Starting phenix.real_space_refine on Sat Nov 16 17:57:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8k_16482/11_2024/8c8k_16482.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8k_16482/11_2024/8c8k_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8k_16482/11_2024/8c8k_16482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8k_16482/11_2024/8c8k_16482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8k_16482/11_2024/8c8k_16482.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8k_16482/11_2024/8c8k_16482.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 7.61, per 1000 atoms: 0.67 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: 2.75 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.89 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: 4.58 Time building geometry restraints manager: 3.13 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: 1.980 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.820 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.630 ------------------------------------------------------------------------------- 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= 0.869 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (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 TRP 0.028 0.006 TRP B1378 HIS 0.029 0.008 HIS B1577 PHE 0.074 0.006 PHE D1393 TYR 0.036 0.005 TYR A1383 ARG 0.019 0.002 ARG D1578 *********************** 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 : 1.376 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: 1.2518 time to fit residues: 371.4001 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 : 1.278 ------------------------------------------------------------------------------- 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 126 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1594 ASN B1373 GLN B1391 HIS B1594 ASN C1373 GLN C1391 HIS C1577 HIS C1594 ASN D1594 ASN E1373 GLN E1391 HIS E1577 HIS E1594 ASN F1373 GLN F1391 HIS F1577 HIS F1594 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 11640 Z= 0.318 Angle : 0.688 5.807 15948 Z= 0.383 Chirality : 0.052 0.165 1884 Planarity : 0.005 0.048 2130 Dihedral : 5.542 17.263 1580 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.99 % Allowed : 10.85 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.18), residues: 1506 helix: -3.05 (0.32), residues: 72 sheet: 0.07 (0.20), residues: 522 loop : -1.60 (0.17), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B1378 HIS 0.004 0.002 HIS E1577 PHE 0.022 0.003 PHE E1442 TYR 0.011 0.003 TYR B1600 ARG 0.005 0.001 ARG B1578 *********************** 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 193 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 1.289 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: 0.7189 (m-30) cc_final: 0.6982 (m-30) REVERT: A 1407 ASP cc_start: 0.7554 (t70) cc_final: 0.7015 (p0) REVERT: A 1417 ASP cc_start: 0.7553 (p0) cc_final: 0.6901 (m-30) REVERT: A 1476 ASP cc_start: 0.7167 (t0) cc_final: 0.6909 (t0) REVERT: A 1486 GLU cc_start: 0.6204 (pt0) cc_final: 0.5848 (pp20) REVERT: A 1590 GLU cc_start: 0.6839 (pt0) cc_final: 0.6329 (pp20) REVERT: A 1608 ILE cc_start: 0.6480 (mm) cc_final: 0.6246 (mt) REVERT: B 1407 ASP cc_start: 0.6840 (t70) cc_final: 0.6475 (p0) REVERT: B 1410 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7775 (ttmt) REVERT: B 1573 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6930 (pt0) REVERT: B 1596 LEU cc_start: 0.7396 (tp) cc_final: 0.6916 (mt) REVERT: C 1405 ASP cc_start: 0.7349 (m-30) cc_final: 0.7098 (m-30) REVERT: C 1417 ASP cc_start: 0.7726 (p0) cc_final: 0.6999 (m-30) REVERT: C 1486 GLU cc_start: 0.6913 (tt0) cc_final: 0.6263 (pm20) REVERT: C 1497 ARG cc_start: 0.7202 (mtm110) cc_final: 0.6892 (ptp-170) REVERT: C 1504 GLN cc_start: 0.6300 (pt0) cc_final: 0.6027 (pt0) REVERT: C 1565 THR cc_start: 0.6519 (p) cc_final: 0.6295 (m) REVERT: C 1608 ILE cc_start: 0.6331 (mm) cc_final: 0.6062 (mt) REVERT: D 1405 ASP cc_start: 0.7264 (m-30) cc_final: 0.7059 (m-30) REVERT: D 1407 ASP cc_start: 0.7490 (t70) cc_final: 0.6979 (p0) REVERT: D 1410 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7998 (ttmt) REVERT: D 1417 ASP cc_start: 0.7551 (p0) cc_final: 0.6888 (m-30) REVERT: D 1590 GLU cc_start: 0.6838 (pt0) cc_final: 0.6330 (pp20) REVERT: D 1608 ILE cc_start: 0.6478 (mm) cc_final: 0.6245 (mt) REVERT: E 1407 ASP cc_start: 0.6832 (t70) cc_final: 