Starting phenix.real_space_refine on Fri Feb 14 13:53:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sie_40507/02_2025/8sie_40507.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sie_40507/02_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_40507/02_2025/8sie_40507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sie_40507/02_2025/8sie_40507.map" model { file = "/net/cci-nas-00/data/ceres_data/8sie_40507/02_2025/8sie_40507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sie_40507/02_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-5592/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: 7.02, per 1000 atoms: 0.68 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: 2.80 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: 1.04 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: 3.61 Time building geometry restraints manager: 3.20 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: 1.200 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.890 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.780 ------------------------------------------------------------------------------- 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= 0.288 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 *********************** 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 : 0.976 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 128 average time/residue: 1.4110 time to fit residues: 193.7853 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 : 1.056 ------------------------------------------------------------------------------- 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 = 0.163047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.127687 restraints weight = 11929.221| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.74 r_work: 0.3303 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.0886 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= 0.174 Angle : 0.606 11.353 14394 Z= 0.288 Chirality : 0.043 0.217 1758 Planarity : 0.004 0.028 1642 Dihedral : 19.325 159.150 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 *********************** 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 : 1.191 Fit side-chains REVERT: D 37 GLU cc_start: 0.6843 (mp0) cc_final: 0.6546 (pt0) REVERT: D 315 TYR cc_start: 0.7390 (t80) cc_final: 0.7029 (t80) REVERT: D 576 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.5536 (mpt90) REVERT: C 37 GLU cc_start: 0.6842 (mp0) cc_final: 0.6564 (pt0) REVERT: C 315 TYR cc_start: 0.7400 (t80) cc_final: 0.7056 (t80) REVERT: C 503 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7317 (mmt) REVERT: C 576 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.5499 (mpt90) outliers start: 17 outliers final: 4 residues processed: 109 average time/residue: 1.4063 time to fit residues: 164.6827 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 : 1.060 ------------------------------------------------------------------------------- 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: 10.0000 chunk 56 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.154155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117976 restraints weight = 12019.008| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.73 r_work: 0.3166 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10618 Z= 0.356 Angle : 0.656 10.835 14394 Z= 0.332 Chirality : 0.049 0.299 1758 Planarity : 0.005 0.037 1642 Dihedral : 17.925 160.639 2714 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.39 % Allowed : 6.60 % 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 (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: 1.08 (0.24), residues: 1210 helix: 1.84 (0.18), residues: 794 sheet: 1.29 (0.57), residues: 50 loop : -2.02 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 482 HIS 0.004 0.001 HIS C 698 PHE 0.021 0.002 PHE D 401 TYR 0.012 0.002 TYR C 371 ARG 0.004 0.001 ARG C 185 *********************** 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 130 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 1.219 Fit side-chains REVERT: D 37 GLU cc_start: 0.7098 (mp0) cc_final: 0.6846 (pt0) REVERT: D 90 SER cc_start: 0.8787 (t) cc_final: 0.8579 (t) REVERT: D 576 ARG cc_start: 0.6673 (OUTLIER) cc_final: 0.5343 (mpt90) REVERT: C 37 GLU cc_start: 0.7068 (mp0) cc_final: 0.6823 (pt0) REVERT: C 503 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7648 (mmt) REVERT: C 576 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.5316 (mpt90) outliers start: 25 outliers final: 11 residues processed: 120 average time/residue: 1.1600 time to fit residues: 151.8049 Evaluate side-chains 110 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 507 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 267 THR 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 576 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 101 