Starting phenix.real_space_refine on Tue Jan 21 09:12:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9flu_50539/01_2025/9flu_50539.cif Found real_map, /net/cci-nas-00/data/ceres_data/9flu_50539/01_2025/9flu_50539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9flu_50539/01_2025/9flu_50539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9flu_50539/01_2025/9flu_50539.map" model { file = "/net/cci-nas-00/data/ceres_data/9flu_50539/01_2025/9flu_50539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9flu_50539/01_2025/9flu_50539.cif" } resolution = 3.4 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= 0.159 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 77 5.16 5 C 10171 2.51 5 N 2660 2.21 5 O 3612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 16520 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2360 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 19, 'TRANS': 312} Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 6.17, per 1000 atoms: 0.37 Number of scatterers: 16520 At special positions: 0 Unit cell: (93.72, 92.655, 183.18, 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 77 16.00 O 3612 8.00 N 2660 7.00 C 10171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A3416 " - pdb=" SG CYS A3555 " distance=2.05 Simple disulfide: pdb=" SG CYS A3498 " - pdb=" SG CYS A3638 " distance=2.03 Simple disulfide: pdb=" SG CYS A3583 " - pdb=" SG CYS A3720 " distance=2.04 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: 3.85 Conformation dependent library (CDL) restraints added in 2.6 seconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4270 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 70 sheets defined 4.8% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'A' and resid 3437 through 3439 No H-bonds generated for 'chain 'A' and resid 3437 through 3439' Processing helix chain 'A' and resid 3454 through 3458 Processing helix chain 'A' and resid 3686 through 3688 No H-bonds generated for 'chain 'A' and resid 3686 through 3688' Processing helix chain 'A' and resid 3703 through 3707 Processing helix chain 'B' and resid 3437 through 3439 No H-bonds generated for 'chain 'B' and resid 3437 through 3439' Processing helix chain 'B' and resid 3454 through 3458 Processing helix chain 'B' and resid 3686 through 3688 No H-bonds generated for 'chain 'B' and resid 3686 through 3688' Processing helix chain 'B' and resid 3703 through 3707 Processing helix chain 'C' and resid 3437 through 3439 No H-bonds generated for 'chain 'C' and resid 3437 through 3439' Processing helix chain 'C' and resid 3454 through 3458 Processing helix chain 'C' and resid 3686 through 3688 No H-bonds generated for 'chain 'C' and resid 3686 through 3688' Processing helix chain 'C' and resid 3703 through 3707 Processing helix chain 'D' and resid 3437 through 3439 No H-bonds generated for 'chain 'D' and resid 3437 through 3439' Processing helix chain 'D' and resid 3454 through 3458 Processing helix chain 'D' and resid 3686 through 3688 No H-bonds generated for 'chain 'D' and resid 3686 through 3688' Processing helix chain 'D' and resid 3703 through 3707 Processing helix chain 'E' and resid 3437 through 3439 No H-bonds generated for 'chain 'E' and resid 3437 through 3439' Processing helix chain 'E' and resid 3454 through 3458 Processing helix chain 'E' and resid 3686 through 3688 No H-bonds generated for 'chain 'E' and resid 3686 through 3688' Processing helix chain 'E' and resid 3703 through 3707 Processing helix chain 'F' and resid 3437 through 3439 No H-bonds generated for 'chain 'F' and resid 3437 through 3439' Processing helix chain 'F' and resid 3454 through 3458 Processing helix chain 'F' and resid 3686 through 3688 No H-bonds generated for 'chain 'F' and resid 3686 through 3688' Processing helix chain 'F' and resid 3703 through 3707 Processing helix chain 'G' and resid 3437 through 3439 No H-bonds generated for 'chain 'G' and resid 3437 through 3439' Processing helix chain 'G' and resid 3454 through 3458 Processing helix chain 'G' and resid 3686 through 3688 No H-bonds generated for 'chain 'G' and resid 3686 through 3688' Processing helix chain 'G' and resid 3703 through 3707 Processing sheet with id=AA1, first strand: chain 'A' and resid 3413 through 3416 removed outlier: 6.880A pdb=" N PHE A3413 " --> pdb=" O THR A3481 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASP A3483 " --> pdb=" O PHE A3413 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL A3415 " --> pdb=" O ASP A3483 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3491 through 3493 Processing sheet with id=AA3, first strand: chain 'A' and resid 3497 through 3498 removed outlier: 6.477A pdb=" N ILE A3497 " --> pdb=" O ASN A3568 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 3523 through 3526 Processing sheet with id=AA5, first strand: chain 'A' and resid 3576 through 3577 Processing sheet with id=AA6, first strand: chain 'A' and resid 3582 through 3583 removed outlier: 6.934A pdb=" N VAL A3582 " --> pdb=" O TYR A3650 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 3586 through 3589 removed outlier: 5.823A pdb=" N GLY A3586 " --> pdb=" O ASN A3622 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 3611 through 3613 Processing sheet with id=AA9, first strand: chain 'A' and resid 3611 through 3613 Processing sheet with id=AB1, first strand: chain 'A' and resid 3662 through 3665 removed outlier: 6.723A pdb=" N PHE A3662 " --> pdb=" O THR A3730 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN A3732 " --> pdb=" O PHE A3662 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL A3664 " --> pdb=" O ASN A3732 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A3680 " --> pdb=" O VAL A3715 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 3413 through 3416 removed outlier: 6.880A pdb=" N PHE B3413 " --> pdb=" O THR B3481 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASP B3483 " --> pdb=" O PHE B3413 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL B3415 " --> pdb=" O ASP B3483 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 3491 through 3493 Processing sheet with id=AB4, first strand: chain 'B' and resid 3497 through 3498 removed outlier: 6.477A pdb=" N ILE B3497 " --> pdb=" O ASN B3568 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 3523 through 3526 Processing sheet with id=AB6, first strand: chain 'B' and resid 3576 through 3577 Processing sheet with id=AB7, first strand: chain 'B' and resid 3582 through 3583 removed outlier: 6.935A pdb=" N VAL B3582 " --> pdb=" O TYR B3650 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 3586 through 3589 removed outlier: 5.822A pdb=" N GLY B3586 " --> pdb=" O ASN B3622 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 3611 through 3613 Processing sheet with id=AC1, first strand: chain 'B' and resid 3611 through 3613 Processing sheet with id=AC2, first strand: chain 'B' and resid 3662 through 3665 removed outlier: 6.723A pdb=" N PHE B3662 " --> pdb=" O THR B3730 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN B3732 " --> pdb=" O PHE B3662 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL B3664 " --> pdb=" O ASN B3732 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY B3680 " --> pdb=" O VAL B3715 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 3413 through 3416 removed outlier: 6.881A pdb=" N PHE C3413 " --> pdb=" O THR C3481 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASP C3483 " --> pdb=" O PHE C3413 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL C3415 " --> pdb=" O ASP C3483 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 3491 through 3493 Processing sheet with id=AC5, first strand: chain 'C' and resid 3497 through 3498 removed outlier: 6.477A pdb=" N ILE C3497 " --> pdb=" O ASN C3568 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 3523 through 3526 Processing sheet with id=AC7, first strand: chain 'C' and resid 3576 through 3577 Processing sheet with id=AC8, first strand: chain 'C' and resid 3582 through 3583 removed outlier: 6.935A pdb=" N VAL C3582 " --> pdb=" O TYR C3650 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 3586 through 3589 removed outlier: 5.822A pdb=" N GLY C3586 " --> pdb=" O ASN C3622 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 3611 through 3613 Processing sheet with id=AD2, first strand: chain 'C' and resid 3611 through 3613 