Starting phenix.real_space_refine on Sat Aug 23 11:04:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c8k_16482/08_2025/8c8k_16482.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c8k_16482/08_2025/8c8k_16482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c8k_16482/08_2025/8c8k_16482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c8k_16482/08_2025/8c8k_16482.map" model { file = "/net/cci-nas-00/data/ceres_data/8c8k_16482/08_2025/8c8k_16482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c8k_16482/08_2025/8c8k_16482.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 7074 2.51 5 N 1758 2.21 5 O 2592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11430 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1905 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 244} Chain: "B" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1905 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 244} Chain: "C" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1905 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 244} Chain: "D" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1905 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 244} Chain: "E" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1905 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 244} Chain: "F" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1905 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 244} Time building chain proxies: 2.67, per 1000 atoms: 0.23 Number of scatterers: 11430 At special positions: 0 Unit cell: (243.516, 258.804, 49.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 2592 8.00 N 1758 7.00 C 7074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 597.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2724 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 30 sheets defined 3.2% alpha, 50.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 1389 through 1392 Processing helix chain 'A' and resid 1523 through 1526 Processing helix chain 'B' and resid 1389 through 1392 Processing helix chain 'B' and resid 1523 through 1526 Processing helix chain 'C' and resid 1389 through 1392 Processing helix chain 'C' and resid 1523 through 1526 Processing helix chain 'D' and resid 1389 through 1392 Processing helix chain 'D' and resid 1523 through 1526 Processing helix chain 'E' and resid 1389 through 1392 Processing helix chain 'E' and resid 1523 through 1526 Processing helix chain 'F' and resid 1389 through 1392 Processing helix chain 'F' and resid 1523 through 1526 Processing sheet with id=AA1, first strand: chain 'A' and resid 1368 through 1371 Processing sheet with id=AA2, first strand: chain 'A' and resid 1368 through 1371 removed outlier: 3.869A pdb=" N GLY A1468 " --> pdb=" O GLU A1436 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1375 through 1376 removed outlier: 7.576A pdb=" N GLU A1488 " --> pdb=" O PHE A1484 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A1484 " --> pdb=" O GLU A1488 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1502 through 1505 removed outlier: 3.514A pdb=" N VAL A1518 " --> pdb=" O GLY A1564 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A1564 " --> pdb=" O VAL A1518 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N THR A1565 " --> pdb=" O THR A1551 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR A1551 " --> pdb=" O THR A1565 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N PHE A1567 " --> pdb=" O ASP A1549 " (cutoff:3.500A) removed outlier: 10.644A pdb=" N ASP A1549 " --> pdb=" O PHE A1567 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N GLU A1536 " --> pdb=" O GLU A1592 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU A1592 " --> pdb=" O GLU A1536 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP A1585 " --> pdb=" O ILE A1614 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A1614 " --> pdb=" O ASP A1585 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A1606 " --> pdb=" O ASP A1593 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1502 through 1505 removed outlier: 3.514A pdb=" N VAL A1518 " --> pdb=" O GLY A1564 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A1564 " --> pdb=" O VAL A1518 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N LEU A1579 " --> pdb=" O THR A1565 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE A1567 " --> pdb=" O LEU A1579 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1368 through 1371 Processing sheet with id=AA7, first strand: chain 'B' and resid 1368 through 1371 removed outlier: 3.863A pdb=" N GLY B1468 " --> pdb=" O GLU B1436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1375 through 1376 removed outlier: 7.562A pdb=" N GLU B1488 " --> pdb=" O PHE B1484 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE B1484 " --> pdb=" O GLU B1488 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1502 through 1505 removed outlier: 3.513A pdb=" N VAL B1518 " --> pdb=" O GLY B1564 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B1564 " --> pdb=" O VAL B1518 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR B1565 " --> pdb=" O THR B1551 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR B1551 " --> pdb=" O THR B1565 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N PHE B1567 " --> pdb=" O ASP B1549 " (cutoff:3.500A) removed outlier: 10.670A pdb=" N ASP B1549 " --> pdb=" O PHE B1567 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N GLU B1536 " --> pdb=" O GLU B1592 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU B1592 " --> pdb=" O GLU B1536 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP B1585 " --> pdb=" O ILE B1614 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B1614 " --> pdb=" O ASP B1585 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B1606 " --> pdb=" O ASP B1593 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1502 through 1505 removed outlier: 3.513A pdb=" N VAL B1518 " --> pdb=" O GLY B1564 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B1564 " --> pdb=" O VAL B1518 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N LEU B1579 " --> pdb=" O THR B1565 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE B1567 " --> pdb=" O LEU B1579 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 1368 through 1371 Processing sheet with id=AB3, first strand: chain 'C' and resid 1368 through 1371 removed outlier: 3.865A pdb=" N GLY C1468 " --> pdb=" O GLU C1436 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 1375 through 1376 removed outlier: 7.555A pdb=" N GLU C1488 " --> pdb=" O PHE C1484 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE C1484 " --> pdb=" O GLU C1488 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 1502 through 1505 removed outlier: 3.514A pdb=" N VAL C1518 " --> pdb=" O GLY C1564 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C1564 " --> pdb=" O VAL C1518 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N THR C1565 " --> pdb=" O THR C1551 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR C1551 " --> pdb=" O THR C1565 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N PHE C1567 " --> pdb=" O ASP C1549 " (cutoff:3.500A) removed outlier: 10.628A pdb=" N ASP C1549 " --> pdb=" O PHE C1567 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N GLU C1536 " --> pdb=" O GLU C1592 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU C1592 " --> pdb=" O GLU C1536 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP C1585 " --> pdb=" O ILE C1614 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C1614 " --> pdb=" O ASP C1585 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C1606 " --> pdb=" O ASP C1593 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1502 through 1505 removed outlier: 3.514A pdb=" N VAL C1518 " --> pdb=" O GLY C1564 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C1564 " --> pdb=" O VAL C1518 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LEU C1579 " --> pdb=" O THR C1565 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE C1567 " --> pdb=" O LEU C1579 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 1368 through 1371 Processing sheet with id=AB8, first strand: chain 'D' and resid 1368 through 1371 removed outlier: 3.868A pdb=" N GLY D1468 " --> pdb=" O GLU D1436 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 1375 