0.6469 (p0) REVERT: E 1410 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7783 (ttmt) REVERT: E 1573 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6650 (pt0) REVERT: E 1596 LEU cc_start: 0.7421 (mt) cc_final: 0.7061 (mt) REVERT: F 1405 ASP cc_start: 0.7436 (m-30) cc_final: 0.7182 (m-30) REVERT: F 1417 ASP cc_start: 0.7726 (p0) cc_final: 0.7001 (m-30) REVERT: F 1486 GLU cc_start: 0.6911 (tt0) cc_final: 0.6258 (pm20) REVERT: F 1497 ARG cc_start: 0.7195 (mtm110) cc_final: 0.6886 (ptp-170) REVERT: F 1608 ILE cc_start: 0.6328 (mm) cc_final: 0.6057 (mt) outliers start: 38 outliers final: 14 residues processed: 182 average time/residue: 0.9946 time to fit residues: 199.4654 Evaluate side-chains 143 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1372 ASP 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 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 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 E residue 1573 GLU Chi-restraints excluded: chain E residue 1601 THR 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 75 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 136 optimal weight: 20.0000 chunk 147 optimal weight: 8.9990 chunk 121 optimal weight: 0.0670 chunk 135 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 overall best weight: 2.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1391 HIS A1452 ASN A1594 ASN B1594 ASN C1452 ASN C1577 HIS C1594 ASN D1391 HIS D1594 ASN E1452 ASN E1594 ASN F1452 ASN F1594 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 11640 Z= 0.180 Angle : 0.577 5.883 15948 Z= 0.317 Chirality : 0.048 0.174 1884 Planarity : 0.004 0.037 2130 Dihedral : 4.969 16.181 1578 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.99 % Allowed : 13.21 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.19), residues: 1506 helix: -2.76 (0.36), residues: 72 sheet: 0.35 (0.20), residues: 546 loop : -1.60 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F1378 HIS 0.002 0.001 HIS A1391 PHE 0.012 0.002 PHE E1442 TYR 0.012 0.002 TYR A1383 ARG 0.009 0.001 ARG F1580 *********************** 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: 38 poor density : 135 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1407 ASP cc_start: 0.7553 (t70) cc_final: 0.7002 (p0) REVERT: A 1417 ASP cc_start: 0.7549 (p0) cc_final: 0.6884 (m-30) REVERT: A 1590 GLU cc_start: 0.6807 (pt0) cc_final: 0.6444 (pp20) REVERT: A 1608 ILE cc_start: 0.6563 (mm) cc_final: 0.6298 (mt) REVERT: B 1407 ASP cc_start: 0.7289 (t70) cc_final: 0.6548 (p0) REVERT: B 1410 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7773 (ttmt) REVERT: B 1596 LEU cc_start: 0.7328 (tp) cc_final: 0.6875 (mt) REVERT: C 1405 ASP cc_start: 0.7378 (m-30) cc_final: 0.7133 (m-30) REVERT: C 1417 ASP cc_start: 0.7688 (p0) cc_final: 0.6969 (m-30) REVERT: C 1429 ASP cc_start: 0.8174 (t70) cc_final: 0.7961 (t0) REVERT: C 1486 GLU cc_start: 0.6894 (tt0) cc_final: 0.6275 (pm20) REVERT: C 1497 ARG cc_start: 0.7092 (mtm110) cc_final: 0.6799 (ptp-170) REVERT: D 1407 ASP cc_start: 0.7542 (t70) cc_final: 0.7028 (p0) REVERT: D 1410 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7997 (ttmt) REVERT: D 1417 ASP cc_start: 0.7550 (p0) cc_final: 0.6905 (m-30) REVERT: D 1590 GLU cc_start: 0.6811 (pt0) cc_final: 0.6447 (pp20) REVERT: D 1608 ILE cc_start: 0.6560 (mm) cc_final: 0.6296 (mt) REVERT: E 1407 ASP cc_start: 0.7285 (t70) cc_final: 0.6535 (p0) REVERT: E 1410 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7773 (ttmt) REVERT: E 1596 LEU cc_start: 0.7410 (mt) cc_final: 0.7058 (mt) REVERT: F 1405 ASP cc_start: 0.7330 (m-30) cc_final: 0.7070 (m-30) REVERT: F 1417 ASP cc_start: 0.7690 (p0) cc_final: 0.6970 (m-30) REVERT: F 1429 ASP cc_start: 0.8179 (t70) cc_final: 0.7967 (t0) REVERT: F 1486 GLU cc_start: 0.6898 (tt0) cc_final: 0.6267 (pm20) REVERT: F 1497 ARG cc_start: 0.7092 (mtm110) cc_final: 0.6806 (ptp-170) REVERT: F 1608 ILE cc_start: 0.6441 (mm) cc_final: 0.6165 (mt) outliers start: 38 outliers final: 17 residues processed: 161 average time/residue: 0.8680 time to fit residues: 156.5764 Evaluate side-chains 152 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1410 LYS Chi-restraints excluded: chain B residue 1536 GLU 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 1520 VAL 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 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 