Processing sheet with id=AD3, first strand: chain 'C' and resid 3662 through 3665 removed outlier: 6.723A pdb=" N PHE C3662 " --> pdb=" O THR C3730 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ASN C3732 " --> pdb=" O PHE C3662 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C3664 " --> pdb=" O ASN C3732 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY C3680 " --> pdb=" O VAL C3715 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 3413 through 3416 removed outlier: 6.881A pdb=" N PHE D3413 " --> pdb=" O THR D3481 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASP D3483 " --> pdb=" O PHE D3413 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL D3415 " --> pdb=" O ASP D3483 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 3491 through 3493 Processing sheet with id=AD6, first strand: chain 'D' and resid 3497 through 3498 removed outlier: 6.477A pdb=" N ILE D3497 " --> pdb=" O ASN D3568 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 3523 through 3526 Processing sheet with id=AD8, first strand: chain 'D' and resid 3576 through 3577 Processing sheet with id=AD9, first strand: chain 'D' and resid 3582 through 3583 removed outlier: 6.934A pdb=" N VAL D3582 " --> pdb=" O TYR D3650 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 3586 through 3589 removed outlier: 5.822A pdb=" N GLY D3586 " --> pdb=" O ASN D3622 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 3611 through 3613 Processing sheet with id=AE3, first strand: chain 'D' and resid 3611 through 3613 Processing sheet with id=AE4, first strand: chain 'D' and resid 3662 through 3665 removed outlier: 6.723A pdb=" N PHE D3662 " --> pdb=" O THR D3730 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN D3732 " --> pdb=" O PHE D3662 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL D3664 " --> pdb=" O ASN D3732 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY D3680 " --> pdb=" O VAL D3715 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 3413 through 3416 removed outlier: 6.881A pdb=" N PHE E3413 " --> pdb=" O THR E3481 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASP E3483 " --> pdb=" O PHE E3413 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL E3415 " --> pdb=" O ASP E3483 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 3491 through 3493 Processing sheet with id=AE7, first strand: chain 'E' and resid 3497 through 3498 removed outlier: 6.477A pdb=" N ILE E3497 " --> pdb=" O ASN E3568 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'E' and resid 3523 through 3526 Processing sheet with id=AE9, first strand: chain 'E' and resid 3576 through 3577 Processing sheet with id=AF1, first strand: chain 'E' and resid 3582 through 3583 removed outlier: 6.934A pdb=" N VAL E3582 " --> pdb=" O TYR E3650 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 3586 through 3589 removed outlier: 5.822A pdb=" N GLY E3586 " --> pdb=" O ASN E3622 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 3611 through 3613 Processing sheet with id=AF4, first strand: chain 'E' and resid 3611 through 3613 Processing sheet with id=AF5, first strand: chain 'E' and resid 3662 through 3665 removed outlier: 6.723A pdb=" N PHE E3662 " --> pdb=" O THR E3730 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN E3732 " --> pdb=" O PHE E3662 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL E3664 " --> pdb=" O ASN E3732 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY E3680 " --> pdb=" O VAL E3715 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 3413 through 3416 removed outlier: 6.880A pdb=" N PHE F3413 " --> pdb=" O THR F3481 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ASP F3483 " --> pdb=" O PHE F3413 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL F3415 " --> pdb=" O ASP F3483 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 3491 through 3493 Processing sheet with id=AF8, first strand: chain 'F' and resid 3497 through 3498 removed outlier: 6.476A pdb=" N ILE F3497 " --> pdb=" O ASN F3568 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'F' and resid 3523 through 3526 Processing sheet with id=AG1, first strand: chain 'F' and resid 3576 through 3577 Processing sheet with id=AG2, first strand: chain 'F' and resid 3582 through 3583 removed outlier: 6.935A pdb=" N VAL F3582 " --> pdb=" O TYR F3650 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'F' and resid 3586 through 3589 removed outlier: 5.823A pdb=" N GLY F3586 " --> pdb=" O ASN F3622 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 3611 through 3613 Processing sheet with id=AG5, first strand: chain 'F' and resid 3611 through 3613 Processing sheet with id=AG6, first strand: chain 'F' and resid 3662 through 3665 removed outlier: 6.723A pdb=" N PHE F3662 " --> pdb=" O THR F3730 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN F3732 " --> pdb=" O PHE F3662 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL F3664 " --> pdb=" O ASN F3732 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY F3680 " --> pdb=" O VAL F3715 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 3413 through 3416 removed outlier: 6.880A pdb=" N PHE G3413 " --> pdb=" O THR G3481 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASP G3483 " --> pdb=" O PHE G3413 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL G3415 " --> pdb=" O ASP G3483 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 3491 through 3493 Processing sheet with id=AG9, first strand: chain 'G' and resid 3497 through 3498 removed outlier: 6.477A pdb=" N ILE G3497 " --> pdb=" O ASN G3568 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'G' and resid 3523 through 3526 Processing sheet with id=AH2, first strand: chain 'G' and resid 3576 through 3577 Processing sheet with id=AH3, first strand: chain 'G' and resid 3582 through 3583 removed outlier: 6.934A pdb=" N VAL G3582 " --> pdb=" O TYR G3650 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'G' and resid 3586 through 3589 removed outlier: 5.823A pdb=" N GLY G3586 " --> pdb=" O ASN G3622 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 3611 through 3613 Processing sheet with id=AH6, first strand: chain 'G' and resid 3611 through 3613 Processing sheet with id=AH7, first strand: chain 'G' and resid 3662 through 3665 removed outlier: 6.723A pdb=" N PHE G3662 " --> pdb=" O THR G3730 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ASN G3732 " --> pdb=" O PHE G3662 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL G3664 " --> pdb=" O ASN G3732 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY G3680 " --> pdb=" O VAL G3715 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1302 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: 6.99 Time building geometry restraints manager: 4.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3249 1.31 - 1.44: 4464 1.44 - 1.57: 9038 1.57 - 1.70: 0 1.70 - 1.83: 98 Bond restraints: 16849 Sorted by residual: bond pdb=" CE2 TRP D3516 " pdb=" CZ2 TRP D3516 " ideal model delta sigma weight residual 1.394 1.305 0.089 2.10e-02 2.27e+03 1.78e+01 bond pdb=" CE2 TRP G3516 " pdb=" CZ2 TRP G3516 " ideal model delta sigma weight residual 1.394 1.305 0.089 2.10e-02 2.27e+03 1.78e+01 bond pdb=" CE2 TRP F3516 " pdb=" CZ2 TRP F3516 " ideal model delta sigma weight residual 1.394 1.306 0.088 2.10e-02 2.27e+03 1.77e+01 bond pdb=" CE2 TRP C3516 " pdb=" CZ2 TRP C3516 " ideal model delta sigma weight residual 1.394 1.306 0.088 2.10e-02 2.27e+03 1.76e+01 bond pdb=" CE2 TRP A3516 " pdb=" CZ2 TRP A3516 " ideal model delta sigma weight residual 1.394 1.306 0.088 2.10e-02 2.27e+03 1.76e+01 ... (remaining 16844 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 20642 2.28 - 4.56: 2376 4.56 - 6.83: 264 6.83 - 9.11: 28 9.11 - 11.39: 14 Bond angle restraints: 23324 Sorted by residual: angle pdb=" CA PHE E3413 " pdb=" CB PHE E3413 " pdb=" CG PHE E3413 " ideal model delta sigma weight residual 113.80 122.86 -9.06 1.00e+00 1.00e+00 8.20e+01 angle pdb=" CA PHE D3413 " pdb=" CB PHE D3413 " pdb=" CG PHE D3413 " ideal model delta sigma weight residual 113.80 122.84 -9.04 1.00e+00 1.00e+00 8.18e+01 angle pdb=" CA PHE F3413 " pdb=" CB PHE F3413 " pdb=" CG PHE F3413 " ideal model delta sigma weight residual 113.80 122.84 -9.04 1.00e+00 1.00e+00 8.17e+01 angle pdb=" CA PHE C3413 " pdb=" CB PHE C3413 " pdb=" CG PHE C3413 " ideal model delta sigma weight residual 113.80 122.84 -9.04 1.00e+00 1.00e+00 8.17e+01 angle pdb=" CA PHE A3413 " pdb=" CB PHE A3413 " pdb=" CG PHE A3413 " ideal model delta sigma weight residual 113.80 122.83 -9.03 1.00e+00 1.00e+00 8.16e+01 ... (remaining 23319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.59: 9319 12.59 - 25.17: 377 25.17 - 37.76: 125 37.76 - 50.35: 7 50.35 - 62.93: 2 Dihedral angle restraints: 9830 sinusoidal: 3173 harmonic: 6657 Sorted by residual: dihedral pdb=" CD ARG G3523 " pdb=" NE ARG G3523 " pdb=" CZ ARG G3523 " pdb=" NH1 ARG G3523 " ideal model delta sinusoidal sigma weight residual 0.00 -46.86 46.86 1 1.00e+01 1.00e-02 3.04e+01 dihedral pdb=" CD ARG D3523 " pdb=" NE ARG D3523 " pdb=" CZ ARG D3523 " pdb=" NH1 ARG D3523 " ideal model delta sinusoidal sigma weight residual 0.00 -46.85 46.85 1 1.00e+01 1.00e-02 3.03e+01 dihedral pdb=" CD ARG C3523 " pdb=" NE ARG C3523 " pdb=" CZ ARG C3523 " pdb=" NH1 ARG C3523 " ideal model delta sinusoidal sigma weight residual 0.00 -46.85 46.85 1 1.00e+01 1.00e-02 3.03e+01 ... (remaining 9827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1586 0.053 - 0.106: 918 0.106 - 0.159: 311 0.159 - 0.212: 125 0.212 - 0.265: 28 Chirality restraints: 2968 Sorted by residual: chirality pdb=" CA ASN B3687 " pdb=" N ASN B3687 " pdb=" C ASN B3687 " pdb=" CB ASN B3687 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA ASN G3687 " pdb=" N ASN G3687 " pdb=" C ASN G3687 " pdb=" CB ASN G3687 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ASN D3687 " pdb=" N ASN D3687 " pdb=" C ASN D3687 " pdb=" CB ASN D3687 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 2965 not shown) Planarity restraints: 3024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E3523 " 0.812 9.50e-02 1.11e+02 3.64e-01 8.05e+01 pdb=" NE ARG E3523 " -0.047 2.00e-02 2.50e+03 pdb=" CZ ARG E3523 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG E3523 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E3523 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B3523 " 0.812 9.50e-02 1.11e+02 3.64e-01 8.04e+01 pdb=" NE ARG B3523 " -0.047 2.00e-02 2.50e+03 pdb=" CZ ARG B3523 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B3523 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B3523 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C3523 " 0.812 9.50e-02 1.11e+02 3.64e-01 8.04e+01 pdb=" NE ARG C3523 " -0.047 2.00e-02 2.50e+03 pdb=" CZ ARG C3523 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C3523 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C3523 " 0.025 2.00e-02 2.50e+03 ... (remaining 3021 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 235 2.60 - 3.18: 14767 3.18 - 3.75: 24753 3.75 - 4.33: 34757 4.33 - 4.90: 57253 Nonbonded interactions: 131765 Sorted by model distance: nonbonded pdb=" SG CYS B3498 " pdb=" SG CYS B3638 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C3498 " pdb=" SG CYS C3638 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS G3498 " pdb=" SG CYS G3638 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS D3498 " pdb=" SG CYS D3638 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS F3498 " pdb=" SG CYS F3638 " model vdw 2.030 3.760 ... (remaining 131760 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' 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: 1.640 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: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 36.980 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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 : 0.018 0.098 16849 Z= 1.193 Angle : 1.515 11.390 23324 Z= 1.017 Chirality : 0.077 0.265 2968 Planarity : 0.019 0.364 3024 Dihedral : 8.060 46.859 5551 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.16), residues: 2310 helix: None (None), residues: 0 sheet: 1.06 (0.16), residues: 882 loop : 1.49 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.007 TRP B3683 PHE 0.056 0.009 PHE B3413 TYR 0.037 0.006 TYR B3540 ARG 0.004 0.002 ARG E3523 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 1.737 Fit side-chains REVERT: A 3416 CYS cc_start: 0.6981 (m) cc_final: 0.6758 (m) REVERT: A 3520 ASP cc_start: 0.7352 (p0) cc_final: 0.7059 (p0) REVERT: B 3416 CYS cc_start: 0.6990 (m) cc_final: 0.6706 (m) REVERT: B 3520 ASP cc_start: 0.7456 (p0) cc_final: 0.7028 (p0) REVERT: D 3416 CYS cc_start: 0.7036 (m) cc_final: 0.6822 (m) REVERT: D 3452 ASN cc_start: 0.8451 (t0) cc_final: 0.8181 (t0) REVERT: D 3520 ASP cc_start: 0.7480 (p0) cc_final: 0.7202 (p0) REVERT: E 3416 CYS cc_start: 0.7142 (m) cc_final: 0.6843 (m) REVERT: E 3452 ASN cc_start: 0.8559 (t0) cc_final: 0.8350 (t0) REVERT: E 3520 ASP cc_start: 0.7601 (p0) cc_final: 0.7376 (p0) REVERT: E 3558 MET cc_start: 0.7603 (mmm) cc_final: 0.7284 (mmt) REVERT: F 3530 ILE cc_start: 0.8505 (mt) cc_final: 0.8293 (pt) REVERT: G 3416 CYS cc_start: 0.6846 (m) cc_final: 0.6429 (m) REVERT: G 3520 ASP cc_start: 0.7560 (p0) cc_final: 0.7170 (p0) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.2005 time to fit residues: 119.3163 Evaluate side-chains 194 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 181 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 134 optimal weight: 6.9990 chunk 209 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3433 ASN A3687 ASN B3433 ASN B3687 ASN C3433 ASN C3687 ASN D3682 ASN D3687 ASN E3433 ASN E3687 ASN F3433 ASN F3687 ASN G3687 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.125098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.100938 restraints weight = 18866.269| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.58 r_work: 0.2925 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16849 Z= 0.203 Angle : 0.507 3.726 23324 Z= 0.287 Chirality : 0.047 0.142 2968 Planarity : 0.005 0.035 3024 Dihedral : 4.400 15.067 2394 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.93 % Allowed : 7.14 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.78 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.72 (0.16), residues: 931 loop : 1.77 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C3683 PHE 0.013 0.002 PHE A3413 TYR 0.012 0.001 TYR C3650 ARG 0.003 0.001 ARG C3523 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 268 time to evaluate : 1.707 Fit side-chains REVERT: A 3416 CYS cc_start: 0.8154 (m) cc_final: 0.7904 (m) REVERT: A 3467 ASP cc_start: 0.7959 (t0) cc_final: 0.7532 (t0) REVERT: B 3467 ASP cc_start: 0.7851 (t0) cc_final: 0.7394 (t0) REVERT: B 3687 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8687 (t0) REVERT: C 3649 VAL cc_start: 0.8542 (t) cc_final: 0.8304 (m) REVERT: D 3467 ASP cc_start: 0.7827 (t0) cc_final: 0.7618 (p0) REVERT: D 3649 VAL cc_start: 0.8379 (t) cc_final: 0.8154 (m) REVERT: E 3467 ASP cc_start: 0.8081 (t0) cc_final: 0.7556 (p0) REVERT: E 3523 ARG cc_start: 0.8394 (mtt-85) cc_final: 0.8132 (mtt90) REVERT: E 3558 MET cc_start: 0.8517 (mmm) cc_final: 0.8272 (mmt) REVERT: F 3530 ILE cc_start: 0.8867 (mt) cc_final: 0.8512 (pt) REVERT: G 3467 ASP cc_start: 0.8091 (t0) cc_final: 0.7449 (p0) REVERT: G 3716 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7696 (m-30) outliers start: 57 outliers final: 33 residues processed: 291 average time/residue: 0.2024 time to fit residues: 99.4362 Evaluate side-chains 214 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3428 VAL Chi-restraints excluded: chain A residue 3530 ILE Chi-restraints excluded: chain A residue 3561 SER Chi-restraints excluded: chain A residue 3709 VAL Chi-restraints excluded: chain A residue 3718 ASN Chi-restraints excluded: chain B residue 3406 THR Chi-restraints excluded: chain B residue 3530 ILE Chi-restraints excluded: chain B residue 3561 SER Chi-restraints excluded: chain B residue 3687 ASN Chi-restraints excluded: chain B residue 3709 VAL Chi-restraints excluded: chain B residue 3718 ASN Chi-restraints excluded: chain C residue 3530 ILE Chi-restraints excluded: chain C residue 3561 SER Chi-restraints excluded: chain C residue 3709 VAL Chi-restraints excluded: chain C residue 3718 ASN Chi-restraints excluded: chain D residue 3419 ASP Chi-restraints excluded: chain D residue 3443 ASN Chi-restraints excluded: chain D residue 3530 ILE Chi-restraints excluded: chain D residue 3561 SER Chi-restraints excluded: chain D residue 3687 ASN Chi-restraints excluded: chain D residue 3709 VAL Chi-restraints excluded: chain D residue 3718 ASN Chi-restraints excluded: chain E residue 