through 1376 removed outlier: 7.561A pdb=" N GLU D1488 " --> pdb=" O PHE D1484 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE D1484 " --> pdb=" O GLU D1488 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 1502 through 1505 removed outlier: 3.515A pdb=" N VAL D1518 " --> pdb=" O GLY D1564 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY D1564 " --> pdb=" O VAL D1518 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N THR D1565 " --> pdb=" O THR D1551 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR D1551 " --> pdb=" O THR D1565 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N PHE D1567 " --> pdb=" O ASP D1549 " (cutoff:3.500A) removed outlier: 10.648A pdb=" N ASP D1549 " --> pdb=" O PHE D1567 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N GLU D1536 " --> pdb=" O GLU D1592 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLU D1592 " --> pdb=" O GLU D1536 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP D1585 " --> pdb=" O ILE D1614 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D1614 " --> pdb=" O ASP D1585 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D1606 " --> pdb=" O ASP D1593 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1502 through 1505 removed outlier: 3.515A pdb=" N VAL D1518 " --> pdb=" O GLY D1564 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY D1564 " --> pdb=" O VAL D1518 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LEU D1579 " --> pdb=" O THR D1565 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE D1567 " --> pdb=" O LEU D1579 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 1368 through 1371 Processing sheet with id=AC4, first strand: chain 'E' and resid 1368 through 1371 removed outlier: 3.864A pdb=" N GLY E1468 " --> pdb=" O GLU E1436 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 1375 through 1376 removed outlier: 7.562A pdb=" N GLU E1488 " --> pdb=" O PHE E1484 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE E1484 " --> pdb=" O GLU E1488 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 1502 through 1505 removed outlier: 3.516A pdb=" N VAL E1518 " --> pdb=" O GLY E1564 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY E1564 " --> pdb=" O VAL E1518 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR E1565 " --> pdb=" O THR E1551 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR E1551 " --> pdb=" O THR E1565 " (cutoff:3.500A) removed outlier: 10.012A pdb=" N PHE E1567 " --> pdb=" O ASP E1549 " (cutoff:3.500A) removed outlier: 10.627A pdb=" N ASP E1549 " --> pdb=" O PHE E1567 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N GLU E1536 " --> pdb=" O GLU E1592 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU E1592 " --> pdb=" O GLU E1536 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP E1585 " --> pdb=" O ILE E1614 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE E1614 " --> pdb=" O ASP E1585 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU E1606 " --> pdb=" O ASP E1593 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 1502 through 1505 removed outlier: 3.516A pdb=" N VAL E1518 " --> pdb=" O GLY E1564 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY E1564 " --> pdb=" O VAL E1518 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N LEU E1579 " --> pdb=" O THR E1565 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE E1567 " --> pdb=" O LEU E1579 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 1368 through 1371 Processing sheet with id=AC9, first strand: chain 'F' and resid 1368 through 1371 removed outlier: 3.865A pdb=" N GLY F1468 " --> pdb=" O GLU F1436 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 1375 through 1376 removed outlier: 7.555A pdb=" N GLU F1488 " --> pdb=" O PHE F1484 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE F1484 " --> pdb=" O GLU F1488 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 1502 through 1505 removed outlier: 3.513A pdb=" N VAL F1518 " --> pdb=" O GLY F1564 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY F1564 " --> pdb=" O VAL F1518 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N THR F1565 " --> pdb=" O THR F1551 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR F1551 " --> pdb=" O THR F1565 " (cutoff:3.500A) removed outlier: 10.016A pdb=" N PHE F1567 " --> pdb=" O ASP F1549 " (cutoff:3.500A) removed outlier: 10.634A pdb=" N ASP F1549 " --> pdb=" O PHE F1567 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N GLU F1536 " --> pdb=" O GLU F1592 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU F1592 " --> pdb=" O GLU F1536 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP F1585 " --> pdb=" O ILE F1614 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE F1614 " --> pdb=" O ASP F1585 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU F1606 " --> pdb=" O ASP F1593 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 1502 through 1505 removed outlier: 3.513A pdb=" N VAL F1518 " --> pdb=" O GLY F1564 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY F1564 " --> pdb=" O VAL F1518 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N LEU F1579 " --> pdb=" O THR F1565 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE F1567 " --> pdb=" O LEU F1579 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1278 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: 2.03 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 2224 1.26 - 1.41: 2617 1.41 - 1.55: 6785 1.55 - 1.69: 2 1.69 - 1.83: 12 Bond restraints: 11640 Sorted by residual: bond pdb=" C THR A1428 " pdb=" O THR A1428 " ideal model delta sigma weight residual 1.237 1.134 0.102 1.19e-02 7.06e+03 7.38e+01 bond pdb=" C LEU E1397 " pdb=" O LEU E1397 " ideal model delta sigma weight residual 1.234 1.136 0.098 1.18e-02 7.18e+03 6.95e+01 bond pdb=" C LEU B1397 " pdb=" O LEU B1397 " ideal model delta sigma weight residual 1.234 1.138 0.097 1.18e-02 7.18e+03 6.70e+01 bond pdb=" C THR D1428 " pdb=" O THR D1428 " ideal model delta sigma weight residual 1.237 1.142 0.095 1.19e-02 7.06e+03 6.35e+01 bond pdb=" C LEU F1397 " pdb=" O LEU F1397 " ideal model delta sigma weight residual 1.234 1.143 0.092 1.18e-02 7.18e+03 6.02e+01 ... (remaining 11635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 14072 2.30 - 4.59: 1782 4.59 - 6.89: 89 6.89 - 9.19: 1 9.19 - 11.48: 4 Bond angle restraints: 15948 Sorted by residual: angle pdb=" CG ARG B1578 " pdb=" CD ARG B1578 " pdb=" NE ARG B1578 " ideal model delta sigma weight residual 112.00 100.52 11.48 2.20e+00 2.07e-01 2.72e+01 angle pdb=" CG ARG D1578 " pdb=" CD ARG D1578 " pdb=" NE ARG D1578 " ideal model delta sigma weight residual 112.00 100.85 11.15 2.20e+00 2.07e-01 2.57e+01 angle pdb=" CG ARG A1578 " pdb=" CD ARG A1578 " pdb=" NE ARG A1578 " ideal model delta sigma weight residual 112.00 100.89 11.11 2.20e+00 2.07e-01 2.55e+01 angle pdb=" CA GLY B1427 " pdb=" C GLY B1427 " pdb=" N THR B1428 " ideal model delta sigma weight residual 114.50 120.16 -5.66 1.19e+00 7.06e-01 2.26e+01 angle pdb=" CA GLY E1427 " pdb=" C GLY E1427 " pdb=" N THR E1428 " ideal model delta sigma weight residual 114.50 120.12 -5.62 1.19e+00 7.06e-01 2.23e+01 ... (remaining 15943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.05: 5772 13.05 - 26.09: 634 26.09 - 39.14: 240 39.14 - 52.18: 32 52.18 - 65.23: 24 Dihedral angle restraints: 6702 sinusoidal: 2430 harmonic: 4272 Sorted by residual: dihedral pdb=" CA PRO A1408 " pdb=" C PRO A1408 " pdb=" N ILE A1409 " pdb=" CA ILE A1409 " ideal model delta harmonic sigma weight residual 180.00 161.00 19.00 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA PRO E1408 " pdb=" C PRO E1408 " pdb=" N ILE E1409 " pdb=" CA ILE E1409 " ideal model delta harmonic sigma weight residual 180.00 161.18 18.82 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA PRO F1408 " pdb=" C PRO F1408 " pdb=" N ILE F1409 " pdb=" CA ILE F1409 " ideal model delta harmonic sigma weight residual 180.00 161.18 18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 6699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 820 0.051 - 0.101: 618 0.101 - 0.152: 353 0.152 - 0.202: 86 0.202 - 0.253: 7 Chirality restraints: 1884 Sorted by residual: chirality pdb=" CA PHE E1365 " pdb=" N PHE E1365 " pdb=" C PHE E1365 " pdb=" CB PHE E1365 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA PHE B1365 " pdb=" N