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 1520 VAL Chi-restraints excluded: chain F residue 1601 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1452 ASN A1594 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 11640 Z= 0.329 Angle : 0.678 6.843 15948 Z= 0.373 Chirality : 0.052 0.178 1884 Planarity : 0.004 0.042 2130 Dihedral : 5.396 16.764 1578 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.25 % Allowed : 15.25 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.18), residues: 1506 helix: -2.95 (0.37), residues: 72 sheet: 0.15 (0.19), residues: 546 loop : -1.71 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B1378 HIS 0.003 0.001 HIS F1391 PHE 0.020 0.003 PHE A1442 TYR 0.014 0.002 TYR A1383 ARG 0.009 0.001 ARG C1580 *********************** 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 180 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 126 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1590 GLU cc_start: 0.6857 (pt0) cc_final: 0.6344 (pp20) REVERT: A 1608 ILE cc_start: 0.6423 (mm) cc_final: 0.6148 (mt) REVERT: B 1407 ASP cc_start: 0.6775 (t70) cc_final: 0.6169 (p0) REVERT: B 1410 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7773 (ttmt) REVERT: B 1596 LEU cc_start: 0.7641 (tp) cc_final: 0.7120 (mt) REVERT: B 1605 GLU cc_start: 0.5487 (mm-30) cc_final: 0.5161 (mm-30) REVERT: C 1405 ASP cc_start: 0.7226 (m-30) cc_final: 0.6968 (m-30) REVERT: C 1417 ASP cc_start: 0.7664 (p0) cc_final: 0.6990 (m-30) REVERT: C 1429 ASP cc_start: 0.8178 (t70) cc_final: 0.7927 (t0) REVERT: C 1486 GLU cc_start: 0.7032 (tt0) cc_final: 0.6228 (pt0) REVERT: C 1497 ARG cc_start: 0.6950 (mtm110) cc_final: 0.6532 (ptp-170) REVERT: C 1504 GLN cc_start: 0.6318 (pt0) cc_final: 0.6008 (pt0) REVERT: C 1608 ILE cc_start: 0.6336 (mm) cc_final: 0.6057 (mt) REVERT: D 1590 GLU cc_start: 0.6860 (pt0) cc_final: 0.6346 (pp20) REVERT: D 1608 ILE cc_start: 0.6420 (mm) cc_final: 0.6146 (mt) REVERT: E 1407 ASP cc_start: 0.6772 (t70) cc_final: 0.6152 (p0) REVERT: E 1410 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7774 (ttmt) REVERT: E 1573 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6574 (pt0) REVERT: E 1596 LEU cc_start: 0.7451 (mt) cc_final: 0.7127 (mt) REVERT: F 1405 ASP cc_start: 0.7227 (m-30) cc_final: 0.6968 (m-30) REVERT: F 1417 ASP cc_start: 0.7667 (p0) cc_final: 0.6994 (m-30) REVERT: F 1429 ASP cc_start: 0.8181 (t70) cc_final: 0.7933 (t0) REVERT: F 1486 GLU cc_start: 0.7027 (tt0) cc_final: 0.6221 (pt0) REVERT: F 1497 ARG cc_start: 0.6950 (mtm110) cc_final: 0.6535 (ptp-170) REVERT: F 1608 ILE cc_start: 0.6331 (mm) cc_final: 0.6052 (mt) outliers start: 54 outliers final: 30 residues processed: 164 average time/residue: 1.0481 time to fit residues: 191.6109 Evaluate side-chains 154 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1372 ASP 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 B residue 1372 ASP Chi-restraints excluded: chain B residue 1410 LYS Chi-restraints excluded: chain B residue 1520 VAL 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 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 D residue 1372 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 E residue 1372 ASP 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 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 1452 ASN Chi-restraints excluded: chain F residue 1518 VAL Chi-restraints excluded: chain F residue 1520 VAL Chi-restraints excluded: chain F residue 1565 THR Chi-restraints excluded: chain F residue 1601 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 123 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 0 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1594 ASN B1452 ASN B1594 ASN C1452 ASN C1577 HIS C1594 ASN D1594 ASN E1594 ASN F1452 ASN F1594 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 11640 Z= 0.344 Angle : 0.687 7.252 15948 Z= 0.377 Chirality : 0.053 0.178 1884 Planarity : 0.004 0.045 2130 Dihedral : 5.520 17.438 1578 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.40 % Allowed : 16.98 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.18), residues: 1506 helix: -3.10 (0.37), residues: 72 sheet: 0.10 (0.20), residues: 546 loop : -1.81 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E1378 HIS 0.003 0.001 HIS F1391 PHE 0.019 0.003 PHE A1567 TYR 0.015 0.002 TYR D1383 ARG 0.010 0.001 ARG F1580 *********************** 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 