312 1758 Planarity : 0.003 0.030 1642 Dihedral : 16.801 164.150 2714 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.20 % Allowed : 6.79 % Favored : 91.01 % 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 aren not related in a simple way. whole: 1.55 (0.25), residues: 1210 helix: 2.25 (0.19), residues: 796 sheet: 1.40 (0.58), residues: 50 loop : -1.97 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 730 TYR 0.010 0.001 TYR D 371 PHE 0.014 0.001 PHE D 385 TRP 0.009 0.001 TRP C 482 HIS 0.002 0.001 HIS D 728 Details of bonding type rmsd covalent geometry : bond 0.00244 (10618) covalent geometry : angle 0.51454 (14394) hydrogen bonds : bond 0.04931 ( 617) hydrogen bonds : angle 3.92230 ( 1803) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.398 Fit side-chains REVERT: D 560 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6416 (m-30) REVERT: D 564 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7916 (tmmt) REVERT: D 576 ARG cc_start: 0.6674 (OUTLIER) cc_final: 0.5394 (mpt90) REVERT: C 315 TYR cc_start: 0.7364 (t80) cc_final: 0.6999 (t80) REVERT: C 560 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6433 (m-30) REVERT: C 564 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7910 (tmmt) REVERT: C 576 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.5384 (mpt90) REVERT: C 730 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7730 (mtt180) outliers start: 23 outliers final: 8 residues processed: 104 average time/residue: 0.5313 time to fit residues: 59.6669 Evaluate side-chains 104 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain D residue 564 LYS Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 564 LYS Chi-restraints excluded: chain C residue 576 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 100 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 93 optimal weight: 0.0980 chunk 58 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN D 464 GLN D 684 GLN C 246 ASN C 464 GLN C 684 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.159305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124012 restraints weight = 11970.514| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.71 r_work: 0.3259 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10618 Z= 0.144 Angle : 0.550 8.002 14394 Z= 0.279 Chirality : 0.044 0.284 1758 Planarity : 0.004 0.032 1642 Dihedral : 15.777 153.515 2714 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.96 % Allowed : 7.46 % Favored : 89.58 % 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 aren not related in a simple way. whole: 1.44 (0.24), residues: 1210 helix: 2.16 (0.18), residues: 794 sheet: 1.36 (0.57), residues: 50 loop : -1.97 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 730 TYR 0.010 0.001 TYR C 371 PHE 0.016 0.002 PHE D 401 TRP 0.009 0.001 TRP C 482 HIS 0.003 0.001 HIS D 698 Details of bonding type rmsd covalent geometry : bond 0.00318 (10618) covalent geometry : angle 0.54956 (14394) hydrogen bonds : bond 0.05825 ( 617) hydrogen bonds : angle 3.94011 ( 1803) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.239 Fit side-chains REVERT: D 37 GLU cc_start: 0.6976 (mp0) cc_final: 0.6713 (pt0) REVERT: D 461 MET cc_start: 0.8622 (mtm) cc_final: 0.8412 (mtm) REVERT: D 576 ARG cc_start: 0.6640 (OUTLIER) cc_final: 0.5335 (mpt90) REVERT: C 37 GLU cc_start: 0.6924 (mp0) cc_final: 0.6658 (mm-30) REVERT: C 320 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6982 (tt0) REVERT: C 576 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.5245 (mpt90) outliers start: 31 outliers final: 18 residues processed: 120 average time/residue: 0.4998 time to fit residues: 64.9809 Evaluate side-chains 113 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 576 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 119 optimal weight: 0.0980 chunk 22 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN D 464 GLN D 684 GLN C 246 ASN C 464 GLN C 684 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.161401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126457 restraints weight = 11976.011| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.71 r_work: 0.3292 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10618 Z= 0.121 Angle : 0.511 7.584 14394 Z= 0.261 Chirality : 0.043 0.286 1758 Planarity : 0.003 0.033 1642 Dihedral : 14.724 152.096 2714 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.15 % Allowed : 8.13 % Favored : 88.72 % 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 aren not related in a simple way. whole: 1.55 (0.24), residues: 1210 helix: 2.23 (0.18), residues: 798 sheet: 1.42 (0.58), residues: 50 loop : -1.95 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 730 TYR 0.010 0.001 TYR C 371 PHE 0.013 0.001 PHE D 401 TRP 0.010 0.001 TRP C 482 HIS 0.002 0.001 HIS C 728 Details of bonding type rmsd covalent geometry : bond 0.00258 (10618) covalent geometry : angle 0.51087 (14394) hydrogen bonds : bond 0.05067 ( 617) hydrogen bonds : angle 3.83936 ( 1803) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.391 Fit side-chains REVERT: D 37 GLU cc_start: 0.6948 (mp0) cc_final: 0.6703 (pt0) REVERT: D 320 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6904 (tt0) REVERT: D 560 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.6464 (m-30) REVERT: D 576 ARG cc_start: 0.6568 (OUTLIER) cc_final: 0.5266 (mpt90) REVERT: D 730 ARG cc_start: 0.7987 (mtm-85) cc_final: 0.7696 (mtt180) REVERT: C 37 GLU cc_start: 0.6882 (mp0) cc_final: 0.6626 (mm-30) REVERT: C 320 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6953 (tt0) REVERT: C 560 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6455 (m-30) REVERT: C 576 ARG cc_start: 0.6538 (OUTLIER) cc_final: 0.5219 (mpt90) REVERT: C 730 ARG cc_start: 0.7984 (mtm-85) cc_final: 0.7696 (mtt180) outliers start: 33 outliers final: 13 residues processed: 113 average time/residue: 0.5076 time to fit residues: 62.0702 Evaluate side-chains 112 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 576 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 1 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 76 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN D 464 GLN D 684 GLN C 246 ASN C 464 GLN C 684 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.159142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.123796 restraints weight = 12006.370| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.72 r_work: 0.3259 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10618 Z= 0.140 Angle : 0.538 8.986 14394 Z= 0.272 Chirality : 0.044 0.344 1758 Planarity : 0.004 0.034 1642 Dihedral : 14.039 147.841 2714 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.25 % Allowed : 8.99 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.24), residues: 1210 helix: 2.21 (0.18), residues: 796 sheet: 1.33 (0.57), residues: 50 loop : -1.97 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 581 TYR 0.010 0.001 TYR C 371 PHE 0.016 0.001 PHE C 401 TRP 0.009 0.001 TRP C 482 HIS 0.003 0.001 HIS C 698 Details of bonding type rmsd covalent geometry : bond 0.00311 (10618) covalent geometry : angle 0.53849 (14394) hydrogen bonds : bond 0.05589 ( 617) hydrogen bonds : angle 3.86713 ( 1803) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.253 Fit side-chains REVERT: D 37 GLU cc_start: 0.6983 (mp0) cc_final: 0.6736 (pt0) REVERT: D 320 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6947 (tt0) REVERT: D 576 ARG cc_start: 0.6565 (OUTLIER) cc_final: 0.5264 (mpt90) REVERT: C 37 GLU cc_start: 0.6904 (mp0) cc_final: 0.6674 (mm-30) REVERT: C 320 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6960 (tt0) REVERT: C 503 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7426 (mmt) REVERT: C 576 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.5228 (mpt90) REVERT: C 730 ARG cc_start: 0.8006 (mtm-85) cc_final: 0.7700 (mtt180) outliers start: 34 outliers final: 22 residues processed: 119 average time/residue: 0.4832 time to fit residues: 62.5113 Evaluate side-chains 120 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 576 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 54 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN D 464 GLN D 684 GLN C 246 ASN C 684 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.160469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.124587 restraints weight = 11986.750| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.75 r_work: 0.3270 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10618 Z= 0.130 Angle : 0.519 8.269 14394 Z= 0.265 Chirality : 0.043 0.339 1758 Planarity : 0.004 0.035 1642 Dihedral : 13.402 144.845 2714 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.25 % Allowed : 9.66 % Favored : 87.09 % 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 aren not related in a