PHE B1365 " pdb=" C PHE B1365 " pdb=" CB PHE B1365 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA PHE C1365 " pdb=" N PHE C1365 " pdb=" C PHE C1365 " pdb=" CB PHE C1365 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1881 not shown) Planarity restraints: 2130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D1393 " -0.013 2.00e-02 2.50e+03 3.99e-02 2.79e+01 pdb=" CG PHE D1393 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE D1393 " 0.074 2.00e-02 2.50e+03 pdb=" CD2 PHE D1393 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE D1393 " -0.033 2.00e-02 2.50e+03 pdb=" CE2 PHE D1393 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE D1393 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D1394 " 0.017 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" CG ASP D1394 " -0.063 2.00e-02 2.50e+03 pdb=" OD1 ASP D1394 " 0.023 2.00e-02 2.50e+03 pdb=" OD2 ASP D1394 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A1394 " -0.017 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" CG ASP A1394 " 0.061 2.00e-02 2.50e+03 pdb=" OD1 ASP A1394 " -0.022 2.00e-02 2.50e+03 pdb=" OD2 ASP A1394 " -0.022 2.00e-02 2.50e+03 ... (remaining 2127 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1962 2.79 - 3.32: 11332 3.32 - 3.84: 17802 3.84 - 4.37: 22906 4.37 - 4.90: 38132 Nonbonded interactions: 92134 Sorted by model distance: nonbonded pdb=" OG SER F1574 " pdb=" N ARG F1580 " model vdw 2.261 3.120 nonbonded pdb=" OG SER E1574 " pdb=" N ARG E1580 " model vdw 2.263 3.120 nonbonded pdb=" OG SER D1574 " pdb=" N ARG D1580 " model vdw 2.264 3.120 nonbonded pdb=" OG SER B1574 " pdb=" N ARG B1580 " model vdw 2.267 3.120 nonbonded pdb=" OG SER C1574 " pdb=" N ARG C1580 " model vdw 2.268 3.120 ... (remaining 92129 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.870 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 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 : 0.013 0.124 11640 Z= 0.969 Angle : 1.500 11.483 15948 Z= 1.048 Chirality : 0.081 0.253 1884 Planarity : 0.006 0.075 2130 Dihedral : 13.311 65.228 3978 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.63 % Allowed : 4.48 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.18), residues: 1506 helix: -3.34 (0.64), residues: 36 sheet: -0.33 (0.20), residues: 528 loop : -1.64 (0.17), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG D1578 TYR 0.036 0.005 TYR A1383 PHE 0.074 0.006 PHE D1393 TRP 0.028 0.006 TRP B1378 HIS 0.029 0.008 HIS B1577 Details of bonding type rmsd covalent geometry : bond 0.01311 (11640) covalent geometry : angle 1.49971 (15948) hydrogen bonds : bond 0.24019 ( 378) hydrogen bonds : angle 8.12836 ( 1278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 267 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1405 ASP cc_start: 0.7128 (m-30) cc_final: 0.6917 (m-30) REVERT: A 1590 GLU cc_start: 0.6782 (pt0) cc_final: 0.6543 (pp20) REVERT: A 1608 ILE cc_start: 0.6487 (mm) cc_final: 0.6251 (mt) REVERT: B 1407 ASP cc_start: 0.6723 (t70) cc_final: 0.6137 (p0) REVERT: B 1419 ASP cc_start: 0.7725 (p0) cc_final: 0.7374 (t0) REVERT: B 1497 ARG cc_start: 0.6845 (mtm110) cc_final: 0.6464 (ptp-170) REVERT: B 1596 LEU cc_start: 0.7154 (tp) cc_final: 0.6951 (mt) REVERT: C 1407 ASP cc_start: 0.6931 (t70) cc_final: 0.6499 (p0) REVERT: C 1476 ASP cc_start: 0.7408 (t0) cc_final: 0.6892 (t0) REVERT: C 1486 GLU cc_start: 0.6305 (tt0) cc_final: 0.6004 (pm20) REVERT: C 1497 ARG cc_start: 0.7210 (mtm110) cc_final: 0.6861 (ptp-170) REVERT: C 1504 GLN cc_start: 0.6664 (pt0) cc_final: 0.6296 (pt0) REVERT: D 1405 ASP cc_start: 0.7347 (m-30) cc_final: 0.7113 (m-30) REVERT: D 1452 ASN cc_start: 0.5764 (p0) cc_final: 0.5387 (p0) REVERT: D 1590 GLU cc_start: 0.6783 (pt0) cc_final: 0.6516 (pp20) REVERT: D 1608 ILE cc_start: 0.6406 (mm) cc_final: 0.6179 (mt) REVERT: E 1407 ASP cc_start: 0.6718 (t70) cc_final: 0.6134 (p0) REVERT: E 1419 ASP cc_start: 0.7725 (p0) cc_final: 0.7373 (t0) REVERT: E 1497 ARG cc_start: 0.6846 (mtm110) cc_final: 0.6462 (ptp-170) REVERT: E 1510 TYR cc_start: 0.6661 (m-80) cc_final: 0.5995 (m-80) REVERT: F 1407 ASP cc_start: 0.6942 (t70) cc_final: 0.6514 (p0) REVERT: F 1476 ASP cc_start: 0.7407 (t0) cc_final: 0.6865 (t0) REVERT: F 1486 GLU cc_start: 0.6331 (tt0) cc_final: 0.6011 (pm20) REVERT: F 1497 ARG cc_start: 0.7209 (mtm110) cc_final: 0.6861 (ptp-170) outliers start: 8 outliers final: 2 residues processed: 275 average time/residue: 0.6344 time to fit residues: 187.4850 Evaluate side-chains 155 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1575 SER Chi-restraints excluded: chain D residue 1575 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1391 HIS A1594 ASN B1373 GLN B1391 HIS B1452 ASN B1594 ASN C1373 GLN C1391 HIS C1577 HIS C1594 ASN D1391 HIS D1594 ASN E1373 GLN E1391 HIS E1577 HIS E1594 ASN F1373 GLN F1391 HIS F1594 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.142917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.129092 restraints weight = 18387.901| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.56 r_work: 0.3763 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11640 Z= 0.144 Angle : 0.614 5.583 15948 Z= 0.341 Chirality : 0.049 0.161 1884 Planarity : 0.004 0.047 2130 Dihedral : 5.148 16.414 1580 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.44 % Allowed : 11.01 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.19), residues: 1506 helix: -2.67 (0.37), residues: 72 sheet: 0.08 (0.20), residues: 522 loop : -1.54 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1580 TYR 0.012 0.002 TYR B1600 PHE 0.017 0.002 PHE E1442 TRP 0.007 0.001 TRP B1378 HIS 0.004 0.001 HIS B1391 Details of bonding type rmsd covalent geometry : bond 0.00320 (11640) covalent geometry : angle 0.61446 (15948) hydrogen bonds : bond 0.04242 ( 378) hydrogen bonds : angle 5.60313 ( 1278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.417 Fit side-chains REVERT: A 1410 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8290 (ttmt) REVERT: B 1410 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8056 (ttmt) REVERT: C 1577 HIS cc_start: 0.7866 (m90) cc_final: 0.7522 (m-70) REVERT: D 1405 ASP cc_start: 0.7326 (m-30) cc_final: 0.7092 (m-30) REVERT: D 1410 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8306 (ttmt) REVERT: E 1410 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8055 (ttmt) REVERT: E 1596 LEU cc_start: 0.7910 (mt) cc_final: 0.7642 (mt) outliers start: 31 outliers final: 12 residues processed: 174 average time/residue: 0.4709 time to fit residues: 90.1160 Evaluate side-chains 133 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1410 LYS Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1601 THR Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1410 LYS Chi-restraints excluded: chain C residue 1372 ASP Chi-restraints excluded: chain C residue 1601 THR Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1410 LYS Chi-restraints excluded: chain D residue 1518 VAL Chi-restraints excluded: chain D residue 1601 THR Chi-restraints excluded: chain E residue 1372 ASP Chi-restraints excluded: chain E residue 1410 LYS Chi-restraints excluded: chain F residue 1372 ASP Chi-restraints excluded: chain F residue 1601 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 71 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 110 optimal weight: 0.0170 chunk 142 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1452 ASN A1594 ASN B1452 ASN B1594 ASN C1452 ASN D1594 ASN E1452 ASN E1594 ASN F1452 ASN F1577 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.140414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.126496 restraints weight = 18754.283| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 1.57 r_work: 0.3720 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11640 Z= 0.169 Angle : 0.646 5.894 15948 Z= 0.355 Chirality : 0.051 0.177 1884 Planarity : 0.004 0.039 2130 Dihedral : 5.201 17.079 1578 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 4.01 % Allowed : 13.44 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.19), residues: 1506 helix: -2.71 (0.37), residues: 72 sheet: 0.29 (0.19), residues: 546 loop : -1.57 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F1580 TYR 0.013 0.002 TYR D1383 PHE 0.017 0.002 PHE D1442 TRP 0.009 0.002 TRP B1378 HIS 0.003 0.001 HIS C1391 Details