177 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 121 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1446 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6670 (t0) REVERT: A 1590 GLU cc_start: 0.6827 (pt0) cc_final: 0.6377 (pp20) REVERT: A 1608 ILE cc_start: 0.6470 (mm) cc_final: 0.6199 (mt) REVERT: B 1407 ASP cc_start: 0.6662 (t70) cc_final: 0.5993 (p0) REVERT: C 1405 ASP cc_start: 0.7200 (m-30) cc_final: 0.6978 (m-30) REVERT: C 1417 ASP cc_start: 0.7608 (p0) cc_final: 0.6958 (m-30) REVERT: C 1429 ASP cc_start: 0.8064 (t70) cc_final: 0.7828 (t0) REVERT: C 1486 GLU cc_start: 0.7149 (tt0) cc_final: 0.6216 (pt0) REVERT: C 1497 ARG cc_start: 0.6990 (mtm110) cc_final: 0.6546 (ptp-170) REVERT: C 1594 ASN cc_start: 0.6198 (m-40) cc_final: 0.5844 (m110) REVERT: C 1605 GLU cc_start: 0.5321 (OUTLIER) cc_final: 0.4534 (mm-30) REVERT: C 1608 ILE cc_start: 0.6355 (mm) cc_final: 0.6050 (mt) REVERT: D 1446 ASP cc_start: 0.7026 (OUTLIER) cc_final: 0.6702 (t70) REVERT: D 1590 GLU cc_start: 0.6827 (pt0) cc_final: 0.6377 (pp20) REVERT: D 1608 ILE cc_start: 0.6469 (mm) cc_final: 0.6198 (mt) REVERT: E 1407 ASP cc_start: 0.6671 (t70) cc_final: 0.5981 (p0) REVERT: E 1573 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6564 (pt0) REVERT: F 1405 ASP cc_start: 0.7201 (m-30) cc_final: 0.6978 (m-30) REVERT: F 1417 ASP cc_start: 0.7600 (p0) cc_final: 0.7078 (m-30) REVERT: F 1429 ASP cc_start: 0.8067 (t70) cc_final: 0.7830 (t0) REVERT: F 1486 GLU cc_start: 0.7149 (tt0) cc_final: 0.6203 (pt0) REVERT: F 1497 ARG cc_start: 0.6990 (mtm110) cc_final: 0.6548 (ptp-170) REVERT: F 1594 ASN cc_start: 0.6194 (m-40) cc_final: 0.5838 (m110) REVERT: F 1605 GLU cc_start: 0.5346 (OUTLIER) cc_final: 0.4572 (mm-30) REVERT: F 1608 ILE cc_start: 0.6343 (mm) cc_final: 0.6038 (mt) outliers start: 56 outliers final: 42 residues processed: 159 average time/residue: 1.0664 time to fit residues: 187.8837 Evaluate side-chains 161 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 114 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 1446 ASP 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 B residue 1372 ASP Chi-restraints excluded: chain B residue 1405 ASP 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 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 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 1557 GLU Chi-restraints excluded: chain C residue 1601 THR Chi-restraints excluded: chain C residue 1605 GLU Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1446 ASP Chi-restraints excluded: chain D residue 1476 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 E residue 1372 ASP Chi-restraints excluded: chain E residue 1405 ASP 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 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 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 1557 GLU Chi-restraints excluded: chain F residue 1565 THR Chi-restraints excluded: chain F residue 1601 THR Chi-restraints excluded: chain F residue 1605 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1594 ASN B1594 ASN C1452 ASN C1577 HIS D1594 ASN E1452 ASN E1594 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.3418 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= 0.230 Angle : 0.605 5.870 15948 Z= 0.332 Chirality : 0.049 0.174 1884 Planarity : 0.004 0.034 2130 Dihedral : 5.186 16.793 1578 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.46 % Allowed : 18.87 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.18), residues: 1506 helix: -2.98 (0.39), residues: 72 sheet: 0.19 (0.20), residues: 546 loop : -1.78 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F1378 HIS 0.003 0.001 HIS C1391 PHE 0.014 0.002 PHE B1442 TYR 0.013 0.002 TYR A1383 ARG 0.008 0.001 ARG F1580 *********************** 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 165 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 121 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1590 GLU cc_start: 0.6808 (pt0) cc_final: 0.6363 (pp20) REVERT: A 1608 ILE cc_start: 0.6480 (mm) cc_final: 0.6203 (mt) REVERT: B 1407 ASP cc_start: 0.6675 (t70) cc_final: 0.6004 (p0) REVERT: B 1596 LEU cc_start: 0.7632 (tp) cc_final: 0.7356 (mt) REVERT: C 1417 ASP cc_start: 0.7702 (p0) cc_final: 0.7043 (m-30) REVERT: C 1429 ASP cc_start: 0.8066 (t70) cc_final: 0.7853 (t0) REVERT: C 1497 ARG cc_start: 0.7084 (mtm110) cc_final: 0.6595 (ptp-170) REVERT: C 