simple way. whole: 1.57 (0.24), residues: 1210 helix: 2.23 (0.18), residues: 798 sheet: 1.33 (0.57), residues: 50 loop : -1.87 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 581 TYR 0.010 0.001 TYR D 371 PHE 0.014 0.001 PHE C 401 TRP 0.010 0.001 TRP C 482 HIS 0.002 0.001 HIS C 698 Details of bonding type rmsd covalent geometry : bond 0.00286 (10618) covalent geometry : angle 0.51891 (14394) hydrogen bonds : bond 0.05305 ( 617) hydrogen bonds : angle 3.84957 ( 1803) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 0.300 Fit side-chains REVERT: D 320 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6922 (tt0) REVERT: D 576 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.5341 (mpt90) REVERT: C 37 GLU cc_start: 0.6905 (mp0) cc_final: 0.6659 (mm-30) REVERT: C 320 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6958 (tt0) REVERT: C 503 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7429 (mmt) REVERT: C 576 ARG cc_start: 0.6540 (OUTLIER) cc_final: 0.5236 (mpt90) REVERT: C 730 ARG cc_start: 0.7980 (mtm-85) cc_final: 0.7695 (mtt180) outliers start: 34 outliers final: 19 residues processed: 116 average time/residue: 0.4549 time to fit residues: 57.3506 Evaluate side-chains 113 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 576 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 120 optimal weight: 0.9980 chunk 58 optimal weight: 0.1980 chunk 28 optimal weight: 0.0060 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN D 684 GLN C 246 ASN C 684 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.160163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.124751 restraints weight = 11925.286| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.72 r_work: 0.3285 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10618 Z= 0.125 Angle : 0.511 8.394 14394 Z= 0.262 Chirality : 0.043 0.289 1758 Planarity : 0.004 0.034 1642 Dihedral : 12.895 141.894 2714 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.87 % Allowed : 10.61 % Favored : 86.52 % 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 aren not related in a simple way. whole: 1.58 (0.24), residues: 1210 helix: 2.24 (0.18), residues: 798 sheet: 1.36 (0.58), residues: 50 loop : -1.87 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 79 TYR 0.011 0.001 TYR D 556 PHE 0.014 0.001 PHE C 555 TRP 0.010 0.001 TRP C 482 HIS 0.002 0.001 HIS D 698 Details of bonding type rmsd covalent geometry : bond 0.00272 (10618) covalent geometry : angle 0.51052 (14394) hydrogen bonds : bond 0.05188 ( 617) hydrogen bonds : angle 3.80975 ( 1803) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.294 Fit side-chains REVERT: D 320 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6948 (tt0) REVERT: D 576 ARG cc_start: 0.6573 (OUTLIER) cc_final: 0.5298 (mpt90) REVERT: C 320 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6942 (tt0) REVERT: C 503 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7431 (mmt) REVERT: C 576 ARG cc_start: 0.6572 (OUTLIER) cc_final: 0.5255 (mpt90) REVERT: C 730 ARG cc_start: 0.7982 (mtm-85) cc_final: 0.7696 (mtt180) outliers start: 30 outliers final: 21 residues processed: 112 average time/residue: 0.4863 time to fit residues: 59.0807 Evaluate side-chains 115 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 576 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 3 optimal weight: 0.0470 chunk 33 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 overall best weight: 2.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN D 684 GLN C 246 ASN C 684 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.119414 restraints weight = 11948.246| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.75 r_work: 0.3188 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10618 Z= 0.193 Angle : 0.601 10.264 14394 Z= 0.307 Chirality : 0.046 0.299 1758 Planarity : 0.004 0.036 1642 Dihedral : 13.138 136.337 2714 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.25 % Allowed : 10.04 % Favored : 86.71 % 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 aren not related in a simple way. whole: 1.38 (0.24), residues: 1210 helix: 2.07 (0.18), residues: 794 sheet: 1.22 (0.56), residues: 50 loop : -1.86 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 185 TYR 0.011 0.002 TYR D 371 PHE 0.019 0.002 PHE C 401 TRP 0.006 0.001 TRP D 482 HIS 0.004 0.001 HIS D 698 Details of bonding type rmsd covalent geometry : bond 0.00449 (10618) covalent geometry : angle 0.60121 (14394) hydrogen bonds : bond 0.06967 ( 617) hydrogen bonds : angle 4.06836 ( 1803) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 0.460 Fit side-chains REVERT: D 37 GLU cc_start: 0.7079 (mp0) cc_final: 0.6806 (mm-30) REVERT: D 320 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6919 (tt0) REVERT: D 576 ARG cc_start: 0.6614 (OUTLIER) cc_final: 0.5327 (mpt90) REVERT: C 37 GLU cc_start: 0.7011 (mp0) cc_final: 0.6783 (mm-30) REVERT: C 320 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6927 (tt0) REVERT: C 503 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7577 (mmt) REVERT: C 576 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.5285 (mpt90) outliers start: 34 outliers final: 21 residues processed: 112 average time/residue: 0.5977 time to fit residues: 72.1470 Evaluate side-chains 116 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 576 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 57 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN D 684 GLN C 246 ASN C 684 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.157025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121461 restraints weight = 11829.630| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.71 r_work: 0.3213 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10618 Z= 0.160 Angle : 0.561 9.203 14394 Z= 0.288 Chirality : 0.044 0.277 1758 Planarity : 0.004 0.036 1642 Dihedral : 12.910 136.715 2714 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.77 % Allowed : 10.71 % Favored : 86.52 % 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 aren not related in a simple way. whole: 1.38 (0.24), residues: 1210 helix: 2.10 (0.18), residues: 794 sheet: 1.06 (0.57), residues: 50 loop : -1.89 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 730 TYR 0.010 0.001 TYR D 371 PHE 0.017 0.002 PHE C 401 TRP 0.008 0.001 TRP C 482 HIS 0.003 0.001 HIS D 698 Details of bonding type rmsd covalent geometry : bond 0.00365 (10618) covalent geometry : angle 0.56109 (14394) hydrogen bonds : bond 0.06189 ( 617) hydrogen bonds : angle 3.97447 ( 1803) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.390 Fit side-chains REVERT: D 320 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6925 (tt0) REVERT: D 576 ARG cc_start: 0.6654 (OUTLIER) cc_final: 0.5372 (mpt90) REVERT: C 37 GLU cc_start: 0.6983 (mp0) cc_final: 0.6760 (mm-30) REVERT: C 320 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6903 (tt0) REVERT: C 461 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8073 (mtm) REVERT: C 503 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7508 (mmt) REVERT: C 576 ARG cc_start: 0.6536 (OUTLIER) cc_final: 0.5228 (mpt90) outliers start: 29 outliers final: 21 residues processed: 107 average time/residue: 0.5743 time to fit residues: 66.1168 Evaluate side-chains 110 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 576 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 43 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 47 optimal weight: 0.5980 chunk 3 optimal weight: 0.0030 chunk 64 optimal weight: 0.0000 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN D 684 GLN C 246 ASN C 684 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.161481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.126405 restraints weight = 11942.178| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.72 r_work: 0.3299 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10618 Z= 0.116 Angle : 0.496 7.503 14394 Z= 0.258 Chirality : 0.042 0.210 1758 Planarity : 0.004 0.040 1642 Dihedral : 12.326 138.268 2714 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.68 % Allowed : 11.19 % Favored : 86.14 % 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 aren not related in a simple way. whole: 1.57 (0.24), residues: 1210 helix: 2.22 (0.19), residues: 800 sheet: 1.16 (0.58), residues: 50 loop : -1.85 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 730 TYR 0.010 0.001 TYR C 371 PHE 0.014 0.001 PHE D 385 TRP 0.012 0.001 TRP C 482 HIS 0.002 0.001 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00245 (10618) covalent geometry : angle 0.49580 (14394) hydrogen bonds : bond 0.04824 ( 617) hydrogen bonds : angle 3.80232 ( 1803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3163.19 seconds wall clock time: 54 minutes 49.02 seconds (3289.02 seconds total)