of bonding type rmsd covalent geometry : bond 0.00393 (11640) covalent geometry : angle 0.64605 (15948) hydrogen bonds : bond 0.04223 ( 378) hydrogen bonds : angle 5.61337 ( 1278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 122 time to evaluate : 0.459 Fit side-chains REVERT: A 1410 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8416 (ttmt) REVERT: A 1476 ASP cc_start: 0.8048 (t0) cc_final: 0.7803 (t0) REVERT: A 1613 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7025 (pp) REVERT: B 1410 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8086 (ttmt) REVERT: B 1419 ASP cc_start: 0.7430 (p0) cc_final: 0.7201 (p0) REVERT: B 1573 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7141 (pt0) REVERT: B 1596 LEU cc_start: 0.7824 (mt) cc_final: 0.7504 (mt) REVERT: C 1613 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6886 (pp) REVERT: D 1405 ASP cc_start: 0.7223 (m-30) cc_final: 0.6974 (m-30) REVERT: D 1410 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8320 (ttmt) REVERT: D 1476 ASP cc_start: 0.8036 (t0) cc_final: 0.7794 (t0) REVERT: D 1613 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7030 (pp) REVERT: E 1410 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8094 (ttmt) REVERT: E 1419 ASP cc_start: 0.7431 (p0) cc_final: 0.7206 (p0) REVERT: E 1573 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7205 (pt0) REVERT: E 1596 LEU cc_start: 0.7714 (mt) cc_final: 0.7429 (mt) REVERT: E 1613 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6877 (pp) REVERT: F 1577 HIS cc_start: 0.7792 (m90) cc_final: 0.7576 (m170) REVERT: F 1613 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6897 (pp) outliers start: 51 outliers final: 23 residues processed: 157 average time/residue: 0.4004 time to fit residues: 70.1155 Evaluate side-chains 144 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1410 LYS Chi-restraints excluded: chain A residue 1452 ASN Chi-restraints excluded: chain A residue 1613 LEU Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1410 LYS Chi-restraints excluded: chain B residue 1452 ASN Chi-restraints excluded: chain B residue 1536 GLU Chi-restraints excluded: chain B residue 1573 GLU Chi-restraints excluded: chain B residue 1601 THR Chi-restraints excluded: chain C residue 1372 ASP Chi-restraints excluded: chain C residue 1397 LEU Chi-restraints excluded: chain C residue 1452 ASN Chi-restraints excluded: chain C residue 1518 VAL Chi-restraints excluded: chain C residue 1520 VAL Chi-restraints excluded: chain C residue 1601 THR Chi-restraints excluded: chain C residue 1613 LEU Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1410 LYS Chi-restraints excluded: chain D residue 1613 LEU Chi-restraints excluded: chain E residue 1372 ASP Chi-restraints excluded: chain E residue 1410 LYS Chi-restraints excluded: chain E residue 1452 ASN Chi-restraints excluded: chain E residue 1536 GLU Chi-restraints excluded: chain E residue 1573 GLU Chi-restraints excluded: chain E residue 1601 THR Chi-restraints excluded: chain E residue 1613 LEU Chi-restraints excluded: chain F residue 1372 ASP Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain F residue 1452 ASN Chi-restraints excluded: chain F residue 1518 VAL Chi-restraints excluded: chain F residue 1520 VAL Chi-restraints excluded: chain F residue 1601 THR Chi-restraints excluded: chain F residue 1613 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 3 optimal weight: 9.9990 chunk 23 optimal weight: 0.1980 chunk 35 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1452 ASN A1594 ASN B1452 ASN B1577 HIS B1594 ASN C1452 ASN C1577 HIS C1594 ASN D1594 ASN E1594 ASN F1452 ASN F1594 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.140271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.126234 restraints weight = 18722.665| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 1.58 r_work: 0.3720 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 11640 Z= 0.170 Angle : 0.639 6.180 15948 Z= 0.350 Chirality : 0.051 0.176 1884 Planarity : 0.003 0.034 2130 Dihedral : 5.199 17.055 1578 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.25 % Allowed : 16.27 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.18), residues: 1506 helix: -2.88 (0.37), residues: 72 sheet: 0.25 (0.19), residues: 546 loop : -1.60 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E1580 TYR 0.014 0.002 TYR A1383 PHE 0.016 0.002 PHE A1442 TRP 0.007 0.001 TRP A1378 HIS 0.003 0.001 HIS C1391 Details of bonding type rmsd covalent geometry : bond 0.00398 (11640) covalent geometry : angle 0.63881 (15948) hydrogen bonds : bond 0.04032 ( 378) hydrogen bonds : angle 5.58525 ( 1278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 118 time to evaluate : 0.454 Fit side-chains REVERT: A 1410 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8373 (ttmt) REVERT: A 1455 ASP cc_start: 0.6311 (m-30) cc_final: 0.5819 (m-30) REVERT: A 1476 ASP cc_start: 0.8054 (t0) cc_final: 0.7831 (t0) REVERT: A 1567 PHE cc_start: 0.4895 (OUTLIER) cc_final: 0.4437 (m-80) REVERT: A 1613 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7087 (pp) REVERT: B 1410 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8165 (ttmt) REVERT: B 1573 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7139 (pt0) REVERT: B 1596 LEU cc_start: 0.7847 (mt) cc_final: 0.7547 (mt) REVERT: C 1486 GLU cc_start: 0.6106 (pm20) cc_final: 0.5501 (pt0) REVERT: C 1580 ARG cc_start: 0.7595 (ttt-90) cc_final: 0.7277 (ttt-90) REVERT: C 1613 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6905 (pp) REVERT: D 1410 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8408 (ttmt) REVERT: D 1476 ASP cc_start: 0.8025 (t0) cc_final: 0.7810 (t0) REVERT: D 1567 PHE cc_start: 0.4935 (OUTLIER) cc_final: 0.4529 (m-80) REVERT: D 1613 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7091 (pp) REVERT: E 1410 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8161 (ttmt) REVERT: E 1573 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7254 (pt0) REVERT: E 1596 LEU cc_start: 0.7902 (mt) cc_final: 0.7636 (mt) REVERT: E 1613 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7073 (pp) REVERT: F 1486 GLU cc_start: 0.6097 (pm20) cc_final: 0.5483 (pt0) REVERT: F 1577 HIS cc_start: 0.7816 (m90) cc_final: 0.7603 (m-70) REVERT: F 1580 ARG cc_start: 0.7523 (ttt-90) cc_final: 0.7229 (ttt-90) REVERT: F 1613 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6909 (pp) outliers start: 54 outliers final: 35 residues processed: 148 average time/residue: 0.3674 time to fit residues: 61.2872 Evaluate side-chains 154 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 106 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1410 LYS Chi-restraints excluded: chain A residue 1452 ASN Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain A residue 1567 PHE Chi-restraints excluded: chain A residue 1613 LEU Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1404 THR Chi-restraints excluded: chain B residue 1410 LYS Chi-restraints excluded: chain B residue 1452 ASN Chi-restraints excluded: chain B residue 1520 VAL Chi-restraints excluded: chain B residue 1557 GLU Chi-restraints excluded: chain B residue 1573 GLU Chi-restraints excluded: chain B residue 1601 THR Chi-restraints excluded: chain C residue 1372 ASP Chi-restraints excluded: chain C residue 1378 TRP Chi-restraints excluded: chain C residue 1380 ASP Chi-restraints excluded: chain C residue 1404 THR Chi-restraints excluded: chain C residue 1452 ASN Chi-restraints excluded: chain C residue 1518 VAL Chi-restraints excluded: chain C residue 1601 THR Chi-restraints excluded: chain C residue 1613 LEU Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1404 THR Chi-restraints excluded: chain D residue 1410 LYS Chi-restraints excluded: chain D residue 1518 VAL Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain D residue 1557 GLU Chi-restraints excluded: chain D residue 1567 PHE Chi-restraints excluded: chain D residue 1613 LEU Chi-restraints excluded: chain E residue 1372 ASP Chi-restraints excluded: chain E residue 1404 THR Chi-restraints excluded: chain E residue 1410 LYS Chi-restraints excluded: chain E residue 1520 VAL Chi-restraints excluded: chain E residue 1573 GLU Chi-restraints excluded: chain E residue 1601 THR Chi-restraints excluded: chain E residue 1613 LEU Chi-restraints excluded: chain F residue 1372 ASP Chi-restraints excluded: chain F residue 1378 TRP Chi-restraints excluded: chain F residue 1380 ASP Chi-restraints excluded: chain F residue 1404 THR Chi-restraints excluded: chain F residue 1452 ASN Chi-restraints excluded: chain F residue 1518 VAL Chi-restraints excluded: chain F residue 1601 THR Chi-restraints excluded: chain F residue 1613 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 30 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 148 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 147 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1452 ASN A1594 ASN B1452 ASN B1594 ASN C1452 ASN C1577 HIS C1594 ASN D1594 ASN E1452 ASN E1594 ASN F1452 ASN F1594 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.138889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.124447 restraints weight = 18686.057| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.65 r_work: 0.3690 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 11640 Z= 0.194 Angle : 0.665 6.582 15948 Z= 0.364 Chirality : 0.052 0.177 1884 Planarity : 0.004 0.033 2130 Dihedral : 5.339 17.333 1578 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.95 % Allowed : 18.08 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.18), residues: 1506 helix: -2.97 (0.37), residues: 72 sheet: 0.24 (0.20), residues: 546 loop : -1.67 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E1580 TYR 0.015 0.002 TYR A1383 PHE 0.018 0.003 PHE A1442 TRP 0.008 0.002 TRP E1378 HIS 0.003 0.001 HIS F1391 Details of bonding type rmsd covalent geometry : bond 0.00460 (11640) covalent geometry : angle 0.66500 (15948) hydrogen bonds : bond 0.04197 ( 378) hydrogen bonds : angle 5.65976 ( 1278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 111 time to evaluate : 0.403 Fit side-chains REVERT: A 1410 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8412 (ttmt) REVERT: A 1455 ASP cc_start: 0.6375 (m-30) cc_final: 0.5895 (m-30) REVERT: A 1567 PHE cc_start: 0.4937 (OUTLIER) cc_final: 0.4483 (m-80) REVERT: A 1613 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7096 (pp) REVERT: B 1413 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8027 (p) REVERT: B 1573 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7358 (pt0) REVERT: B 1596 LEU cc_start: 0.7824 (mt) cc_final: 0.7547 (mt) REVERT: C 1580 ARG cc_start: 0.7638 (ttt-90) cc_final: 0.7409 (ttt-90) REVERT: C 1613 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6923 (pp) REVERT: D 1410 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8428 (ttmt) REVERT: D 1446 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7485 (t70) REVERT: D 1476 ASP cc_start: 0.8062 (t0) cc_final: 0.7852 (t0) REVERT: D 1567 PHE cc_start: 0.4984 (OUTLIER) cc_final: 0.4525 (m-80) REVERT: D 1613 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7144 (pp) REVERT: E 1413 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.8025 (p) REVERT: E 1573 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7180 (pt0) REVERT: E 1596 LEU cc_start: 0.7868 (mt) cc_final: 0.7645 (mt) REVERT: E 1613 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7065 (pp) REVERT: F 1580 ARG cc_start: 0.7571 (ttt-90) cc_final: 0.7348 (ttt-90) REVERT: F 1613 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6925 (pp) outliers start: 63 outliers final: 44 residues processed: 150 average time/residue: 0.3692 time to fit residues: 62.2238 Evaluate side-chains 162 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 104 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1378 TRP Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1410 LYS Chi-restraints excluded: chain A residue 1452 ASN Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain A residue 1567 PHE Chi-restraints excluded: chain A residue 1613 LEU Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1405 ASP Chi-restraints excluded: chain B residue 1413 THR Chi-restraints excluded: chain B residue 1452 ASN Chi-restraints excluded: chain B residue 1520 VAL Chi-restraints excluded: chain B residue 1557 GLU Chi-restraints excluded: chain B residue 1573 GLU Chi-restraints excluded: chain B residue 1601 THR Chi-restraints excluded: chain C residue 1372 ASP Chi-restraints excluded: chain C residue 1380 ASP Chi-restraints excluded: chain C residue 1397 LEU Chi-restraints excluded: chain C residue 1404 THR Chi-restraints excluded: chain C residue 1452 ASN Chi-restraints excluded: chain C residue 1518 VAL Chi-restraints excluded: chain C residue 1520 VAL Chi-restraints excluded: chain C residue 1557 GLU Chi-restraints excluded: chain C residue 1565 THR Chi-restraints excluded: chain C residue 1601 THR Chi-restraints excluded: chain C residue 1613 LEU Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1378 TRP Chi-restraints excluded: chain D residue 1404 THR Chi-restraints excluded: chain D residue 1410 LYS Chi-restraints excluded: chain D residue 1446 ASP Chi-restraints excluded: chain D residue 1518 VAL Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain D residue 1557 GLU Chi-restraints excluded: chain D residue 1567 PHE Chi-restraints excluded: chain D residue 1613 LEU Chi-restraints excluded: chain E residue 1372 ASP Chi-restraints excluded: chain E residue 1405 ASP Chi-restraints excluded: chain E residue 1413 THR Chi-restraints excluded: chain E residue 1452 ASN Chi-restraints excluded: chain E residue 1520 VAL Chi-restraints excluded: chain E residue 1557 GLU Chi-restraints excluded: chain E residue 1573 GLU Chi-restraints excluded: chain E residue 1601 THR Chi-restraints excluded: chain E residue 1613 LEU Chi-restraints excluded: chain F residue 1372 ASP Chi-restraints excluded: chain F residue 1380 ASP Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain F residue 1404 THR Chi-restraints excluded: chain F residue 1452 ASN Chi-restraints excluded: chain F residue 1518 VAL Chi-restraints excluded: chain F residue 1520 VAL Chi-restraints excluded: chain F residue 1557 GLU Chi-restraints excluded: chain F residue 1601 THR Chi-restraints excluded: chain F residue 1613 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 45 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1452 ASN A1594 ASN B1452 ASN B1594 ASN C1452 ASN C1577 HIS C1594 ASN D1594 ASN E1452 ASN E1594 ASN F1452 ASN F1594 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.139631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.125350 restraints weight = 18754.194| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.65 r_work: 0.3706 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 11640 Z= 0.183 Angle : 0.653 6.686 15948 Z= 0.357 Chirality : 0.051 0.177 1884 Planarity : 0.003 0.032 2130 Dihedral : 5.314 17.179 1578 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 5.58 % Allowed : 18.16 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.19), residues: 1506 helix: -2.96 (0.38), residues: 72 sheet: 0.26 (0.20), residues: 546 loop : -1.72 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E1580 TYR 0.015 0.002 TYR A1383 PHE 0.016 0.003 PHE A1442 TRP 0.007 0.001 TRP D1378 HIS 0.003 0.001 HIS F1391 Details of bonding type rmsd covalent geometry : bond 0.00430 (11640) covalent geometry : angle 0.65293 (15948) hydrogen bonds : bond 0.04086 ( 378) hydrogen bonds : angle 5.64674 ( 1278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 111 time to evaluate : 0.438 Fit side-chains REVERT: A 1410 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8385 (ttmt) REVERT: A 1455 ASP cc_start: 0.6516 (m-30) cc_final: 0.6075 (m-30) REVERT: A 1567 PHE cc_start: 0.4944 (OUTLIER) cc_final: 0.4495 (m-80) REVERT: A 1613 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7080 (pp) REVERT: B 1413 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.8004 (p) REVERT: B 1573 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7280 (pt0) REVERT: B 1613 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.6819 (pp) REVERT: C 1405 ASP cc_start: 0.6884 (OUTLIER) cc_final: 0.6662 (m-30) REVERT: C 1580 ARG cc_start: 0.7621 (ttt-90) cc_final: 0.7400 (ttt-90) REVERT: C 1613 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6901 (pp) REVERT: D 1410 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8411 (ttmt) REVERT: D 1446 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7429 (t70) REVERT: D 1476 ASP cc_start: 