1594 ASN cc_start: 0.6396 (m-40) cc_final: 0.6072 (m110) REVERT: C 1605 GLU cc_start: 0.5329 (OUTLIER) cc_final: 0.4560 (mm-30) REVERT: C 1608 ILE cc_start: 0.6366 (mm) cc_final: 0.6055 (mt) REVERT: D 1417 ASP cc_start: 0.7686 (p0) cc_final: 0.7047 (m-30) REVERT: D 1446 ASP cc_start: 0.7054 (OUTLIER) cc_final: 0.6754 (t70) REVERT: D 1486 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6228 (pm20) REVERT: D 1590 GLU cc_start: 0.6809 (pt0) cc_final: 0.6362 (pp20) REVERT: D 1608 ILE cc_start: 0.6478 (mm) cc_final: 0.6200 (mt) REVERT: E 1407 ASP cc_start: 0.6686 (t70) cc_final: 0.5960 (p0) REVERT: E 1573 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6607 (pt0) REVERT: F 1417 ASP cc_start: 0.7650 (p0) cc_final: 0.6980 (m-30) REVERT: F 1429 ASP cc_start: 0.8056 (t70) cc_final: 0.7845 (t0) REVERT: F 1497 ARG cc_start: 0.7082 (mtm110) cc_final: 0.6594 (ptp-170) REVERT: F 1594 ASN cc_start: 0.6392 (m-40) cc_final: 0.6069 (m110) REVERT: F 1605 GLU cc_start: 0.5328 (OUTLIER) cc_final: 0.4559 (mm-30) REVERT: F 1608 ILE cc_start: 0.6359 (mm) cc_final: 0.6049 (mt) outliers start: 44 outliers final: 25 residues processed: 147 average time/residue: 0.9965 time to fit residues: 161.8575 Evaluate side-chains 140 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1476 ASP Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1405 ASP Chi-restraints excluded: chain B residue 1520 VAL Chi-restraints excluded: chain C residue 1372 ASP Chi-restraints excluded: chain C residue 1378 TRP Chi-restraints excluded: chain C residue 1397 LEU 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 1605 GLU Chi-restraints excluded: chain D residue 1372 ASP 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 E residue 1372 ASP Chi-restraints excluded: chain E residue 1405 ASP 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 F residue 1372 ASP Chi-restraints excluded: chain F residue 1378 TRP Chi-restraints excluded: chain F residue 1397 LEU 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 1605 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1594 ASN C1452 ASN C1577 HIS E1452 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 11640 Z= 0.257 Angle : 0.621 6.054 15948 Z= 0.341 Chirality : 0.050 0.174 1884 Planarity : 0.004 0.034 2130 Dihedral : 5.208 16.868 1578 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.48 % Allowed : 19.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.19), residues: 1506 helix: -2.98 (0.40), residues: 72 sheet: 0.17 (0.20), residues: 546 loop : -1.78 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D1378 HIS 0.003 0.001 HIS F1391 PHE 0.015 0.002 PHE D1567 TYR 0.014 0.002 TYR D1383 ARG 0.007 0.001 ARG F1580 *********************** 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 171 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 114 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1446 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6689 (t70) REVERT: A 1590 GLU cc_start: 0.6812 (pt0) cc_final: 0.6365 (pp20) REVERT: A 1608 ILE cc_start: 0.6521 (mm) cc_final: 0.6249 (mt) REVERT: B 1407 ASP cc_start: 0.6694 (t70) cc_final: 0.6015 (p0) REVERT: C 1417 ASP cc_start: 0.7663 (p0) cc_final: 0.7027 (m-30) REVERT: C 1429 ASP cc_start: 0.8029 (t70) cc_final: 0.7819 (t0) REVERT: C 1497 ARG cc_start: 0.7066 (mtm110) cc_final: 0.6566 (ptp-170) REVERT: C 1594 ASN cc_start: 0.6207 (m-40) cc_final: 0.5860 (m110) REVERT: C 1605 GLU cc_start: 0.5202 (OUTLIER) cc_final: 0.4487 (mm-30) REVERT: C 1608 ILE cc_start: 0.6491 (mm) cc_final: 0.6189 (mt) REVERT: C 1613 LEU cc_start: 0.5045 (OUTLIER) cc_final: 0.4825 (pp) REVERT: D 1446 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6709 (t70) REVERT: D 1486 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6232 (pm20) REVERT: D 1590 GLU cc_start: 0.6812 (pt0) cc_final: 0.6363 (pp20) REVERT: D 1608 ILE cc_start: 0.6520 (mm) cc_final: 0.6247 (mt) REVERT: E 1407 ASP cc_start: 0.6636 (t70) cc_final: 0.6012 (p0) REVERT: E 1573 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6555 (pt0) REVERT: F 1417 ASP cc_start: 0.7612 (p0) cc_final: 0.6967 (m-30) REVERT: F 1429 ASP cc_start: 0.8034 (t70) cc_final: 0.7823 (t0) REVERT: F 1476 ASP cc_start: 0.7192 (t0) cc_final: 0.6536 (t0) REVERT: F 1497 ARG cc_start: 0.7062 (mtm110) cc_final: 0.6571 (ptp-170) REVERT: F 1594 ASN cc_start: 0.6205 (m-40) cc_final: 0.5861 (m110) REVERT: F 1605 GLU cc_start: 