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN D 248 ASN D 464 GLN D 684 GLN C 246 ASN C 464 GLN C 684 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.158359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122652 restraints weight = 11924.549| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.74 r_work: 0.3247 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10618 Z= 0.206 Angle : 0.543 7.103 14394 Z= 0.279 Chirality : 0.044 0.304 1758 Planarity : 0.004 0.034 1642 Dihedral : 16.231 151.592 2714 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.15 % Allowed : 8.03 % Favored : 88.81 % 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: 1.33 (0.24), residues: 1210 helix: 2.06 (0.18), residues: 794 sheet: 1.18 (0.57), residues: 50 loop : -1.95 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 482 HIS 0.002 0.001 HIS C 728 PHE 0.014 0.001 PHE D 401 TYR 0.014 0.001 TYR D 323 ARG 0.003 0.000 ARG C 185 *********************** 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 131 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 1.077 Fit side-chains REVERT: D 37 GLU cc_start: 0.7011 (mp0) cc_final: 0.6752 (pt0) REVERT: D 320 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6955 (tt0) REVERT: D 461 MET cc_start: 0.8566 (mtm) cc_final: 0.8353 (mtm) REVERT: D 576 ARG cc_start: 0.6570 (OUTLIER) cc_final: 0.5264 (mpt90) REVERT: D 730 ARG cc_start: 0.7940 (mtm-85) cc_final: 0.7705 (mtt180) REVERT: C 37 GLU cc_start: 0.7009 (mp0) cc_final: 0.6726 (pt0) REVERT: C 320 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7027 (tt0) REVERT: C 461 MET cc_start: 0.8640 (mtm) cc_final: 0.8404 (mtm) REVERT: C 503 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7618 (mmt) REVERT: C 576 ARG cc_start: 0.6573 (OUTLIER) cc_final: 0.5239 (mpt90) REVERT: C 730 ARG cc_start: 0.7919 (mtm-85) cc_final: 0.7675 (mtt180) outliers start: 33 outliers final: 16 residues processed: 114 average time/residue: 1.2346 time to fit residues: 152.2482 Evaluate side-chains 112 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 111 VAL 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 559 VAL Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 80 ILE 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 503 MET Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 559 VAL 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: 0.9980 chunk 79 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN D 248 ASN 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 = 0.3833 r_free = 0.3833 target = 0.160978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.126054 restraints weight = 11897.960| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.71 r_work: 0.3292 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10618 Z= 0.162 Angle : 0.511 8.144 14394 Z= 0.259 Chirality : 0.043 0.251 1758 Planarity : 0.003 0.033 1642 Dihedral : 14.629 151.071 2714 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.15 % Allowed : 8.80 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.49 (0.24), residues: 1210 helix: 2.19 (0.18), residues: 798 sheet: 1.21 (0.57), residues: 50 loop : -1.96 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 482 HIS 0.002 0.001 HIS D 698 PHE 0.013 0.001 PHE D 555 TYR 0.010 0.001 TYR C 371 ARG 0.004 0.000 ARG D 730 *********************** 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 : 1.118 Fit side-chains REVERT: D 37 GLU cc_start: 0.6898 (mp0) cc_final: 0.6603 (pt0) REVERT: D 461 MET cc_start: 0.8533 (mtm) cc_final: 0.8329 (mtm) REVERT: D 576 ARG cc_start: 0.6596 (OUTLIER) cc_final: 0.5299 (mpt90) REVERT: C 37 GLU cc_start: 0.6894 (mp0) cc_final: 0.6659 (mm-30) REVERT: C 320 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6940 (tt0) REVERT: C 576 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.5198 (mpt90) outliers start: 33 outliers final: 17 residues processed: 114 average time/residue: 1.1333 time to fit residues: 140.7839 Evaluate side-chains 113 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 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 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 576 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 59 optimal weight: 0.0370 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 0.5980 overall best weight: 0.6860 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.161947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.127044 restraints weight = 11958.304| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.72 r_work: 0.3325 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1595 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= 0.153 Angle : 0.499 7.583 14394 Z= 0.253 Chirality : 0.042 0.344 1758 Planarity : 0.003 0.033 1642 Dihedral : 13.567 146.827 2714 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.58 % Allowed : 9.85 % Favored : 87.57 % 