0.8050 (t0) cc_final: 0.7849 (t0) REVERT: D 1567 PHE cc_start: 0.4972 (OUTLIER) cc_final: 0.4527 (m-80) REVERT: D 1613 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7099 (pp) REVERT: E 1413 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8017 (p) REVERT: E 1573 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7176 (pt0) REVERT: E 1613 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.6789 (pp) REVERT: F 1405 ASP cc_start: 0.6906 (OUTLIER) cc_final: 0.6688 (m-30) REVERT: F 1476 ASP cc_start: 0.8037 (t0) cc_final: 0.7524 (t0) REVERT: F 1580 ARG cc_start: 0.7552 (ttt-90) cc_final: 0.7340 (ttt-90) REVERT: F 1613 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6965 (pp) outliers start: 71 outliers final: 45 residues processed: 147 average time/residue: 0.3777 time to fit residues: 62.7003 Evaluate side-chains 165 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 103 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1410 LYS Chi-restraints excluded: chain A residue 1452 ASN Chi-restraints excluded: chain A residue 1476 ASP Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain A residue 1567 PHE Chi-restraints excluded: chain A residue 1613 LEU Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1405 ASP Chi-restraints excluded: chain B residue 1413 THR Chi-restraints excluded: chain B residue 1452 ASN Chi-restraints excluded: chain B residue 1520 VAL Chi-restraints excluded: chain B residue 1524 ASP Chi-restraints excluded: chain B residue 1557 GLU Chi-restraints excluded: chain B residue 1573 GLU Chi-restraints excluded: chain B residue 1601 THR Chi-restraints excluded: chain B residue 1613 LEU Chi-restraints excluded: chain C residue 1372 ASP Chi-restraints excluded: chain C residue 1380 ASP Chi-restraints excluded: chain C residue 1397 LEU Chi-restraints excluded: chain C residue 1404 THR Chi-restraints excluded: chain C residue 1405 ASP Chi-restraints excluded: chain C residue 1452 ASN Chi-restraints excluded: chain C residue 1518 VAL Chi-restraints excluded: chain C residue 1520 VAL Chi-restraints excluded: chain C residue 1557 GLU Chi-restraints excluded: chain C residue 1565 THR Chi-restraints excluded: chain C residue 1601 THR Chi-restraints excluded: chain C residue 1613 LEU Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1404 THR Chi-restraints excluded: chain D residue 1410 LYS Chi-restraints excluded: chain D residue 1446 ASP Chi-restraints excluded: chain D residue 1518 VAL Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain D residue 1557 GLU Chi-restraints excluded: chain D residue 1567 PHE Chi-restraints excluded: chain D residue 1613 LEU Chi-restraints excluded: chain E residue 1372 ASP Chi-restraints excluded: chain E residue 1405 ASP Chi-restraints excluded: chain E residue 1413 THR Chi-restraints excluded: chain E residue 1452 ASN Chi-restraints excluded: chain E residue 1520 VAL Chi-restraints excluded: chain E residue 1524 ASP Chi-restraints excluded: chain E residue 1557 GLU Chi-restraints excluded: chain E residue 1573 GLU Chi-restraints excluded: chain E residue 1601 THR Chi-restraints excluded: chain E residue 1613 LEU Chi-restraints excluded: chain F residue 1372 ASP Chi-restraints excluded: chain F residue 1380 ASP Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain F residue 1404 THR Chi-restraints excluded: chain F residue 1405 ASP Chi-restraints excluded: chain F residue 1452 ASN Chi-restraints excluded: chain F residue 1518 VAL Chi-restraints excluded: chain F residue 1520 VAL Chi-restraints excluded: chain F residue 1557 GLU Chi-restraints excluded: chain F residue 1601 THR Chi-restraints excluded: chain F residue 1613 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 83 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 147 optimal weight: 4.9990 chunk 21 optimal weight: 0.0980 chunk 61 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 34 optimal weight: 0.0770 overall best weight: 4.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1452 ASN B1452 ASN B1594 ASN C1452 ASN C1577 HIS C1594 ASN E1452 ASN E1594 ASN F1452 ASN F1594 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.140539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.126330 restraints weight = 18723.329| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.65 r_work: 0.3716 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 11640 Z= 0.150 Angle : 0.614 6.330 15948 Z= 0.335 Chirality : 0.050 0.174 1884 Planarity : 0.003 0.032 2130 Dihedral : 5.149 16.924 1578 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 5.11 % Allowed : 19.03 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.19), residues: 1506 helix: -2.89 (0.39), residues: 72 sheet: 0.29 (0.20), residues: 546 loop : -1.71 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E1580 TYR 0.014 0.002 TYR D1383 PHE 0.014 0.002 PHE E1442 TRP 0.007 0.001 TRP A1378 HIS 0.003 0.001 HIS F1391 Details of bonding type rmsd covalent geometry : bond 0.00347 (11640) covalent geometry : angle 0.61404 (15948) hydrogen bonds : bond 0.03889 ( 378) hydrogen bonds : angle 5.51353 ( 1278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 112 time to evaluate : 0.503 Fit side-chains REVERT: A 1446 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7379 (t70) REVERT: A 1455 ASP cc_start: 0.6391 (m-30) cc_final: 0.6053 (m-30) REVERT: A 1567 PHE cc_start: 0.4882 (OUTLIER) cc_final: 0.4482 (m-80) REVERT: A 1613 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6918 (pp) REVERT: B 1413 THR cc_start: 0.8350 (OUTLIER) cc_final: 0.7994 (p) REVERT: B 1573 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7146 (pt0) REVERT: B 1613 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6714 (pp) REVERT: C 1580 ARG cc_start: 0.7581 (ttt-90) cc_final: 0.7364 (ttt-90) REVERT: C 1613 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6761 (pp) REVERT: D 1446 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7484 (t70) REVERT: D 1486 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6848 (pm20) REVERT: D 1567 PHE cc_start: 0.4925 (OUTLIER) cc_final: 0.4526 (m-80) REVERT: D 1613 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6944 (pp) REVERT: E 1413 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.7926 (p) REVERT: E 1573 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7105 (pt0) REVERT: E 1613 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6667 (pp) REVERT: F 1580 ARG cc_start: 0.7563 (ttt-90) cc_final: 0.7359 (ttt-90) REVERT: F 1613 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6758 (pp) outliers start: 65 outliers final: 31 residues processed: 145 average time/residue: 0.4004 time to fit residues: 65.2054 Evaluate side-chains 151 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 105 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1446 ASP Chi-restraints excluded: chain A residue 1452 ASN Chi-restraints excluded: chain A residue 1476 ASP Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain A residue 1567 PHE Chi-restraints excluded: chain A residue 1613 LEU Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1413 THR Chi-restraints excluded: chain B residue 1452 ASN Chi-restraints excluded: chain B residue 1520 VAL Chi-restraints excluded: chain B residue 1524 ASP Chi-restraints excluded: chain B residue 1557 GLU Chi-restraints excluded: chain B residue 1573 GLU Chi-restraints excluded: chain B residue 1613 LEU Chi-restraints excluded: chain C residue 1372 ASP Chi-restraints excluded: chain C residue 1397 LEU Chi-restraints excluded: chain C residue 1404 THR Chi-restraints excluded: chain C residue 1452 ASN Chi-restraints excluded: chain C residue 1520 VAL Chi-restraints excluded: chain C residue 1557 GLU Chi-restraints excluded: chain C residue 1613 LEU Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1404 THR Chi-restraints excluded: chain D residue 1446 ASP Chi-restraints excluded: chain D residue 1486 GLU Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain D residue 1557 GLU Chi-restraints excluded: chain D residue 1567 PHE Chi-restraints excluded: chain D residue 1613 LEU Chi-restraints excluded: chain E residue 1372 ASP Chi-restraints excluded: chain E residue 1413 THR Chi-restraints excluded: chain E residue 1452 ASN Chi-restraints excluded: chain E residue 1520 VAL Chi-restraints excluded: chain E residue 