3419 ASP Chi-restraints excluded: chain E residue 3443 ASN Chi-restraints excluded: chain E residue 3530 ILE Chi-restraints excluded: chain E residue 3561 SER Chi-restraints excluded: chain E residue 3709 VAL Chi-restraints excluded: chain F residue 3561 SER Chi-restraints excluded: chain F residue 3709 VAL Chi-restraints excluded: chain G residue 3406 THR Chi-restraints excluded: chain G residue 3530 ILE Chi-restraints excluded: chain G residue 3561 SER Chi-restraints excluded: chain G residue 3709 VAL Chi-restraints excluded: chain G residue 3716 ASP Chi-restraints excluded: chain G residue 3718 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 82 optimal weight: 0.5980 chunk 212 optimal weight: 3.9990 chunk 89 optimal weight: 0.0050 chunk 186 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 83 optimal weight: 0.2980 chunk 190 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 49 optimal weight: 0.0060 overall best weight: 0.2210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3636 ASN A3687 ASN C3687 ASN D3687 ASN E3636 ASN F3636 ASN G3636 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.128397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.104880 restraints weight = 18660.915| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.57 r_work: 0.2973 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16849 Z= 0.117 Angle : 0.435 3.435 23324 Z= 0.244 Chirality : 0.045 0.140 2968 Planarity : 0.004 0.043 3024 Dihedral : 3.737 14.702 2394 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.21 % Allowed : 10.23 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 1.24 (0.16), residues: 826 loop : 1.64 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D3434 PHE 0.005 0.001 PHE G3662 TYR 0.009 0.001 TYR E3650 ARG 0.006 0.001 ARG C3523 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 234 time to evaluate : 1.630 Fit side-chains REVERT: A 3467 ASP cc_start: 0.7897 (t70) cc_final: 0.7410 (t0) REVERT: A 3506 SER cc_start: 0.8829 (p) cc_final: 0.8586 (t) REVERT: A 3716 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.8068 (m-30) REVERT: B 3467 ASP cc_start: 0.7832 (t70) cc_final: 0.7435 (t70) REVERT: B 3506 SER cc_start: 0.8942 (p) cc_final: 0.8685 (t) REVERT: B 3551 ASN cc_start: 0.8039 (p0) cc_final: 0.7665 (p0) REVERT: B 3716 ASP cc_start: 0.8175 (m-30) cc_final: 0.7675 (m-30) REVERT: C 3506 SER cc_start: 0.8846 (p) cc_final: 0.8616 (t) REVERT: D 3443 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8281 (p0) REVERT: E 3467 ASP cc_start: 0.7870 (t0) cc_final: 0.7588 (p0) REVERT: E 3523 ARG cc_start: 0.8412 (mtt-85) cc_final: 0.8113 (mtt90) REVERT: F 3443 ASN cc_start: 0.8377 (m-40) cc_final: 0.8145 (p0) REVERT: F 3530 ILE cc_start: 0.8980 (mt) cc_final: 0.8653 (pt) REVERT: G 3443 ASN cc_start: 0.8595 (m-40) cc_final: 0.8380 (p0) REVERT: G 3467 ASP cc_start: 0.7841 (t0) cc_final: 0.7562 (p0) REVERT: G 3506 SER cc_start: 0.8856 (p) cc_final: 0.8635 (t) REVERT: G 3716 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7755 (m-30) outliers start: 43 outliers final: 27 residues processed: 254 average time/residue: 0.2208 time to fit residues: 94.5451 Evaluate side-chains 203 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3428 VAL Chi-restraints excluded: chain A residue 3431 SER Chi-restraints excluded: chain A residue 3596 SER Chi-restraints excluded: chain A residue 3687 ASN Chi-restraints excluded: chain A residue 3709 VAL Chi-restraints excluded: chain A residue 3716 ASP Chi-restraints excluded: chain B residue 3535 SER Chi-restraints excluded: chain B residue 3596 SER Chi-restraints excluded: chain B residue 3718 ASN Chi-restraints excluded: chain C residue 3535 SER Chi-restraints excluded: chain C residue 3596 SER Chi-restraints excluded: chain C residue 3624 SER Chi-restraints excluded: chain C residue 3687 ASN Chi-restraints excluded: chain C residue 3718 ASN Chi-restraints excluded: chain D residue 3443 ASN Chi-restraints excluded: chain D residue 3535 SER Chi-restraints excluded: chain D residue 3596 SER Chi-restraints excluded: chain D residue 3718 ASN Chi-restraints excluded: chain E residue 3443 ASN Chi-restraints excluded: chain E residue 3535 SER Chi-restraints excluded: chain E residue 3596 SER Chi-restraints excluded: chain E residue 3624 SER Chi-restraints excluded: chain E residue 3677 VAL Chi-restraints excluded: chain E residue 3709 VAL Chi-restraints excluded: chain F residue 3535 SER Chi-restraints excluded: chain F residue 3596 SER Chi-restraints excluded: chain G residue 3406 THR Chi-restraints excluded: chain G residue 3596 SER Chi-restraints excluded: chain G residue 3716 ASP Chi-restraints excluded: chain G residue 3718 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 147 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 221 optimal weight: 0.4980 chunk 85 optimal weight: 0.4980 chunk 12 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3687 ASN B3687 ASN C3687 ASN D3687 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.120741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.096659 restraints weight = 18952.755| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.60 r_work: 0.2854 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16849 Z= 0.250 Angle : 0.467 3.686 23324 Z= 0.259 Chirality : 0.047 0.140 2968 Planarity : 0.005 0.041 3024 Dihedral : 4.030 16.028 2394 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.19 % Allowed : 10.53 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.94 (0.15), residues: 917 loop : 1.69 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B3434 PHE 0.009 0.002 PHE E3413 TYR 0.011 0.001 TYR E3650 ARG 0.005 0.001 ARG C3523 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 181 time to evaluate : 1.757 Fit side-chains REVERT: A 3467 ASP cc_start: 0.7918 (t70) cc_final: 0.7426 (t70) REVERT: B 3467 ASP cc_start: 0.7873 (t70) cc_final: 0.7391 (t70) REVERT: B 3687 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.8817 (t0) REVERT: B 3716 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7723 (m-30) REVERT: C 3506 SER cc_start: 0.8990 (p) cc_final: 0.8641 (t) REVERT: D 3443 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8377 (p0) REVERT: D 3716 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7792 (m-30) REVERT: E 3454 THR cc_start: 0.8733 (t) cc_final: 0.8483 (p) REVERT: E 3467 ASP cc_start: 0.7836 (t0) cc_final: 0.7544 (p0) REVERT: E 3523 ARG cc_start: 0.8530 (mtt-85) cc_final: 0.8174 (mtt90) REVERT: F 3523 ARG cc_start: 0.8503 (mtt90) cc_final: 0.8301 (mtt180) REVERT: F 3530 ILE cc_start: 0.8998 (mt) cc_final: 0.8569 (pt) REVERT: F 3716 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7825 (m-30) REVERT: G 3443 ASN cc_start: 0.8630 (m-40) cc_final: 0.8419 (p0) REVERT: G 3540 TYR cc_start: 0.9083 (t80) cc_final: 0.8684 (t80) REVERT: G 3716 ASP cc_start: 0.8168 (t0) cc_final: 0.7762 (m-30) outliers start: 62 outliers final: 41 residues processed: 215 average time/residue: 0.2130 time to fit residues: 77.1352 Evaluate side-chains 207 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3428 VAL Chi-restraints excluded: chain A residue 3431 SER Chi-restraints excluded: chain A residue 3530 ILE Chi-restraints excluded: chain A residue 3561 SER Chi-restraints excluded: chain A residue 3709 VAL Chi-restraints excluded: chain A residue 3718 ASN Chi-restraints excluded: chain B residue 3406 THR Chi-restraints excluded: chain B residue 3530 ILE Chi-restraints excluded: chain B residue 3535 SER Chi-restraints excluded: chain B residue 3561 SER Chi-restraints excluded: chain B residue 3596 SER Chi-restraints excluded: chain B residue 3687 ASN Chi-restraints excluded: chain B residue 3709 VAL Chi-restraints excluded: chain B residue 3716 ASP Chi-restraints excluded: chain B residue 3718 ASN Chi-restraints excluded: chain C residue 3530 ILE Chi-restraints excluded: chain C residue 3535 SER Chi-restraints excluded: chain C residue 3561 SER Chi-restraints excluded: chain C residue 3709 VAL Chi-restraints excluded: chain C residue 3711 THR Chi-restraints excluded: chain C residue 3716 ASP Chi-restraints excluded: chain C residue 3718 ASN Chi-restraints excluded: chain D residue 3443 ASN Chi-restraints excluded: chain D residue 3535 SER Chi-restraints excluded: chain D residue 3561 SER Chi-restraints excluded: chain D residue 3596 SER Chi-restraints excluded: chain