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: 1.63 (0.25), residues: 1210 helix: 2.27 (0.19), residues: 802 sheet: 1.31 (0.58), residues: 50 loop : -1.86 (0.29), residues: 358 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 0.012 0.001 PHE C 385 TYR 0.011 0.001 TYR C 371 ARG 0.004 0.000 ARG C 730 *********************** 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 123 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 1.126 Fit side-chains REVERT: D 320 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6858 (tt0) REVERT: D 576 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.5255 (mpt90) REVERT: C 320 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6882 (tt0) REVERT: C 576 ARG cc_start: 0.6535 (OUTLIER) cc_final: 0.5228 (mpt90) REVERT: C 730 ARG cc_start: 0.7985 (mtm-85) cc_final: 0.7702 (mtt180) outliers start: 27 outliers final: 13 residues processed: 111 average time/residue: 1.0915 time to fit residues: 132.1546 Evaluate side-chains 110 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 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 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 545 VAL Chi-restraints excluded: chain C residue 556 TYR 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: 6.9990 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.158652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.123308 restraints weight = 11959.427| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.71 r_work: 0.3256 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10618 Z= 0.206 Angle : 0.537 8.948 14394 Z= 0.273 Chirality : 0.044 0.360 1758 Planarity : 0.004 0.033 1642 Dihedral : 13.327 143.327 2714 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.06 % Allowed : 10.52 % Favored : 86.42 % 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: 1.51 (0.24), residues: 1210 helix: 2.21 (0.18), residues: 796 sheet: 1.22 (0.58), residues: 50 loop : -1.94 (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 D 698 PHE 0.017 0.001 PHE C 401 TYR 0.011 0.001 TYR C 371 ARG 0.004 0.000 ARG C 79 *********************** 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 126 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 1.141 Fit side-chains REVERT: D 320 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6967 (tt0) REVERT: D 576 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.5305 (mpt90) REVERT: C 320 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6976 (tt0) REVERT: C 576 ARG cc_start: 0.6517 (OUTLIER) cc_final: 0.5184 (mpt90) outliers start: 32 outliers final: 22 residues processed: 116 average time/residue: 1.0923 time to fit residues: 138.6405 Evaluate side-chains 118 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 111 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 72 optimal weight: 0.0070 chunk 29 optimal weight: 2.9990 overall best weight: 1.3604 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.158995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.123672 restraints weight = 11916.720| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.71 r_work: 0.3250 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10618 Z= 0.198 Angle : 0.529 8.714 14394 Z= 0.272 Chirality : 0.043 0.315 1758 Planarity : 0.004 0.033 1642 Dihedral : 12.982 141.250 2714 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.06 % Allowed : 11.28 % Favored : 85.66 % 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: 1.52 (0.24), residues: 1210 helix: 2.21 (0.18), residues: 796 sheet: 1.22 (0.58), residues: 50 loop : -1.90 (0.30), residues: 364 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 0.001 PHE D 401 TYR 0.010 0.001 TYR C 371 ARG 0.004 0.000 ARG C 730 *********************** 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 125 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 1.038 Fit side-chains REVERT: D 320 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6966 (tt0) REVERT: D 576 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.5324 (mpt90) REVERT: C 37 GLU cc_start: 0.6915 (mp0) cc_final: 0.6685 (mm-30) REVERT: C 320 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6963 (tt0) REVERT: C 461 MET cc_start: 0.8118 (mtm) cc_final: 0.7899 (mtm) REVERT: C 503 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7382 (mmt) REVERT: C 576 ARG cc_start: 0.6502 (OUTLIER) cc_final: 0.5174 (mpt90) outliers start: 32 outliers final: 22 residues processed: 114 average time/residue: 1.1483 time to fit residues: 142.5376 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 : 1.153 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 23 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.157705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121630 restraints weight = 12090.690| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.75 r_work: 0.3232 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10618 