1524 ASP Chi-restraints excluded: chain E residue 1573 GLU Chi-restraints excluded: chain E residue 1613 LEU Chi-restraints excluded: chain F residue 1372 ASP Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain F residue 1404 THR Chi-restraints excluded: chain F residue 1452 ASN Chi-restraints excluded: chain F residue 1520 VAL Chi-restraints excluded: chain F residue 1557 GLU Chi-restraints excluded: chain F residue 1613 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 17 optimal weight: 8.9990 chunk 121 optimal weight: 30.0000 chunk 58 optimal weight: 20.0000 chunk 137 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 136 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1452 ASN A1594 ASN B1452 ASN C1452 ASN C1594 ASN D1594 ASN E1452 ASN F1452 ASN F1594 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.138226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.123996 restraints weight = 18927.421| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.65 r_work: 0.3682 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 11640 Z= 0.239 Angle : 0.718 7.243 15948 Z= 0.393 Chirality : 0.054 0.179 1884 Planarity : 0.004 0.034 2130 Dihedral : 5.548 16.170 1578 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 5.74 % Allowed : 19.18 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.18), residues: 1506 helix: -3.02 (0.39), residues: 72 sheet: 0.14 (0.20), residues: 546 loop : -1.85 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E1580 TYR 0.016 0.002 TYR A1383 PHE 0.021 0.003 PHE A1442 TRP 0.010 0.002 TRP E1378 HIS 0.003 0.001 HIS A1577 Details of bonding type rmsd covalent geometry : bond 0.00572 (11640) covalent geometry : angle 0.71797 (15948) hydrogen bonds : bond 0.04357 ( 378) hydrogen bonds : angle 5.84494 ( 1278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 104 time to evaluate : 0.491 Fit side-chains REVERT: A 1446 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7380 (t70) REVERT: A 1455 ASP cc_start: 0.6469 (m-30) cc_final: 0.6047 (m-30) REVERT: A 1613 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7048 (pp) REVERT: B 1410 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8185 (ttmt) REVERT: B 1413 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.8053 (p) REVERT: B 1613 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6710 (pp) REVERT: C 1605 GLU cc_start: 0.6431 (mm-30) cc_final: 0.6192 (mm-30) REVERT: D 1446 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7543 (t70) REVERT: D 1486 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.6852 (pm20) REVERT: D 1613 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7053 (pp) REVERT: E 1410 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8188 (ttmt) REVERT: E 1413 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.8048 (p) REVERT: E 1573 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7123 (pt0) REVERT: E 1613 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6729 (pp) REVERT: F 1476 ASP cc_start: 0.8040 (t0) cc_final: 0.7520 (t0) REVERT: F 1605 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.4834 (mm-30) outliers start: 73 outliers final: 42 residues processed: 146 average time/residue: 0.4006 time to fit residues: 65.6457 Evaluate side-chains 157 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 102 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1446 ASP Chi-restraints excluded: chain A residue 1452 ASN Chi-restraints excluded: chain A residue 1476 ASP Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain A residue 1613 LEU Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1410 LYS Chi-restraints excluded: chain B residue 1413 THR Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1452 ASN Chi-restraints excluded: chain B residue 1520 VAL Chi-restraints excluded: chain B residue 1524 ASP Chi-restraints excluded: chain B residue 1557 GLU Chi-restraints excluded: chain B residue 1613 LEU Chi-restraints excluded: chain C residue 1372 ASP Chi-restraints excluded: chain C residue 1380 ASP Chi-restraints excluded: chain C residue 1397 LEU Chi-restraints excluded: chain C residue 1404 THR Chi-restraints excluded: chain C residue 1452 ASN Chi-restraints excluded: chain C residue 1518 VAL Chi-restraints excluded: chain C residue 1520 VAL Chi-restraints excluded: chain C residue 1557 GLU Chi-restraints excluded: chain C residue 1601 THR Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1398 VAL Chi-restraints excluded: chain D residue 1404 THR Chi-restraints excluded: chain D residue 1446 ASP Chi-restraints excluded: chain D residue 1486 GLU Chi-restraints excluded: chain D residue 1518 VAL Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain D residue 1557 GLU Chi-restraints excluded: chain D residue 1613 LEU Chi-restraints excluded: chain E residue 1372 ASP Chi-restraints excluded: chain E residue 1410 LYS Chi-restraints excluded: chain E residue 1413 THR Chi-restraints excluded: chain E residue 1419 ASP Chi-restraints excluded: chain E residue 1452 ASN Chi-restraints excluded: chain E residue 1520 VAL Chi-restraints excluded: chain E residue 1524 ASP Chi-restraints excluded: chain E residue 1573 GLU Chi-restraints excluded: chain E residue 1613 LEU Chi-restraints excluded: chain F residue 1372 ASP Chi-restraints excluded: chain F residue 1380 ASP Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain F residue 1404 THR Chi-restraints excluded: chain F residue 1452 ASN Chi-restraints excluded: chain F residue 1518 VAL Chi-restraints excluded: chain F residue 1520 VAL Chi-restraints excluded: chain F residue 1557 GLU Chi-restraints excluded: chain F residue 1601 THR Chi-restraints excluded: chain F residue 1605 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1452 ASN A1594 ASN B1452 ASN B1594 ASN C1452 ASN D1594 ASN E1452 ASN E1594 ASN F1452 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.140579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.126455 restraints weight = 18577.628| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.64 r_work: 0.3718 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 11640 Z= 0.143 Angle : 0.613 6.337 15948 Z= 0.335 Chirality : 0.049 0.173 1884 Planarity : 0.003 0.033 2130 Dihedral : 5.176 15.922 1578 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.32 % Allowed : 20.52 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.19), residues: 1506 helix: -2.90 (0.41), residues: 72 sheet: 0.23 (0.20), residues: 546 loop : -1.76 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E1580 TYR 0.013 0.002 TYR A1383 PHE 0.015 0.002 PHE A1567 TRP 0.006 0.001 TRP D1378 HIS 0.002 0.001 HIS F1391 Details of bonding type rmsd covalent geometry : bond 0.00329 (11640) covalent geometry : angle 0.61254 (15948) hydrogen bonds : bond 0.03836 ( 378) hydrogen bonds : angle 5.51154 ( 1278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 115 time to evaluate : 0.443 Fit side-chains REVERT: A 1446 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7379 (t70) REVERT: A 1455 ASP cc_start: 0.6322 (m-30) cc_final: 0.5989 (m-30) REVERT: A 1473 ASP cc_start: 0.7268 (t0) cc_final: 0.7025 (t0) REVERT: A 1613 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6929 (pp) REVERT: B 1410 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8196 (ttmt) REVERT: B 1413 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.7880 (p) REVERT: B 1613 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6602 (pp) REVERT: C 1476 ASP cc_start: 0.7938 (t0) cc_final: 0.7432 (t0) REVERT: D 1446 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7482 (t70) REVERT: D 1486 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6872 (pm20) REVERT: D 1567 PHE cc_start: 0.4912 (OUTLIER) cc_final: 0.4465 (m-80) REVERT: D 1613 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6943 (pp) REVERT: E 1410 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8259 (ttmt) REVERT: E 1413 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.7878 (p) REVERT: E 1573 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7203 (pt0) REVERT: E 1613 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6599 (pp) REVERT: F 1476 ASP cc_start: 0.7909 (t0) cc_final: 0.7473 (t0) outliers start: 55 outliers final: 34 residues processed: 145 average time/residue: 0.3301 time to fit residues: 54.0895 Evaluate side-chains 