0.5202 (OUTLIER) cc_final: 0.4487 (mm-30) REVERT: F 1608 ILE cc_start: 0.6522 (mm) cc_final: 0.6215 (mt) REVERT: F 1613 LEU cc_start: 0.5041 (OUTLIER) cc_final: 0.4829 (pp) outliers start: 57 outliers final: 32 residues processed: 145 average time/residue: 0.9364 time to fit residues: 151.3542 Evaluate side-chains 152 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1446 ASP Chi-restraints excluded: chain A residue 1476 ASP Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1405 ASP 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 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 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 C residue 1605 GLU Chi-restraints excluded: chain C residue 1613 LEU Chi-restraints excluded: chain D residue 1372 ASP 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 E residue 1372 ASP Chi-restraints excluded: chain E residue 1405 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 1557 GLU Chi-restraints excluded: chain E residue 1573 GLU 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 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 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 86 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 28 optimal weight: 0.0070 chunk 91 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 overall best weight: 2.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1594 ASN C1452 ASN D1594 ASN E1452 ASN E1594 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.3539 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= 0.171 Angle : 0.558 5.669 15948 Z= 0.306 Chirality : 0.047 0.169 1884 Planarity : 0.003 0.033 2130 Dihedral : 4.880 16.111 1578 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.62 % Allowed : 20.20 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.19), residues: 1506 helix: -2.82 (0.42), residues: 72 sheet: 0.28 (0.20), residues: 546 loop : -1.67 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C1540 HIS 0.003 0.001 HIS E1391 PHE 0.011 0.002 PHE B1442 TYR 0.012 0.002 TYR D1383 ARG 0.006 0.001 ARG F1580 *********************** 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 181 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 135 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1417 ASP cc_start: 0.7480 (p0) cc_final: 0.6873 (m-30) REVERT: A 1446 ASP cc_start: 0.7232 (OUTLIER) cc_final: 0.6878 (t70) REVERT: A 1590 GLU cc_start: 0.6780 (pt0) cc_final: 0.6341 (pp20) REVERT: B 1407 ASP cc_start: 0.6707 (t70) cc_final: 0.5998 (p0) REVERT: C 1417 ASP cc_start: 0.7639 (p0) cc_final: 0.6993 (m-30) REVERT: C 1429 ASP cc_start: 0.8066 (t70) cc_final: 0.7861 (t0) REVERT: C 1446 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7123 (t70) REVERT: C 1497 ARG cc_start: 0.7039 (mtm110) cc_final: 0.6723 (ptp-170) REVERT: C 1594 ASN cc_start: 0.6434 (m-40) cc_final: 0.6138 (m110) REVERT: C 1605 GLU cc_start: 0.5270 (OUTLIER) cc_final: 0.4597 (mm-30) REVERT: C 1608 ILE cc_start: 0.6528 (mm) cc_final: 0.6215 (mt) REVERT: D 1417 ASP cc_start: 0.7469 (p0) cc_final: 0.6841 (m-30) REVERT: D 1446 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6813 (t70) REVERT: D 1486 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6243 (pm20) REVERT: D 1590 GLU cc_start: 0.6765 (pt0) cc_final: 0.6322 (pp20) REVERT: E 1407 ASP cc_start: 0.6703 (t70) cc_final: 0.6023 (p0) REVERT: F 1417 ASP cc_start: 0.7641 (p0) cc_final: 0.7028 (m-30) REVERT: F 1429 ASP cc_start: 0.8071 (t70) cc_final: 0.7866 (t0) REVERT: F 1476 ASP cc_start: 0.7007 (t0) cc_final: 0.6355 (t0) REVERT: F 1497 ARG cc_start: 0.7021 (mtm110) cc_final: 0.6713 (ptp-170) REVERT: F 1594 ASN cc_start: 0.6429 (m-40) cc_final: 0.6123 (m110) REVERT: F 1605 GLU cc_start: 0.5269 (OUTLIER) cc_final: 0.4596 (mm-30) REVERT: F 1608 ILE cc_start: 0.6536 (mm) cc_final: 0.6222 (mt) outliers start: 46 outliers final: 23 residues processed: 163 average time/residue: 0.9131 time to fit residues: 167.1292 Evaluate side-chains 145 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1446 ASP Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1405 ASP Chi-restraints excluded: chain B residue 1520 VAL 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 1446 ASP 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 1605 GLU Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1398 VAL 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 E residue 1372 ASP Chi-restraints