Starting phenix.real_space_refine on Thu May 1 05:15:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sie_40507/05_2025/8sie_40507.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sie_40507/05_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_40507/05_2025/8sie_40507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sie_40507/05_2025/8sie_40507.map" model { file = "/net/cci-nas-00/data/ceres_data/8sie_40507/05_2025/8sie_40507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sie_40507/05_2025/8sie_40507.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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-2': 6, 'LBN:plan-3': 7, 'LBN:plan-1': 7} 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-2': 6, 'LBN:plan-3': 7, 'LBN:plan-1': 7} Unresolved non-hydrogen planarities: 72 Time building chain proxies: 7.01, per 1000 atoms: 0.67 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: 2.82 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.01 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: 3.46 Time building geometry restraints manager: 3.22 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: 0.05 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: 35.660 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: 2.840 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 27.210 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:38.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.920 ------------------------------------------------------------------------------- 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 : 5.47 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP C 482 HIS 0.002 0.001 HIS C 728 PHE 0.029 0.001 PHE D 385 TYR 0.012 0.001 TYR D 323 ARG 0.005 0.000 ARG C 730 Details of bonding type rmsd hydrogen bonds : bond 0.13372 ( 617) hydrogen bonds : angle 5.23381 ( 1803) covalent geometry : bond 0.00475 (10618) covalent geometry : angle 0.67187 (14394) *********************** 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 : 1.034 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 128 average time/residue: 1.9354 time to fit residues: 265.2035 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 : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 0.0970 chunk 49 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 58 optimal weight: 0.0870 chunk 71 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 overall best weight: 0.8156 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.163035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.127689 restraints weight = 11930.060| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.74 r_work: 0.3304 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10618 Z= 0.131 Angle : 0.606 11.350 14394 Z= 0.288 Chirality : 0.043 0.216 1758 Planarity : 0.004 0.028 1642 Dihedral : 19.333 159.154 2714 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.63 % Allowed : 5.64 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.24), residues: 1210 helix: 2.14 (0.19), residues: 794 sheet: 1.48 (0.59), residues: 50 loop : -2.04 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 482 HIS 0.003 0.001 HIS D 728 PHE 0.015 0.001 PHE C 385 TYR 0.011 0.001 TYR D 371 ARG 0.004 0.000 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.05294 ( 617) hydrogen bonds : angle 4.10770 ( 1803) covalent geometry : bond 0.00270 (10618) covalent geometry : angle 0.60610 (14394) *********************** 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 124 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.077 Fit side-chains REVERT: D 37 GLU cc_start: 0.6839 (mp0) cc_final: 0.6544 (pt0) REVERT: D 315 TYR cc_start: 0.7390 (t80) cc_final: 0.7028 (t80) REVERT: D 576 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.5536 (mpt90) REVERT: C 37 GLU cc_start: 0.6840 (mp0) cc_final: 0.6564 (pt0) REVERT: C 315 TYR cc_start: 0.7400 (t80) cc_final: 0.7055 (t80) REVERT: C 503 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7313 (mmt) REVERT: C 576 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.5498 (mpt90) outliers start: 17 outliers final: 4 residues processed: 109 average time/residue: 1.3437 time to fit residues: 157.3579 Evaluate side-chains 107 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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: 9.9990 chunk 56 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.158762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122844 restraints weight = 12012.406| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.75 r_work: 0.3238 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10618 Z= 0.151 Angle : 0.562 8.640 14394 Z= 0.284 Chirality : 0.045 0.310 1758 Planarity : 0.004 0.033 1642 Dihedral : 17.215 163.037 2714 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.01 % Allowed : 6.60 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.24), residues: 1210 helix: 2.13 (0.19), residues: 794 sheet: 1.35 (0.57), residues: 50 loop : -1.99 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 482 HIS 0.003 0.001 HIS C 698 PHE 0.016 0.002 PHE D 401 TYR 0.011 0.001 TYR D 323 ARG 0.003 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.06052 ( 617) hydrogen bonds : angle 4.03656 ( 1803) covalent geometry : bond 0.00338 (10618) covalent geometry : angle 0.56173 (14394) *********************** 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 123 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 1.121 Fit side-chains REVERT: D 37 GLU cc_start: 0.7032 (mp0) cc_final: 0.6769 (pt0) REVERT: D 564 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7945 (tmmt) REVERT: D 576 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.5374 (mpt90) REVERT: C 37 GLU cc_start: 0.7018 (mp0) cc_final: 0.6751 (pt0) REVERT: C 503 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7546 (mmt) REVERT: C 564 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7944 (tmmt) REVERT: C 576 ARG cc_start: 0.6671 (OUTLIER) cc_final: 0.5340 (mpt90) outliers start: 21 outliers final: 8 residues processed: 110 average time/residue: 1.1711 time to fit residues: 139.7169 Evaluate side-chains 105 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 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 503 MET Chi-restraints excluded: chain C residue 507 LEU 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 101 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 89 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 9 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.159813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124087 restraints weight = 11935.354| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.75 r_work: 0.3264 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10618 Z= 0.135 Angle : 0.533 7.196 14394 Z= 0.271 Chirality : 0.044 0.272 1758 Planarity : 0.004 0.032 1642 Dihedral : 15.643 151.683 2714 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.35 % Allowed : 6.60 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.24), residues: 1210 helix: 2.16 (0.18), residues: 794 sheet: 1.33 (0.57), residues: 50 loop : -1.95 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 482 HIS 0.002 0.001 HIS C 698 PHE 0.015 0.001 PHE C 401 TYR 0.010 0.001 TYR C 536 ARG 0.003 0.000 ARG C 730 Details of bonding type rmsd hydrogen bonds : bond 0.05507 ( 617) hydrogen bonds : angle 3.91222 ( 1803) covalent geometry : bond 0.00295 (10618) covalent geometry : angle 0.53258 (14394) *********************** 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 137 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 1.045 Fit side-chains REVERT: D 37 GLU cc_start: 0.6988 (mp0) cc_final: 0.6720 (pt0) REVERT: D 320 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6938 (tt0) REVERT: D 461 MET cc_start: 0.8556 (mtm) cc_final: 0.8352 (mtm) REVERT: D 564 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7944 (tmmt) REVERT: D 576 ARG cc_start: 0.6559 (OUTLIER) cc_final: 0.5257 (mpt90) REVERT: C 37 GLU cc_start: 0.6942 (mp0) cc_final: 0.6681 (pt0) REVERT: C 320 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6989 (tt0) REVERT: C 564 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7946 (tmmt) REVERT: C 576 ARG cc_start: 0.6569 (OUTLIER) cc_final: 0.5253 (mpt90) outliers start: 35 outliers final: 19 residues processed: 122 average time/residue: 1.1459 time to fit residues: 151.6402 Evaluate side-chains 121 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 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 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 267 THR Chi-restraints excluded: chain C residue 283 MET 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 564 LYS 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 68 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 82 optimal weight: 0.3980 chunk 69 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.162183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.127243 restraints weight = 11880.081| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.72 r_work: 0.3307 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10618 Z= 0.116 Angle : 0.504 7.785 14394 Z= 0.255 Chirality : 0.043 0.308 1758 Planarity : 0.003 0.033 1642 Dihedral : 14.304 151.618 2714 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.15 % Allowed : 8.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.24), residues: 1210 helix: 2.26 (0.19), residues: 800 sheet: 1.29 (0.57), residues: 50 loop : -1.95 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 482 HIS 0.002 0.001 HIS D 728 PHE 0.014 0.001 PHE D 385 TYR 0.010 0.001 TYR C 371 ARG 0.003 0.000 ARG D 730 Details of bonding type rmsd hydrogen bonds : bond 0.04785 ( 617) hydrogen bonds : angle 3.79307 ( 1803) covalent geometry : bond 0.00248 (10618) covalent geometry : angle 0.50402 (14394) *********************** 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 134 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 1.060 Fit side-chains REVERT: D 537 LYS cc_start: 0.7094 (mmpt) cc_final: 0.6493 (mptp) REVERT: D 564 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7936 (tmmt) REVERT: D 576 ARG cc_start: 0.6588 (OUTLIER) cc_final: 0.5292 (mpt90) REVERT: D 730 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7709 (mtt180) REVERT: C 320 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6910 (tt0) REVERT: C 564 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7935 (tmmt) REVERT: C 576 ARG cc_start: 0.6511 (OUTLIER) cc_final: 0.5187 (mpt90) REVERT: C 730 ARG cc_start: 0.7979 (mtm-85) cc_final: 0.7693 (mtt180) outliers start: 33 outliers final: 18 residues processed: 120 average time/residue: 1.1692 time to fit residues: 152.9107 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 : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 219 LEU 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 564 LYS 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 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 564 LYS Chi-restraints excluded: chain C residue 575 ILE 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 59 optimal weight: 0.0020 chunk 51 optimal weight: 0.0980 chunk 54 