D residue 3658 VAL Chi-restraints excluded: chain D residue 3687 ASN Chi-restraints excluded: chain D residue 3709 VAL Chi-restraints excluded: chain D residue 3716 ASP Chi-restraints excluded: chain D residue 3718 ASN Chi-restraints excluded: chain E residue 3443 ASN Chi-restraints excluded: chain E residue 3530 ILE Chi-restraints excluded: chain E residue 3535 SER Chi-restraints excluded: chain E residue 3561 SER Chi-restraints excluded: chain E residue 3677 VAL Chi-restraints excluded: chain E residue 3709 VAL Chi-restraints excluded: chain E residue 3716 ASP Chi-restraints excluded: chain F residue 3561 SER Chi-restraints excluded: chain F residue 3596 SER Chi-restraints excluded: chain F residue 3709 VAL Chi-restraints excluded: chain F residue 3716 ASP Chi-restraints excluded: chain G residue 3406 THR Chi-restraints excluded: chain G residue 3561 SER Chi-restraints excluded: chain G residue 3709 VAL Chi-restraints excluded: chain G residue 3718 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 187 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 108 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3687 ASN B3687 ASN C3687 ASN D3687 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.115227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.091645 restraints weight = 19546.511| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.50 r_work: 0.2803 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16849 Z= 0.433 Angle : 0.542 4.856 23324 Z= 0.300 Chirality : 0.050 0.146 2968 Planarity : 0.005 0.048 3024 Dihedral : 4.627 17.927 2394 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.85 % Allowed : 9.97 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.58 (0.16), residues: 896 loop : 1.24 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C3683 PHE 0.014 0.002 PHE E3413 TYR 0.015 0.002 TYR E3650 ARG 0.005 0.001 ARG C3523 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 151 time to evaluate : 1.912 Fit side-chains REVERT: A 3467 ASP cc_start: 0.7934 (t70) cc_final: 0.7361 (t0) REVERT: B 3467 ASP cc_start: 0.7948 (t70) cc_final: 0.7347 (t70) REVERT: C 3454 THR cc_start: 0.8711 (t) cc_final: 0.8427 (p) REVERT: E 3454 THR cc_start: 0.8738 (t) cc_final: 0.8366 (p) REVERT: E 3467 ASP cc_start: 0.8010 (t0) cc_final: 0.7483 (p0) REVERT: E 3523 ARG cc_start: 0.8557 (mtt-85) cc_final: 0.8114 (mtt90) REVERT: E 3718 ASN cc_start: 0.8491 (p0) cc_final: 0.8274 (p0) REVERT: F 3409 VAL cc_start: 0.9036 (t) cc_final: 0.8781 (m) REVERT: F 3530 ILE cc_start: 0.8930 (mt) cc_final: 0.8584 (pt) REVERT: F 3716 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7716 (m-30) REVERT: G 3443 ASN cc_start: 0.8697 (m-40) cc_final: 0.8427 (p0) outliers start: 75 outliers final: 58 residues processed: 205 average time/residue: 0.2152 time to fit residues: 74.0146 Evaluate side-chains 202 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 143 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3406 THR Chi-restraints excluded: chain A residue 3428 VAL Chi-restraints excluded: chain A residue 3431 SER Chi-restraints excluded: chain A residue 3443 ASN Chi-restraints excluded: chain A residue 3478 VAL Chi-restraints excluded: chain A residue 3530 ILE Chi-restraints excluded: chain A residue 3561 SER Chi-restraints excluded: chain A residue 3676 THR Chi-restraints excluded: chain A residue 3687 ASN Chi-restraints excluded: chain A residue 3709 VAL Chi-restraints excluded: chain B residue 3406 THR Chi-restraints excluded: chain B residue 3530 ILE Chi-restraints excluded: chain B residue 3561 SER Chi-restraints excluded: chain B residue 3596 SER Chi-restraints excluded: chain B residue 3658 VAL Chi-restraints excluded: chain B residue 3676 THR Chi-restraints excluded: chain B residue 3709 VAL Chi-restraints excluded: chain C residue 3530 ILE Chi-restraints excluded: chain C residue 3535 SER Chi-restraints excluded: chain C residue 3561 SER Chi-restraints excluded: chain C residue 3596 SER Chi-restraints excluded: chain C residue 3626 ASP Chi-restraints excluded: chain C residue 3687 ASN Chi-restraints excluded: chain C residue 3709 VAL Chi-restraints excluded: chain C residue 3711 THR Chi-restraints excluded: chain C residue 3716 ASP Chi-restraints excluded: chain C residue 3718 ASN Chi-restraints excluded: chain D residue 3478 VAL Chi-restraints excluded: chain D residue 3535 SER Chi-restraints excluded: chain D residue 3561 SER Chi-restraints excluded: chain D residue 3596 SER Chi-restraints excluded: chain D residue 3658 VAL Chi-restraints excluded: chain D residue 3676 THR Chi-restraints excluded: chain D residue 3709 VAL Chi-restraints excluded: chain D residue 3716 ASP Chi-restraints excluded: chain D residue 3718 ASN Chi-restraints excluded: chain E residue 3443 ASN Chi-restraints excluded: chain E residue 3478 VAL Chi-restraints excluded: chain E residue 3530 ILE Chi-restraints excluded: chain E residue 3535 SER Chi-restraints excluded: chain E residue 3561 SER Chi-restraints excluded: chain E residue 3676 THR Chi-restraints excluded: chain E residue 3709 VAL Chi-restraints excluded: chain E residue 3716 ASP Chi-restraints excluded: chain F residue 3478 VAL Chi-restraints excluded: chain F residue 3561 SER Chi-restraints excluded: chain F residue 3676 THR Chi-restraints excluded: chain F residue 3709 VAL Chi-restraints excluded: chain F residue 3716 ASP Chi-restraints excluded: chain G residue 3406 THR Chi-restraints excluded: chain G residue 3530 ILE Chi-restraints excluded: chain G residue 3533 ILE Chi-restraints excluded: chain G residue 3561 SER Chi-restraints excluded: chain G residue 3596 SER Chi-restraints excluded: chain G residue 3658 VAL Chi-restraints excluded: chain G residue 3676 THR Chi-restraints excluded: chain G residue 3709 VAL Chi-restraints excluded: chain G residue 3711 THR Chi-restraints excluded: chain G residue 3718 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 148 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 209 optimal weight: 0.4980 chunk 158 optimal weight: 7.9990 chunk 215 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3687 ASN B3687 ASN C3687 ASN D3687 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.119223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.095083 restraints weight = 19211.880| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.63 r_work: 0.2806 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16849 Z= 0.191 Angle : 0.436 3.457 23324 Z= 0.240 Chirality : 0.046 0.143 2968 Planarity : 0.005 0.043 3024 Dihedral : 3.905 17.070 2394 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.19 % Allowed : 11.05 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.77 (0.16), residues: 854 loop : 1.39 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G3683 PHE 0.007 0.001 PHE F3413 TYR 0.010 0.001 TYR E3650 ARG 0.005 0.001 ARG C3523 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 178 time to evaluate : 1.674 Fit side-chains REVERT: A 3467 ASP cc_start: 0.8015 (t70) cc_final: 0.7596 (t70) REVERT: B 3467 ASP cc_start: 0.7941 (t70) cc_final: 0.7512 (t70) REVERT: B 3551 ASN cc_start: 0.8478 (p0) cc_final: 0.8261 (p0) REVERT: B 3687 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8677 (t0) REVERT: C 3454 THR cc_start: 0.8796 (t) cc_final: 0.8478 (m) REVERT: C 3684 SER cc_start: 0.8872 (p) cc_final: 0.8666 (m) REVERT: E 3454 THR cc_start: 0.8793 (t) cc_final: 0.8550 (m) REVERT: E 3467 ASP cc_start: 0.7839 (t0) cc_final: 0.7601 (p0) REVERT: F 3454 THR cc_start: 0.8832 (t) cc_final: 0.8555 (p) REVERT: F 3530 ILE cc_start: 0.9019 (mt) cc_final: 0.8659 (pt) REVERT: F 3716 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7952 (m-30) outliers start: 62 outliers final: 54 residues processed: 215 average time/residue: 0.2135 time to fit residues: 76.9697 Evaluate side-chains 224 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 168 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3406 THR Chi-restraints excluded: chain A residue 3428 VAL Chi-restraints excluded: chain A residue 3431 SER Chi-restraints excluded: chain A residue 3530 ILE Chi-restraints excluded: chain A residue 3561 SER Chi-restraints excluded: chain A residue 3596 SER Chi-restraints excluded: chain A residue 3676 THR Chi-restraints excluded: chain A residue 3687 ASN Chi-restraints excluded: chain A residue 3709 VAL Chi-restraints excluded: chain B residue 3406 THR Chi-restraints excluded: chain B residue 3478 VAL Chi-restraints excluded: chain B residue 3561 SER Chi-restraints excluded: chain B residue 3596 SER Chi-restraints excluded: chain B residue 3658 VAL Chi-restraints excluded: chain B residue 3676 THR Chi-restraints excluded: chain B residue 3687 ASN Chi-restraints excluded: chain B residue 3709 VAL Chi-restraints excluded: chain B residue 3727 VAL Chi-restraints excluded: chain C residue 3478 VAL Chi-restraints excluded: chain C residue 3530 ILE Chi-restraints excluded: chain C residue 3535 SER Chi-restraints excluded: chain C residue 3596 SER Chi-restraints excluded: chain C residue 3626 ASP Chi-restraints excluded: chain C residue 3716 ASP Chi-restraints excluded: chain D residue 3535 SER Chi-restraints excluded: chain D residue 3561 SER Chi-restraints excluded: chain D residue 3596 SER Chi-restraints excluded: chain D residue 3658 VAL Chi-restraints excluded: chain D residue 3676 THR Chi-restraints excluded: chain D residue 3687 ASN Chi-restraints excluded: chain D residue 3709 VAL Chi-restraints excluded: chain D residue 3716 ASP Chi-restraints excluded: chain D residue 3718 ASN Chi-restraints excluded: chain E residue 3443 ASN Chi-restraints excluded: chain E residue 3530 ILE Chi-restraints excluded: chain E residue 3535 SER Chi-restraints excluded: chain E residue 3561 SER Chi-restraints excluded: chain E residue 3596 SER Chi-restraints excluded: chain E residue 3676 THR Chi-restraints excluded: chain E residue 3709 VAL Chi-restraints excluded: chain E residue 3716 ASP Chi-restraints excluded: chain F residue 3561 SER Chi-restraints excluded: chain F residue 3596 SER Chi-restraints excluded: chain F residue 3655 THR Chi-restraints excluded: chain F residue 3676 THR Chi-restraints excluded: chain F residue 3716 ASP Chi-restraints excluded: chain G residue 3406 THR Chi-restraints excluded: chain G residue 3478 VAL Chi-restraints excluded: chain G residue 3533 ILE Chi-restraints excluded: chain G residue 3561 SER Chi-restraints excluded: chain G residue 3596 SER Chi-restraints excluded: chain G residue 3658 VAL Chi-restraints excluded: chain G residue 3676 THR Chi-restraints excluded: chain G residue 3709 VAL Chi-restraints excluded: chain G residue 3718 ASN Chi-restraints excluded: chain G residue 3727 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 23 optimal weight: 0.6980 chunk 210 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 229 optimal weight: 0.5980 chunk 178 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3687 ASN B3687 ASN C3687 ASN D3687 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.119584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.095815 restraints weight = 19217.371| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.59 r_work: 0.2829 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16849 Z= 0.184 Angle : 0.428 3.257 23324 Z= 0.235 Chirality : 0.046 0.143 2968 Planarity : 0.005 0.043 3024 Dihedral : 3.760 16.652 2394 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.39 % Allowed : 11.41 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.82 (0.16), residues: 854 loop : 1.43 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C3683 PHE 0.006 0.001 PHE F3413 TYR 0.009 0.001 TYR E3650 ARG 0.004 0.001 ARG C3523 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 179 time to evaluate : 1.803 Fit side-chains REVERT: A 3443 ASN cc_start: 0.8527 (m-40) cc_final: 0.8275 (p0) REVERT: A 3467 ASP cc_start: 0.7984 (t70) cc_final: 0.7566 (t70) REVERT: B 3467 ASP cc_start: 0.7952 (t70) cc_final: 0.7505 (t70) REVERT: B 3501 ASP cc_start: 0.8891 (m-30) cc_final: 0.8646 (m-30) REVERT: B 3551 ASN cc_start: 0.8453 (p0) cc_final: 0.8208 (p0) REVERT: B 3687 ASN cc_start: 0.9006 (OUTLIER) cc_final: 0.8757 (t0) REVERT: C 3454 THR cc_start: 0.8773 (t) cc_final: 0.8467 (m) REVERT: C 3475 ASP cc_start: 0.7559 (m-30) cc_final: 0.7263 (m-30) REVERT: C 3684 SER cc_start: 0.8850 (p) cc_final: 0.8649 (m) REVERT: E 3454 THR cc_start: 0.8767 (t) cc_final: 0.8517 (m) REVERT: E 3467 ASP cc_start: 0.7823 (t0) cc_final: 0.7595 (p0) REVERT: E 3718 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8240 (p0) REVERT: F 3443 ASN cc_start: 0.8559 (m-40) cc_final: 0.8289 (p0) REVERT: F 3454 THR cc_start: 0.8808 (t) cc_final: 0.8511 (m) REVERT: F 3530 ILE cc_start: 0.9030 (mt) cc_final: 0.8650 (pt) REVERT: F 3579 ASP cc_start: 0.7592 (p0) cc_final: 0.7169 (t0) REVERT: F 3716 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7924 (m-30) outliers start: 66 outliers final: 59 residues processed: 224 average time/residue: 0.2065 time to fit residues: 77.4616 Evaluate side-chains 228 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 166 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3406 THR Chi-restraints excluded: chain A residue 3428 VAL Chi-restraints excluded: chain A residue 3431 SER Chi-restraints excluded: chain A residue 3478 VAL Chi-restraints excluded: chain A residue 3530 ILE Chi-restraints excluded: chain A residue 3596 SER Chi-restraints excluded: chain A residue 3676 THR Chi-restraints excluded: chain A residue 3709 VAL Chi-restraints excluded: chain B residue 3406 THR Chi-restraints excluded: chain B residue 3478 VAL Chi-restraints excluded: chain B residue 3561 SER Chi-restraints excluded: chain B residue 3596 SER Chi-restraints excluded: chain B residue 3658 VAL Chi-restraints excluded: chain B residue 3676 THR Chi-restraints excluded: chain B residue 3687 ASN Chi-restraints excluded: chain B residue 3727 VAL Chi-restraints excluded: chain C residue 3478 VAL Chi-restraints excluded: chain C residue 3530 ILE Chi-restraints excluded: chain C residue 3535 SER Chi-restraints excluded: chain C residue 3561 SER Chi-restraints excluded: chain C residue 3596 SER Chi-restraints excluded: chain C residue 3619 MET Chi-restraints excluded: chain C residue 3626 ASP Chi-restraints excluded: chain C residue 3687 ASN Chi-restraints excluded: chain C residue 3709 VAL Chi-restraints excluded: chain C residue 3716 ASP Chi-restraints excluded: chain C residue 3727 VAL Chi-restraints excluded: chain D residue 3478 VAL Chi-restraints excluded: chain D residue 3535 SER Chi-restraints excluded: chain D residue 3561 SER Chi-restraints excluded: chain D residue 3596 SER Chi-restraints excluded: chain D residue 3658 VAL Chi-restraints excluded: chain D residue 3676 THR Chi-restraints excluded: chain D residue 3687 ASN Chi-restraints excluded: chain D residue 3716 ASP Chi-restraints excluded: chain D residue 3718 ASN Chi-restraints excluded: chain D residue 3727 VAL Chi-restraints excluded: chain E residue 3443 ASN Chi-restraints excluded: chain E residue 3478 VAL Chi-restraints excluded: chain E residue 3530 ILE Chi-restraints excluded: chain E residue 3535 SER Chi-restraints excluded: chain E residue 3561 SER Chi-restraints excluded: chain E residue 3676 THR Chi-restraints excluded: chain E residue 3709 VAL Chi-restraints excluded: chain E residue 3718 ASN Chi-restraints excluded: chain F residue 3478 VAL Chi-restraints excluded: chain F residue 3561 SER Chi-restraints excluded: chain F residue 3596 SER Chi-restraints excluded: chain F residue 3655 THR Chi-restraints excluded: chain F residue 3709 VAL Chi-restraints excluded: chain F residue 3716 ASP Chi-restraints excluded: chain F residue 3727 VAL Chi-restraints excluded: chain G residue 3406 THR Chi-restraints excluded: chain G residue 3478 VAL Chi-restraints excluded: chain G residue 3533 ILE Chi-restraints excluded: chain G residue 3561 SER Chi-restraints excluded: chain G residue 3596 SER Chi-restraints excluded: chain G residue 3658 VAL Chi-restraints excluded: chain G residue 3676 THR Chi-restraints excluded: chain G residue 3709 VAL Chi-restraints excluded: chain G residue 3718 ASN Chi-restraints excluded: chain G residue 3727 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 113 optimal weight: 0.8980 chunk 139 optimal weight: 8.9990 chunk 201 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 119 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3687 ASN C3687 ASN D3687 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.115135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.091048 restraints weight = 19445.923| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 1.59 r_work: 0.2757 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 