152 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 105 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1446 ASP Chi-restraints excluded: chain A residue 1452 ASN Chi-restraints excluded: chain A residue 1476 ASP Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain A residue 1613 LEU Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1410 LYS Chi-restraints excluded: chain B residue 1413 THR Chi-restraints excluded: chain B residue 1452 ASN Chi-restraints excluded: chain B residue 1520 VAL Chi-restraints excluded: chain B residue 1557 GLU Chi-restraints excluded: chain B residue 1613 LEU Chi-restraints excluded: chain C residue 1372 ASP Chi-restraints excluded: chain C residue 1380 ASP Chi-restraints excluded: chain C residue 1397 LEU Chi-restraints excluded: chain C residue 1404 THR Chi-restraints excluded: chain C residue 1452 ASN Chi-restraints excluded: chain C residue 1520 VAL Chi-restraints excluded: chain C residue 1557 GLU Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1398 VAL Chi-restraints excluded: chain D residue 1404 THR Chi-restraints excluded: chain D residue 1446 ASP Chi-restraints excluded: chain D residue 1476 ASP Chi-restraints excluded: chain D residue 1486 GLU Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain D residue 1557 GLU Chi-restraints excluded: chain D residue 1567 PHE Chi-restraints excluded: chain D residue 1613 LEU Chi-restraints excluded: chain E residue 1372 ASP Chi-restraints excluded: chain E residue 1410 LYS Chi-restraints excluded: chain E residue 1413 THR Chi-restraints excluded: chain E residue 1452 ASN Chi-restraints excluded: chain E residue 1520 VAL Chi-restraints excluded: chain E residue 1573 GLU Chi-restraints excluded: chain E residue 1613 LEU Chi-restraints excluded: chain F residue 1372 ASP Chi-restraints excluded: chain F residue 1380 ASP Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain F residue 1404 THR Chi-restraints excluded: chain F residue 1452 ASN Chi-restraints excluded: chain F residue 1518 VAL Chi-restraints excluded: chain F residue 1520 VAL Chi-restraints excluded: chain F residue 1557 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 10 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 136 optimal weight: 9.9990 overall best weight: 4.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1452 ASN B1452 ASN C1452 ASN D1594 ASN E1452 ASN F1452 ASN F1594 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.140434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.126376 restraints weight = 18627.089| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.63 r_work: 0.3716 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 11640 Z= 0.152 Angle : 0.621 6.291 15948 Z= 0.340 Chirality : 0.049 0.173 1884 Planarity : 0.003 0.034 2130 Dihedral : 5.121 15.764 1578 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.32 % Allowed : 21.23 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.19), residues: 1506 helix: -2.91 (0.41), residues: 72 sheet: 0.24 (0.20), residues: 546 loop : -1.75 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E1580 TYR 0.013 0.002 TYR D1383 PHE 0.014 0.002 PHE B1442 TRP 0.006 0.001 TRP D1378 HIS 0.003 0.001 HIS A1391 Details of bonding type rmsd covalent geometry : bond 0.00354 (11640) covalent geometry : angle 0.62070 (15948) hydrogen bonds : bond 0.03884 ( 378) hydrogen bonds : angle 5.50176 ( 1278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 104 time to evaluate : 0.410 Fit side-chains REVERT: A 1455 ASP cc_start: 0.6293 (m-30) cc_final: 0.5953 (m-30) REVERT: A 1476 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7782 (m-30) REVERT: A 1613 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6921 (pp) REVERT: B 1410 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8253 (ttmt) REVERT: B 1413 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.7776 (p) REVERT: B 1613 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6592 (pp) REVERT: C 1476 ASP cc_start: 0.7890 (t0) cc_final: 0.7427 (t0) REVERT: D 1446 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7489 (t70) REVERT: D 1486 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6866 (pm20) REVERT: D 1567 PHE cc_start: 0.4877 (OUTLIER) cc_final: 0.4464 (m-80) REVERT: D 1613 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6955 (pp) REVERT: E 1410 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8249 (ttmt) REVERT: E 1413 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.7790 (p) REVERT: E 1573 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7205 (pt0) REVERT: E 1613 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6533 (pp) REVERT: F 1476 ASP cc_start: 0.7893 (t0) cc_final: 0.7444 (t0) outliers start: 55 outliers final: 33 residues processed: 136 average time/residue: 0.3636 time to fit residues: 55.9772 Evaluate side-chains 149 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 103 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1452 ASN Chi-restraints excluded: chain A residue 1476 ASP Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain A residue 1613 LEU Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1410 LYS Chi-restraints excluded: chain B residue 1413 THR Chi-restraints excluded: chain B residue 1452 ASN Chi-restraints excluded: chain B residue 1520 VAL Chi-restraints excluded: chain B residue 1557 GLU Chi-restraints excluded: chain B residue 1613 LEU Chi-restraints excluded: chain C residue 1372 ASP Chi-restraints excluded: chain C residue 1380 ASP Chi-restraints excluded: chain C residue 1397 LEU Chi-restraints excluded: chain C residue 1404 THR Chi-restraints excluded: chain C residue 1452 ASN Chi-restraints excluded: chain C residue 1520 VAL Chi-restraints excluded: chain C residue 1557 GLU Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1398 VAL Chi-restraints excluded: chain D residue 1404 THR Chi-restraints excluded: chain D residue 1446 ASP Chi-restraints excluded: chain D residue 1476 ASP Chi-restraints excluded: chain D residue 1486 GLU Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain D residue 1557 GLU Chi-restraints excluded: chain D residue 1567 PHE Chi-restraints excluded: chain D residue 1613 LEU Chi-restraints excluded: chain E residue 1372 ASP Chi-restraints excluded: chain E residue 1410 LYS Chi-restraints excluded: chain E residue 1413 THR Chi-restraints excluded: chain E residue 1452 ASN Chi-restraints excluded: chain E residue 1520 VAL Chi-restraints excluded: chain E residue 1573 GLU Chi-restraints excluded: chain E residue 1613 LEU Chi-restraints excluded: chain F residue 1372 ASP Chi-restraints excluded: chain F residue 1380 ASP Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain F residue 1404 THR Chi-restraints excluded: chain F residue 1452 ASN Chi-restraints excluded: chain F residue 1518 VAL Chi-restraints excluded: chain F residue 1520 VAL Chi-restraints excluded: chain F residue 1557 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 63 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 56 optimal weight: 0.0970 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1452 ASN A1594 ASN B1452 ASN B1594 ASN C1452 ASN D1594 ASN E1452 ASN E1594 ASN F1452 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.140802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.126685 restraints weight = 18715.823| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 1.64 r_work: 0.3721 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 11640 Z= 0.144 Angle : 0.610 6.198 15948 Z= 0.334 Chirality : 0.049 0.172 1884 Planarity : 0.003 0.034 2130 Dihedral : 5.063 16.191 1578 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.48 % Allowed : 20.91 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.19), residues: 1506 helix: -2.88 (0.41), residues: 72 sheet: 0.26 (0.20), residues: 546 loop : -1.73 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E1580 TYR 0.013 0.002 TYR D1383 PHE 0.013 0.002 PHE A1567 TRP 0.006 0.001 TRP A1378 HIS 0.003 0.001 HIS A1391 Details of bonding type rmsd covalent geometry : bond 0.00334 (11640) covalent geometry : angle 0.60990 (15948) hydrogen bonds : bond 0.03833 ( 378) hydrogen bonds : angle 5.44963 ( 1278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3978.30 seconds wall clock time: 68 minutes 34.97 seconds (4114.97 seconds total)