Z= 0.234 Angle : 0.554 9.240 14394 Z= 0.284 Chirality : 0.044 0.295 1758 Planarity : 0.004 0.034 1642 Dihedral : 12.914 138.708 2714 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.35 % Allowed : 11.19 % Favored : 85.47 % 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: 1.47 (0.24), residues: 1210 helix: 2.16 (0.18), residues: 794 sheet: 1.17 (0.58), residues: 50 loop : -1.84 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 482 HIS 0.003 0.001 HIS D 698 PHE 0.018 0.002 PHE C 401 TYR 0.010 0.001 TYR D 371 ARG 0.004 0.000 ARG C 79 *********************** 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 128 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 1.073 Fit side-chains REVERT: D 37 GLU cc_start: 0.7002 (mp0) cc_final: 0.6760 (mm-30) REVERT: D 320 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6889 (tt0) REVERT: D 576 ARG cc_start: 0.6608 (OUTLIER) cc_final: 0.5329 (mpt90) REVERT: C 37 GLU cc_start: 0.6947 (mp0) cc_final: 0.6709 (mm-30) REVERT: C 320 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6967 (tt0) REVERT: C 461 MET cc_start: 0.8247 (mtm) cc_final: 0.8030 (mtm) REVERT: C 503 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7430 (mmt) REVERT: C 576 ARG cc_start: 0.6595 (OUTLIER) cc_final: 0.5262 (mpt90) outliers start: 35 outliers final: 25 residues processed: 115 average time/residue: 1.1736 time to fit residues: 146.5096 Evaluate side-chains 124 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 LYS 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 575 ILE Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain C residue 66 LYS 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 349 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 10 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 47 optimal weight: 0.0270 chunk 72 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.162271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.127442 restraints weight = 11999.289| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.72 r_work: 0.3312 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1751 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= 0.152 Angle : 0.488 7.353 14394 Z= 0.254 Chirality : 0.041 0.226 1758 Planarity : 0.004 0.038 1642 Dihedral : 12.356 139.795 2714 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.68 % Allowed : 11.95 % Favored : 85.37 % 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: 1.63 (0.25), residues: 1210 helix: 2.26 (0.19), residues: 800 sheet: 1.30 (0.59), residues: 50 loop : -1.83 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 482 HIS 0.002 0.001 HIS D 656 PHE 0.013 0.001 PHE D 128 TYR 0.010 0.001 TYR C 371 ARG 0.004 0.000 ARG C 730 ********************** 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 131 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 1.082 Fit side-chains REVERT: D 66 LYS cc_start: 0.5184 (OUTLIER) cc_final: 0.4976 (pptt) REVERT: D 576 ARG cc_start: 0.6549 (OUTLIER) cc_final: 0.5276 (mpt90) REVERT: D 730 ARG cc_start: 0.7930 (mtm-85) cc_final: 0.7675 (mtt180) REVERT: C 66 LYS cc_start: 0.5179 (OUTLIER) cc_final: 0.4975 (pptt) REVERT: C 320 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6875 (tt0) REVERT: C 503 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7294 (mmt) REVERT: C 576 ARG cc_start: 0.6542 (OUTLIER) cc_final: 0.5230 (mpt90) REVERT: C 730 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7624 (mtt180) outliers start: 28 outliers final: 17 residues processed: 117 average time/residue: 1.1896 time to fit residues: 151.0048 Evaluate side-chains 119 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 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 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 349 MET 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: 0.9980 chunk 80 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 47 optimal weight: 0.0050 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.160655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.125605 restraints weight = 11889.461| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.71 r_work: 0.3285 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10618 Z= 0.173 Angle : 0.505 8.482 14394 Z= 0.262 Chirality : 0.042 0.208 1758 Planarity : 0.004 0.041 1642 Dihedral : 12.153 137.215 2714 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.68 % Allowed : 12.14 % Favored : 85.18 % 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: 1.64 (0.24), residues: 1210 helix: 2.26 (0.19), residues: 800 sheet: 1.24 (0.59), residues: 50 loop : -1.80 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 482 HIS 0.002 0.001 HIS D 698 PHE 0.014 0.001 PHE C 401 TYR 0.011 0.001 TYR C 371 ARG 0.004 0.000 ARG C 730 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6968.25 seconds wall clock time: 123 minutes 56.36 seconds (7436.36 seconds total)