16849 Z= 0.476 Angle : 0.549 4.891 23324 Z= 0.302 Chirality : 0.051 0.150 2968 Planarity : 0.005 0.049 3024 Dihedral : 4.529 17.961 2394 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.85 % Allowed : 11.66 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.38 (0.16), residues: 896 loop : 1.03 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G3683 PHE 0.014 0.002 PHE E3413 TYR 0.014 0.002 TYR G3650 ARG 0.003 0.001 ARG C3523 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 147 time to evaluate : 1.717 Fit side-chains revert: symmetry clash REVERT: A 3467 ASP cc_start: 0.8019 (t70) cc_final: 0.7440 (t0) REVERT: B 3467 ASP cc_start: 0.8069 (t70) cc_final: 0.7574 (t70) REVERT: B 3551 ASN cc_start: 0.8616 (p0) cc_final: 0.8360 (p0) REVERT: C 3454 THR cc_start: 0.8837 (t) cc_final: 0.8547 (p) REVERT: C 3684 SER cc_start: 0.8892 (p) cc_final: 0.8673 (m) REVERT: E 3467 ASP cc_start: 0.8072 (t0) cc_final: 0.7599 (p0) REVERT: E 3718 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8240 (p0) REVERT: F 3454 THR cc_start: 0.8891 (t) cc_final: 0.8654 (p) REVERT: F 3530 ILE cc_start: 0.8992 (mt) cc_final: 0.8674 (pt) REVERT: F 3579 ASP cc_start: 0.7684 (p0) cc_final: 0.7264 (t0) REVERT: F 3716 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7816 (m-30) outliers start: 75 outliers final: 70 residues processed: 204 average time/residue: 0.2116 time to fit residues: 73.0023 Evaluate side-chains 211 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 139 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3406 THR Chi-restraints excluded: chain A residue 3428 VAL Chi-restraints excluded: chain A residue 3431 SER Chi-restraints excluded: chain A residue 3478 VAL Chi-restraints excluded: chain A residue 3530 ILE Chi-restraints excluded: chain A residue 3561 SER Chi-restraints excluded: chain A residue 3596 SER Chi-restraints excluded: chain A residue 3676 THR Chi-restraints excluded: chain A residue 3687 ASN Chi-restraints excluded: chain A residue 3709 VAL Chi-restraints excluded: chain A residue 3727 VAL Chi-restraints excluded: chain B residue 3406 THR Chi-restraints excluded: chain B residue 3478 VAL Chi-restraints excluded: chain B residue 3530 ILE Chi-restraints excluded: chain B residue 3561 SER Chi-restraints excluded: chain B residue 3658 VAL Chi-restraints excluded: chain B residue 3676 THR Chi-restraints excluded: chain B residue 3709 VAL Chi-restraints excluded: chain B residue 3727 VAL Chi-restraints excluded: chain C residue 3478 VAL Chi-restraints excluded: chain C residue 3530 ILE Chi-restraints excluded: chain C residue 3535 SER Chi-restraints excluded: chain C residue 3561 SER Chi-restraints excluded: chain C residue 3596 SER Chi-restraints excluded: chain C residue 3619 MET Chi-restraints excluded: chain C residue 3626 ASP Chi-restraints excluded: chain C residue 3687 ASN Chi-restraints excluded: chain C residue 3709 VAL Chi-restraints excluded: chain C residue 3711 THR Chi-restraints excluded: chain C residue 3716 ASP Chi-restraints excluded: chain C residue 3718 ASN Chi-restraints excluded: chain C residue 3727 VAL Chi-restraints excluded: chain D residue 3478 VAL Chi-restraints excluded: chain D residue 3535 SER Chi-restraints excluded: chain D residue 3561 SER Chi-restraints excluded: chain D residue 3596 SER Chi-restraints excluded: chain D residue 3658 VAL Chi-restraints excluded: chain D residue 3676 THR Chi-restraints excluded: chain D residue 3687 ASN Chi-restraints excluded: chain D residue 3709 VAL Chi-restraints excluded: chain D residue 3716 ASP Chi-restraints excluded: chain D residue 3718 ASN Chi-restraints excluded: chain D residue 3727 VAL Chi-restraints excluded: chain E residue 3443 ASN Chi-restraints excluded: chain E residue 3478 VAL Chi-restraints excluded: chain E residue 3530 ILE Chi-restraints excluded: chain E residue 3535 SER Chi-restraints excluded: chain E residue 3561 SER Chi-restraints excluded: chain E residue 3596 SER Chi-restraints excluded: chain E residue 3676 THR Chi-restraints excluded: chain E residue 3709 VAL Chi-restraints excluded: chain E residue 3716 ASP Chi-restraints excluded: chain E residue 3718 ASN Chi-restraints excluded: chain F residue 3478 VAL Chi-restraints excluded: chain F residue 3561 SER Chi-restraints excluded: chain F residue 3596 SER Chi-restraints excluded: chain F residue 3655 THR Chi-restraints excluded: chain F residue 3676 THR Chi-restraints excluded: chain F residue 3709 VAL Chi-restraints excluded: chain F residue 3716 ASP Chi-restraints excluded: chain F residue 3727 VAL Chi-restraints excluded: chain G residue 3406 THR Chi-restraints excluded: chain G residue 3478 VAL Chi-restraints excluded: chain G residue 3530 ILE Chi-restraints excluded: chain G residue 3533 ILE Chi-restraints excluded: chain G residue 3561 SER Chi-restraints excluded: chain G residue 3596 SER Chi-restraints excluded: chain G residue 3658 VAL Chi-restraints excluded: chain G residue 3676 THR Chi-restraints excluded: chain G residue 3709 VAL Chi-restraints excluded: chain G residue 3718 ASN Chi-restraints excluded: chain G residue 3727 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 66 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 193 optimal weight: 0.4980 chunk 191 optimal weight: 7.9990 chunk 152 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3687 ASN B3687 ASN C3687 ASN D3687 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.118379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.094104 restraints weight = 19206.182| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.64 r_work: 0.2830 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16849 Z= 0.182 Angle : 0.435 3.400 23324 Z= 0.239 Chirality : 0.046 0.141 2968 Planarity : 0.005 0.043 3024 Dihedral : 3.859 16.913 2394 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.24 % Allowed : 12.33 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.68 (0.16), residues: 854 loop : 1.25 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A3683 PHE 0.007 0.001 PHE D3689 TYR 0.009 0.001 TYR G3650 ARG 0.004 0.001 ARG C3523 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 167 time to evaluate : 1.813 Fit side-chains REVERT: A 3443 ASN cc_start: 0.8568 (m-40) cc_final: 0.8321 (p0) REVERT: A 3467 ASP cc_start: 0.8022 (t70) cc_final: 0.7198 (t0) REVERT: B 3467 ASP cc_start: 0.8052 (t70) cc_final: 0.7577 (t70) REVERT: B 3551 ASN cc_start: 0.8447 (p0) cc_final: 0.8215 (p0) REVERT: B 3687 ASN cc_start: 0.9135 (OUTLIER) cc_final: 0.8801 (t0) REVERT: C 3454 THR cc_start: 0.8803 (t) cc_final: 0.8519 (m) REVERT: E 3467 ASP cc_start: 0.7925 (t0) cc_final: 0.7627 (p0) REVERT: E 3718 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8293 (p0) REVERT: F 3454 THR cc_start: 0.8913 (t) cc_final: 0.8606 (m) REVERT: F 3530 ILE cc_start: 0.9033 (mt) cc_final: 0.8677 (pt) REVERT: F 3579 ASP cc_start: 0.7538 (p0) cc_final: 0.7190 (t0) REVERT: F 3716 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7949 (m-30) outliers start: 63 outliers final: 57 residues processed: 213 average time/residue: 0.2160 time to fit residues: 77.8654 Evaluate side-chains 222 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 162 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3428 VAL Chi-restraints excluded: chain A residue 3431 SER Chi-restraints excluded: chain A residue 3530 ILE Chi-restraints excluded: chain A residue 3561 SER Chi-restraints excluded: chain A residue 3596 SER Chi-restraints excluded: chain A residue 3676 THR Chi-restraints excluded: chain A residue 3709 VAL Chi-restraints excluded: chain B residue 3406 THR Chi-restraints excluded: chain B residue 3478 VAL Chi-restraints excluded: chain B residue 3561 SER Chi-restraints excluded: chain B residue 3658 VAL Chi-restraints excluded: chain B residue 3676 THR Chi-restraints excluded: chain B residue 3687 ASN Chi-restraints excluded: chain B residue 3727 VAL Chi-restraints excluded: chain C residue 3530 ILE Chi-restraints excluded: chain C residue 3535 SER Chi-restraints excluded: chain C residue 3561 SER Chi-restraints excluded: chain C residue 3596 SER Chi-restraints excluded: chain C residue 3619 MET Chi-restraints excluded: chain C residue 3626 ASP Chi-restraints excluded: chain C residue 3687 ASN Chi-restraints excluded: chain C residue 3709 VAL Chi-restraints excluded: chain C residue 3716 ASP Chi-restraints