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 overall best weight: 0.7992 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.162147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.127129 restraints weight = 11899.647| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.71 r_work: 0.3309 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10618 Z= 0.116 Angle : 0.498 7.894 14394 Z= 0.254 Chirality : 0.042 0.348 1758 Planarity : 0.003 0.034 1642 Dihedral : 13.295 145.743 2714 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.96 % Allowed : 9.18 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1210 helix: 2.28 (0.19), residues: 800 sheet: 1.43 (0.58), residues: 50 loop : -1.92 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 482 HIS 0.002 0.001 HIS C 728 PHE 0.013 0.001 PHE D 385 TYR 0.011 0.001 TYR C 371 ARG 0.003 0.000 ARG C 730 Details of bonding type rmsd hydrogen bonds : bond 0.04863 ( 617) hydrogen bonds : angle 3.74929 ( 1803) covalent geometry : bond 0.00246 (10618) covalent geometry : angle 0.49844 (14394) *********************** 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 129 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 1.131 Fit side-chains REVERT: D 320 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6886 (tt0) REVERT: D 564 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7952 (tmmt) REVERT: D 576 ARG cc_start: 0.6546 (OUTLIER) cc_final: 0.5275 (mpt90) REVERT: C 320 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6882 (tt0) REVERT: C 564 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7959 (tmmt) REVERT: C 576 ARG cc_start: 0.6536 (OUTLIER) cc_final: 0.5243 (mpt90) REVERT: C 730 ARG cc_start: 0.7962 (mtm-85) cc_final: 0.7659 (mtt180) outliers start: 31 outliers final: 16 residues processed: 118 average time/residue: 1.0648 time to fit residues: 137.1835 Evaluate side-chains 119 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 219 LEU 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 564 LYS Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 219 LEU 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 556 TYR Chi-restraints excluded: chain C residue 559 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 50 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 0.0970 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.163664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.128233 restraints weight = 12056.087| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.75 r_work: 0.3324 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10618 Z= 0.109 Angle : 0.480 7.767 14394 Z= 0.247 Chirality : 0.041 0.284 1758 Planarity : 0.003 0.034 1642 Dihedral : 12.786 144.237 2714 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.58 % Allowed : 9.75 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.24), residues: 1210 helix: 2.32 (0.19), residues: 800 sheet: 1.45 (0.58), residues: 50 loop : -1.88 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 482 HIS 0.002 0.001 HIS C 728 PHE 0.014 0.001 PHE D 385 TYR 0.010 0.001 TYR D 371 ARG 0.002 0.000 ARG C 730 Details of bonding type rmsd hydrogen bonds : bond 0.04561 ( 617) hydrogen bonds : angle 3.70751 ( 1803) covalent geometry : bond 0.00231 (10618) covalent geometry : angle 0.47994 (14394) *********************** 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: 27 poor density : 101 time to evaluate : 1.057 Fit side-chains REVERT: D 564 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7959 (tmmt) REVERT: D 576 ARG cc_start: 0.6533 (OUTLIER) cc_final: 0.5250 (mpt90) REVERT: C 576 ARG cc_start: 0.6540 (OUTLIER) cc_final: 0.5231 (mpt90) outliers start: 27 outliers final: 17 residues processed: 116 average time/residue: 1.0381 time to fit residues: 131.7680 Evaluate side-chains 118 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 219 LEU 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 564 LYS Chi-restraints excluded: chain D residue 576 ARG 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 385 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 111 optimal weight: 0.9980 chunk 114 optimal weight: 0.2980 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.161140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.125244 restraints weight = 11956.147| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.75 r_work: 0.3281 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10618 Z= 0.130 Angle : 0.510 8.608 14394 Z= 0.262 Chirality : 0.042 0.260 1758 Planarity : 0.004 0.033 1642 Dihedral : 12.590 140.223 2714 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.06 % Allowed : 9.56 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.24), residues: 1210 helix: 2.29 (0.18), residues: 796 sheet: 1.36 (0.58), residues: 50 loop : -1.91 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 482 HIS 0.003 0.001 HIS C 698 PHE 0.015 0.001 PHE D 401 TYR 0.011 0.001 TYR C 371 ARG 0.004 0.000 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.05303 ( 617) hydrogen bonds : angle 3.78717 ( 1803) covalent geometry : bond 0.00286 (10618) covalent geometry : angle 0.51000 (14394) *********************** 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 134 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 1.143 Fit side-chains REVERT: D 320 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6899 (tt0) REVERT: D 576 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.5329 (mpt90) REVERT: C 503 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7395 (mmt) REVERT: C 576 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.5250 (mpt90) outliers start: 32 outliers final: 18 residues processed: 121 average time/residue: 1.0349 time to fit residues: 136.9240 Evaluate side-chains 120 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 111 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 267 THR 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 23 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 109 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.160347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124219 restraints weight = 12102.624| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.76 r_work: 0.3268 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10618 Z= 0.135 Angle : 0.517 8.730 14394 Z= 0.267 Chirality : 0.042 0.231 1758 Planarity : 0.004 0.034 1642 Dihedral : 12.351 137.701 2714 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.15 % Allowed : 10.04 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.24), residues: 1210 helix: 2.25 (0.18), residues: 796 sheet: 1.31 (0.57), residues: 50 loop : -1.85 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 482 HIS 0.003 0.001 HIS D 698 PHE 0.016 0.001 PHE C 401 TYR 0.010 0.001 TYR D 371 ARG 0.004 0.000 ARG C 730 Details of bonding type rmsd hydrogen bonds : bond 0.05464 ( 617) hydrogen bonds : angle 3.82386 ( 1803) covalent geometry : bond 0.00298 (10618) covalent geometry : angle 0.51718 (14394) *********************** 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 126 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 1.190 Fit side-chains REVERT: D 320 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6946 (tt0) REVERT: D 576 ARG cc_start: 0.6594 (OUTLIER) cc_final: 0.5320 (mpt90) REVERT: C 320 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6913 (tt0) REVERT: C 503 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7407 (mmt) REVERT: C 576 ARG cc_start: 0.6549 (OUTLIER) cc_final: 0.5236 (mpt90) REVERT: C 730 ARG cc_start: 0.7927 (mtm-85) cc_final: 0.7666 (mtt180) outliers start: 33 outliers final: 20 residues processed: 117 average time/residue: 1.0567 time to fit residues: 135.4299 Evaluate side-chains 116 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 10 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 0.0170 chunk 72 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 29 optimal weight: 0.0050 chunk 36 optimal weight: 9.9990 overall best weight: 0.4632 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.165010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.130174 restraints weight = 12027.415| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.73 r_work: 0.3348 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10618 Z= 0.105 Angle : 0.471 7.398 14394 Z= 0.244 Chirality : 0.041 0.182 1758 Planarity : 0.003 0.035 1642 Dihedral : 11.864 138.361 2714 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.39 % Allowed : 10.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.25), residues: 1210 helix: 2.29 (0.19), residues: 802 sheet: 1.49 (0.60), residues: 50 loop : -1.71 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 482 HIS 0.002 0.001 HIS C 656 PHE 0.014 0.001 PHE D 385 TYR 0.010 0.001 TYR C 371 ARG 0.003 0.000 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 617) hydrogen bonds : angle 3.67472 ( 1803) covalent geometry : bond 0.00223 (10618) covalent geometry : angle 0.47147 (14394) ********************** 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 134 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 1.191 Fit side-chains REVERT: D 559 VAL cc_start: 0.7624 (OUTLIER) cc_final: 0.7375 (m) REVERT: D 576 ARG cc_start: 0.6560 (OUTLIER) cc_final: 0.5281 (mpt90) REVERT: C 315 TYR cc_start: 0.7362 (t80) cc_final: 0.7030 (t80) REVERT: C 503 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7294 (mmt) REVERT: C 559 VAL cc_start: 0.7617 (OUTLIER) cc_final: 0.7373 (m) REVERT: C 576 ARG cc_start: 0.6540 (OUTLIER) cc_final: 0.5233 (mpt90) REVERT: C 730 ARG cc_start: 0.7909 (mtm-85) cc_final: 0.7637 (mtt180) outliers start: 25 outliers final: 11 residues processed: 123 average time/residue: 1.2299 time to fit residues: 167.5195 Evaluate side-chains 113 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 VAL 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 111 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 503 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 105 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 47 optimal weight: 0.0980 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.154236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.118311 restraints weight = 11916.453| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.71 r_work: 0.3198 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10618 Z= 0.230 Angle : 0.655 11.881 14394 Z= 0.334 Chirality : 0.047 0.260 1758 Planarity : 0.005 0.042 1642 Dihedral : 12.534 130.687 2714 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.77 % Allowed : 11.19 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1210 helix: 1.98 (0.18), residues: 794 sheet: 1.25 (0.55), residues: 50 loop : -1.78 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 472 HIS 0.006 0.001 HIS D 698 PHE 0.023 0.002 PHE C 401 TYR 0.013 0.002 TYR D 371 ARG 0.006 0.001 ARG C 185 Details of bonding type rmsd hydrogen bonds : bond 0.07658 ( 617) hydrogen bonds : angle 4.14332 ( 1803) covalent geometry : bond 0.00548 (10618) covalent geometry : angle 0.65454 (14394) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8103.88 seconds wall clock time: 142 minutes 32.40 seconds (8552.40 seconds total)