excluded: chain E residue 1405 ASP Chi-restraints excluded: chain E residue 1452 ASN Chi-restraints excluded: chain E residue 1520 VAL Chi-restraints excluded: chain E residue 1536 GLU Chi-restraints excluded: chain F residue 1372 ASP Chi-restraints excluded: chain F residue 1380 ASP Chi-restraints excluded: chain F residue 1520 VAL Chi-restraints excluded: chain F residue 1557 GLU 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 134 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1594 ASN C1452 ASN D1594 ASN E1452 ASN F1452 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11640 Z= 0.317 Angle : 0.665 6.635 15948 Z= 0.366 Chirality : 0.052 0.175 1884 Planarity : 0.004 0.035 2130 Dihedral : 5.306 15.481 1578 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.01 % Allowed : 20.75 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.19), residues: 1506 helix: -2.99 (0.40), residues: 72 sheet: 0.16 (0.20), residues: 546 loop : -1.78 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B1378 HIS 0.003 0.001 HIS C1391 PHE 0.019 0.003 PHE D1442 TYR 0.015 0.002 TYR D1383 ARG 0.006 0.001 ARG F1580 *********************** 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 167 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 116 time to evaluate : 1.284 Fit side-chains REVERT: A 1590 GLU cc_start: 0.6783 (pt0) cc_final: 0.6320 (pp20) REVERT: A 1605 GLU cc_start: 0.5703 (OUTLIER) cc_final: 0.5343 (mm-30) REVERT: A 1608 ILE cc_start: 0.6525 (mm) cc_final: 0.6254 (mt) REVERT: B 1407 ASP cc_start: 0.6624 (t70) cc_final: 0.5961 (p0) REVERT: C 1417 ASP cc_start: 0.7840 (p0) cc_final: 0.7145 (m-30) REVERT: C 1429 ASP cc_start: 0.8007 (t70) cc_final: 0.7797 (t0) REVERT: C 1476 ASP cc_start: 0.7206 (t0) cc_final: 0.6441 (t0) REVERT: C 1497 ARG cc_start: 0.6885 (mtm110) cc_final: 0.6496 (ptp-170) REVERT: C 1594 ASN cc_start: 0.6212 (m-40) cc_final: 0.5871 (m110) REVERT: C 1605 GLU cc_start: 0.5316 (OUTLIER) cc_final: 0.4580 (mm-30) REVERT: C 1608 ILE cc_start: 0.6502 (mm) cc_final: 0.6189 (mt) REVERT: D 1410 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8095 (ttmt) REVERT: D 1446 ASP cc_start: 0.6959 (OUTLIER) cc_final: 0.6709 (t70) REVERT: D 1486 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6215 (pm20) REVERT: D 1590 GLU cc_start: 0.6782 (pt0) cc_final: 0.6318 (pp20) REVERT: D 1605 GLU cc_start: 0.5717 (OUTLIER) cc_final: 0.5359 (mm-30) REVERT: D 1608 ILE cc_start: 0.6527 (mm) cc_final: 0.6256 (mt) REVERT: E 1407 ASP cc_start: 0.6627 (t70) cc_final: 0.5914 (p0) REVERT: F 1417 ASP cc_start: 0.7622 (p0) cc_final: 0.7124 (m-30) REVERT: F 1429 ASP cc_start: 0.8052 (t70) cc_final: 0.7846 (t0) REVERT: F 1476 ASP cc_start: 0.7111 (t0) cc_final: 0.6459 (t0) REVERT: F 1497 ARG cc_start: 0.6895 (mtm110) cc_final: 0.6493 (ptp-170) REVERT: F 1594 ASN cc_start: 0.6202 (m-40) cc_final: 0.5860 (m110) REVERT: F 1605 GLU cc_start: 0.5310 (OUTLIER) cc_final: 0.4573 (mm-30) REVERT: F 1608 ILE cc_start: 0.6518 (mm) cc_final: 0.6206 (mt) outliers start: 51 outliers final: 29 residues processed: 151 average time/residue: 0.9017 time to fit residues: 151.7981 Evaluate side-chains 149 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1605 GLU Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1405 ASP Chi-restraints excluded: chain B residue 1520 VAL Chi-restraints excluded: chain B residue 1524 ASP Chi-restraints excluded: chain B residue 1548 ILE 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 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 C residue 1605 GLU Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1398 VAL Chi-restraints excluded: chain D residue 1410 LYS 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 1605 GLU Chi-restraints excluded: chain E residue 1372 ASP Chi-restraints excluded: chain E residue 1405 ASP Chi-restraints excluded: chain E residue 1452 ASN Chi-restraints excluded: chain E residue 1520 VAL 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 1452 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1594 ASN C1452 ASN D1594 ASN E1452 ASN E1594 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.3625 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= 0.268 Angle : 0.635 6.159 15948 Z= 0.350 Chirality : 0.050 0.174 1884 Planarity : 0.004 0.037 2130 Dihedral : 5.210 15.510 1578 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.38 % Allowed : 21.31 