excluded: chain D residue 3478 VAL Chi-restraints excluded: chain D residue 3535 SER Chi-restraints excluded: chain D residue 3561 SER Chi-restraints excluded: chain D residue 3596 SER Chi-restraints excluded: chain D residue 3658 VAL Chi-restraints excluded: chain D residue 3676 THR Chi-restraints excluded: chain D residue 3687 ASN Chi-restraints excluded: chain D residue 3716 ASP Chi-restraints excluded: chain D residue 3718 ASN Chi-restraints excluded: chain D residue 3727 VAL Chi-restraints excluded: chain E residue 3478 VAL Chi-restraints excluded: chain E residue 3530 ILE Chi-restraints excluded: chain E residue 3535 SER Chi-restraints excluded: chain E residue 3561 SER Chi-restraints excluded: chain E residue 3596 SER Chi-restraints excluded: chain E residue 3676 THR Chi-restraints excluded: chain E residue 3709 VAL Chi-restraints excluded: chain E residue 3716 ASP Chi-restraints excluded: chain E residue 3718 ASN Chi-restraints excluded: chain F residue 3478 VAL Chi-restraints excluded: chain F residue 3561 SER Chi-restraints excluded: chain F residue 3596 SER Chi-restraints excluded: chain F residue 3655 THR Chi-restraints excluded: chain F residue 3676 THR Chi-restraints excluded: chain F residue 3709 VAL Chi-restraints excluded: chain F residue 3716 ASP Chi-restraints excluded: chain F residue 3727 VAL Chi-restraints excluded: chain G residue 3406 THR Chi-restraints excluded: chain G residue 3478 VAL Chi-restraints excluded: chain G residue 3533 ILE Chi-restraints excluded: chain G residue 3561 SER Chi-restraints excluded: chain G residue 3596 SER Chi-restraints excluded: chain G residue 3658 VAL Chi-restraints excluded: chain G residue 3676 THR Chi-restraints excluded: chain G residue 3709 VAL Chi-restraints excluded: chain G residue 3718 ASN Chi-restraints excluded: chain G residue 3727 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 136 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 201 optimal weight: 0.2980 chunk 79 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3687 ASN B3687 ASN C3687 ASN D3687 ASN E3669 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.114215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.090091 restraints weight = 19629.021| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.59 r_work: 0.2763 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 16849 Z= 0.390 Angle : 0.508 4.160 23324 Z= 0.279 Chirality : 0.049 0.149 2968 Planarity : 0.005 0.049 3024 Dihedral : 4.305 17.257 2394 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.55 % Allowed : 12.54 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.50 (0.16), residues: 882 loop : 1.01 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A3683 PHE 0.012 0.002 PHE E3413 TYR 0.012 0.002 TYR G3650 ARG 0.003 0.001 ARG C3523 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 156 time to evaluate : 1.732 Fit side-chains REVERT: A 3467 ASP cc_start: 0.7901 (t70) cc_final: 0.7440 (t0) REVERT: B 3467 ASP cc_start: 0.8093 (t70) cc_final: 0.7606 (t70) REVERT: B 3551 ASN cc_start: 0.8574 (p0) cc_final: 0.8321 (p0) REVERT: B 3687 ASN cc_start: 0.9240 (OUTLIER) cc_final: 0.8872 (t0) REVERT: C 3454 THR cc_start: 0.8838 (t) cc_final: 0.8534 (m) REVERT: D 3454 THR cc_start: 0.8778 (t) cc_final: 0.8527 (p) REVERT: E 3467 ASP cc_start: 0.8014 (t0) cc_final: 0.7626 (p0) REVERT: E 3718 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8290 (p0) REVERT: F 3454 THR cc_start: 0.8887 (t) cc_final: 0.8634 (p) REVERT: F 3530 ILE cc_start: 0.9049 (mt) cc_final: 0.8698 (pt) REVERT: F 3579 ASP cc_start: 0.7656 (p0) cc_final: 0.7243 (t0) REVERT: F 3716 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7887 (m-30) REVERT: G 3454 THR cc_start: 0.8889 (t) cc_final: 0.8626 (m) outliers start: 69 outliers final: 65 residues processed: 208 average time/residue: 0.2462 time to fit residues: 85.4204 Evaluate side-chains 219 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 151 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3428 VAL Chi-restraints excluded: chain A residue 3431 SER Chi-restraints excluded: chain A residue 3478 VAL Chi-restraints excluded: chain A residue 3530 ILE Chi-restraints excluded: chain A residue 3561 SER Chi-restraints excluded: chain A residue 3596 SER Chi-restraints excluded: chain A residue 3676 THR Chi-restraints excluded: chain A residue 3687 ASN Chi-restraints excluded: chain A residue 3709 VAL Chi-restraints excluded: chain A residue 3718 ASN Chi-restraints excluded: chain B residue 3406 THR Chi-restraints excluded: chain B residue 3478 VAL Chi-restraints excluded: chain B residue 3530 ILE Chi-restraints excluded: chain B residue 3561 SER Chi-restraints excluded: chain B residue 3596 SER Chi-restraints excluded: chain B residue 3658 VAL Chi-restraints excluded: chain B residue 3676 THR Chi-restraints excluded: chain B residue 3687 ASN Chi-restraints excluded: chain B residue 3709 VAL Chi-restraints excluded: chain B residue 3727 VAL Chi-restraints excluded: chain C residue 3478 VAL Chi-restraints excluded: chain C residue 3530 ILE Chi-restraints excluded: chain C residue 3535 SER Chi-restraints excluded: chain C residue 3561 SER Chi-restraints excluded: chain C residue 3596 SER Chi-restraints excluded: chain C residue 3619 MET Chi-restraints excluded: chain C residue 3626 ASP Chi-restraints excluded: chain C residue 3687 ASN Chi-restraints excluded: chain C residue 3709 VAL Chi-restraints excluded: chain C residue 3716 ASP Chi-restraints excluded: chain D residue 3478 VAL Chi-restraints excluded: chain D residue 3535 SER Chi-restraints excluded: chain D residue 3561 SER Chi-restraints excluded: chain D residue 3596 SER Chi-restraints excluded: chain D residue 3658 VAL Chi-restraints excluded: chain D residue 3676 THR Chi-restraints excluded: chain D residue 3687 ASN Chi-restraints excluded: chain D residue 3716 ASP Chi-restraints excluded: chain D residue 3718 ASN Chi-restraints excluded: chain D residue 3727 VAL Chi-restraints excluded: chain E residue 3478 VAL Chi-restraints excluded: chain E residue 3530 ILE Chi-restraints excluded: chain E residue 3535 SER Chi-restraints excluded: chain E residue 3561 SER Chi-restraints excluded: chain E residue 3596 SER Chi-restraints excluded: chain E residue 3676 THR Chi-restraints excluded: chain E residue 3709 VAL Chi-restraints excluded: chain E residue 3716 ASP Chi-restraints excluded: chain E residue 3718 ASN Chi-restraints excluded: chain F residue 3478 VAL Chi-restraints excluded: chain F residue 3561 SER Chi-restraints excluded: chain F residue 3596 SER Chi-restraints excluded: chain F residue 3655 THR Chi-restraints excluded: chain F residue 3676 THR Chi-restraints excluded: chain F residue 3709 VAL Chi-restraints excluded: chain F residue 3716 ASP Chi-restraints excluded: chain F residue 3727 VAL Chi-restraints excluded: chain G residue 3406 THR Chi-restraints excluded: chain G residue 3478 VAL Chi-restraints excluded: chain G residue 3530 ILE Chi-restraints excluded: chain G residue 3533 ILE Chi-restraints excluded: chain G residue 3561 SER Chi-restraints excluded: chain G residue 3596 SER Chi-restraints excluded: chain G residue 3658 VAL Chi-restraints excluded: chain G residue 3676 THR Chi-restraints excluded: chain G residue 3709 VAL Chi-restraints excluded: chain G residue 3718 ASN Chi-restraints excluded: chain G residue 3727 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 224 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3687 ASN B3687 ASN C3687 ASN D3687 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.117592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.093520 restraints weight = 19380.572| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.63 r_work: 0.2782 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16849 Z= 0.242 Angle : 0.453 3.517 23324 Z= 0.248 Chirality : 0.047 0.143 2968 Planarity : 0.005 0.046 3024 Dihedral : 4.026 16.941 2394 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.34 % Allowed : 12.80 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.78 (0.17), residues: 819 loop : 1.01 (0.17), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C3683 PHE 0.008 0.001 PHE E3413 TYR 0.010 0.001 TYR G3650 ARG 0.004 0.001 ARG C3523 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7180.08 seconds wall clock time: 129 minutes 31.98 seconds (7771.98 seconds total)