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.19), residues: 1506 helix: -2.97 (0.40), residues: 72 sheet: 0.15 (0.20), residues: 546 loop : -1.79 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D1378 HIS 0.003 0.001 HIS A1391 PHE 0.016 0.002 PHE A1567 TYR 0.014 0.002 TYR D1383 ARG 0.006 0.001 ARG F1580 ********************** 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 154 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 111 time to evaluate : 1.278 Fit side-chains REVERT: A 1417 ASP cc_start: 0.7663 (p0) cc_final: 0.7045 (m-30) REVERT: A 1476 ASP cc_start: 0.7307 (t0) cc_final: 0.7069 (m-30) REVERT: A 1590 GLU cc_start: 0.6777 (pt0) cc_final: 0.6312 (pp20) REVERT: A 1605 GLU cc_start: 0.5719 (OUTLIER) cc_final: 0.5354 (mm-30) REVERT: A 1608 ILE cc_start: 0.6529 (mm) cc_final: 0.6257 (mt) REVERT: B 1407 ASP cc_start: 0.6629 (t70) cc_final: 0.5992 (p0) REVERT: C 1417 ASP cc_start: 0.7715 (p0) cc_final: 0.7056 (m-30) REVERT: C 1429 ASP cc_start: 0.8012 (t70) cc_final: 0.7803 (t0) REVERT: C 1476 ASP cc_start: 0.7147 (t0) cc_final: 0.6428 (t0) REVERT: C 1497 ARG cc_start: 0.7032 (mtm110) cc_final: 0.6592 (ptp-170) REVERT: C 1594 ASN cc_start: 0.6194 (m-40) cc_final: 0.5850 (m110) REVERT: C 1605 GLU cc_start: 0.5294 (OUTLIER) cc_final: 0.4552 (mm-30) REVERT: C 1608 ILE cc_start: 0.6507 (mm) cc_final: 0.6190 (mt) REVERT: D 1417 ASP cc_start: 0.7576 (p0) cc_final: 0.7016 (m-30) REVERT: D 1446 ASP cc_start: 0.7020 (OUTLIER) cc_final: 0.6731 (t70) REVERT: D 1476 ASP cc_start: 0.7317 (t0) cc_final: 0.7074 (m-30) REVERT: D 1486 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6221 (pm20) REVERT: D 1590 GLU cc_start: 0.6775 (pt0) cc_final: 0.6310 (pp20) REVERT: D 1605 GLU cc_start: 0.5723 (OUTLIER) cc_final: 0.5355 (mm-30) REVERT: D 1608 ILE cc_start: 0.6529 (mm) cc_final: 0.6257 (mt) REVERT: E 1407 ASP cc_start: 0.6640 (t70) cc_final: 0.5966 (p0) REVERT: F 1417 ASP cc_start: 0.7669 (p0) cc_final: 0.7037 (m-30) REVERT: F 1429 ASP cc_start: 0.8016 (t70) cc_final: 0.7813 (t0) REVERT: F 1476 ASP cc_start: 0.7092 (t0) cc_final: 0.6453 (t0) REVERT: F 1497 ARG cc_start: 0.7029 (mtm110) cc_final: 0.6574 (ptp-170) REVERT: F 1594 ASN cc_start: 0.6471 (m-40) cc_final: 0.6136 (m110) REVERT: F 1605 GLU cc_start: 0.5290 (OUTLIER) cc_final: 0.4544 (mm-30) REVERT: F 1608 ILE cc_start: 0.6525 (mm) cc_final: 0.6209 (mt) outliers start: 43 outliers final: 34 residues processed: 142 average time/residue: 0.9087 time to fit residues: 144.2654 Evaluate side-chains 151 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1446 ASP Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain A residue 1605 GLU Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1405 ASP Chi-restraints excluded: chain B residue 1520 VAL Chi-restraints excluded: chain B residue 1524 ASP Chi-restraints excluded: chain B residue 1548 ILE 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 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 C residue 1605 GLU Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1398 VAL 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 1605 GLU Chi-restraints excluded: chain E residue 1372 ASP Chi-restraints excluded: chain E residue 1405 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 1548 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 30.0000 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 122 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1594 ASN C1452 ASN E1452 ASN F1452 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.137664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.123728 restraints weight = 18554.257| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.62 r_work: 0.3681 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11640 Z= 0.413 Angle : 0.734 7.130 15948 Z= 0.405 Chirality : 0.055 0.178 1884 Planarity : 0.005 0.042 2130 Dihedral : 5.595 16.245 1578 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.25 % Allowed : 20.75 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.18), residues: 1506 helix: -3.12 (0.39), residues: 72 sheet: 0.05 (0.20), residues: 546 loop : -1.95 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B1378 HIS 0.004 0.002 HIS C1391 PHE 0.021 0.004 PHE D1442 TYR 0.017 0.003 TYR D1383 ARG 0.006 0.001 ARG F1580 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3847.87 seconds wall clock time: 75 minutes 1.66 seconds (4501.66 seconds total)