Starting phenix.real_space_refine on Mon Nov 18 14:10:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9flu_50539/11_2024/9flu_50539.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9flu_50539/11_2024/9flu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9flu_50539/11_2024/9flu_50539.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9flu_50539/11_2024/9flu_50539.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9flu_50539/11_2024/9flu_50539.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9flu_50539/11_2024/9flu_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-5513/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: 5.99, per 1000 atoms: 0.36 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: 4.23 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: 3.29 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: 6.95 Time building geometry restraints manager: 4.88 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 37.390 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.140 ------------------------------------------------------------------------------- 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 : 1.766 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: 0.2007 time to fit residues: 119.1859 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 : 1.787 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 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 : 1.890 Fit side-chains REVERT: A 3416 CYS cc_start: 0.6753 (m) cc_final: 0.6531 (m) REVERT: B 3687 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8653 (t0) REVERT: E 3523 ARG cc_start: 0.7904 (mtt-85) cc_final: 0.7674 (mtt90) REVERT: F 3530 ILE cc_start: 0.8531 (mt) cc_final: 0.8310 (pt) outliers start: 57 outliers final: 33 residues processed: 291 average time/residue: 0.2151 time to fit residues: 104.5983 Evaluate side-chains 200 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 1.926 ------------------------------------------------------------------------------- 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 3718 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 174 optimal weight: 0.0040 chunk 142 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3636 ASN A3687 ASN B3687 ASN C3687 ASN D3687 ASN E3636 ASN F3636 ASN G3636 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16849 Z= 0.227 Angle : 0.475 3.789 23324 Z= 0.266 Chirality : 0.046 0.141 2968 Planarity : 0.005 0.041 3024 Dihedral : 4.135 15.450 2394 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.88 % Allowed : 9.61 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.76 (0.16), residues: 917 loop : 1.67 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C3683 PHE 0.009 0.001 PHE E3413 TYR 0.012 0.001 TYR E3650 ARG 0.005 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 242 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 186 time to evaluate : 1.779 Fit side-chains REVERT: C 3506 SER cc_start: 0.8905 (p) cc_final: 0.8664 (t) REVERT: E 3506 SER cc_start: 0.8879 (p) cc_final: 0.8649 (t) REVERT: E 3523 ARG cc_start: 0.8030 (mtt-85) cc_final: 0.7761 (mtt90) REVERT: F 3530 ILE cc_start: 0.8766 (mt) cc_final: 0.8484 (pt) REVERT: G 3648 ILE cc_start: 0.8645 (mm) cc_final: 0.8445 (mt) outliers start: 56 outliers final: 43 residues processed: 217 average time/residue: 0.2165 time to fit residues: 79.0520 Evaluate side-chains 193 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 1.860 ------------------------------------------------------------------------------- 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 3596 SER 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 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 3709 VAL 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 3596 SER Chi-restraints excluded: chain C residue 3687 ASN Chi-restraints excluded: chain C residue 3709 VAL Chi-restraints excluded: chain C residue 3718 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 3709 VAL 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 3709 VAL Chi-restraints excluded: chain E residue 3716 ASP Chi-restraints excluded: chain F residue 3535 SER 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 3711 THR Chi-restraints excluded: chain G residue 3406 THR Chi-restraints excluded: chain G residue 3561 SER Chi-restraints excluded: chain G residue 3596 SER Chi-restraints excluded: chain G residue 3649 VAL Chi-restraints excluded: chain G residue 3709 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 0.0980 chunk 158 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 chunk 210 optimal weight: 4.9990 chunk 223 optimal weight: 0.8980 chunk 110 optimal weight: 0.4980 chunk 199 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16849 Z= 0.165 Angle : 0.434 3.383 23324 Z= 0.241 Chirality : 0.045 0.142 2968 Planarity : 0.004 0.036 3024 Dihedral : 3.833 16.113 2394 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.62 % Allowed : 10.89 % Favored : 86.49 % 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: 1.86 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 1.06 (0.16), residues: 889 loop : 1.58 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G3683 PHE 0.008 0.001 PHE C3689 TYR 0.009 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 234 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 1.575 Fit side-chains REVERT: B 3551 ASN cc_start: 0.8459 (p0) cc_final: 0.8181 (p0) REVERT: C 3506 SER cc_start: 0.8848 (p) cc_final: 0.8579 (t) REVERT: C 3684 SER cc_start: 0.8665 (p) cc_final: 0.8389 (m) REVERT: E 3506 SER cc_start: 0.8877 (p) cc_final: 0.8624 (t) REVERT: F 3530 ILE cc_start: 0.8792 (mt) cc_final: 0.8486 (pt) outliers start: 51 outliers final: 34 residues processed: 209 average time/residue: 0.2181 time to fit residues: 76.5074 Evaluate side-chains 199 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 1.737 ------------------------------------------------------------------------------- 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 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 3535 SER Chi-restraints excluded: chain B residue 3596 SER Chi-restraints excluded: chain B residue 3658 VAL 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 3535 SER Chi-restraints excluded: chain C residue 3626 ASP Chi-restraints excluded: chain C residue 3709 VAL Chi-restraints excluded: chain C residue 3718 ASN Chi-restraints excluded: chain D residue 3535 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 3677 VAL Chi-restraints excluded: chain E residue 3709 VAL Chi-restraints excluded: chain E residue 3716 ASP Chi-restraints excluded: chain F residue 3709 VAL Chi-restraints excluded: chain G residue 3406 THR Chi-restraints excluded: chain G residue 3709 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 166 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 190 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3540 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= 0.239 Angle : 0.455 3.479 23324 Z= 0.251 Chirality : 0.047 0.141 2968 Planarity : 0.005 0.039 3024 Dihedral : 3.963 16.390 2394 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.39 % Allowed : 10.28 % Favored : 86.33 % 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: 1.77 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 1.02 (0.16), residues: 882 loop : 1.49 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C3683 PHE 0.009 0.001 PHE E3413 TYR 0.010 0.001 TYR E3650 ARG 0.004 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 252 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 186 time to evaluate : 1.858 Fit side-chains REVERT: B 3551 ASN cc_start: 0.8472 (p0) cc_final: 0.8208 (p0) REVERT: B 3687 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8648 (t0) REVERT: C 3506 SER cc_start: 0.8879 (p) cc_final: 0.8539 (t) REVERT: C 3684 SER cc_start: 0.8628 (p) cc_final: 0.8355 (m) REVERT: E 3454 THR cc_start: 0.8849 (p) cc_final: 0.8380 (m) REVERT: F 3409 VAL cc_start: 0.8700 (t) cc_final: 0.8417 (m) REVERT: F 3530 ILE cc_start: 0.8804 (mt) cc_final: 0.8511 (pt) outliers start: 66 outliers final: 54 residues processed: 222 average time/residue: 0.2137 time to fit residues: 79.5849 Evaluate side-chains 212 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 157 time to evaluate : 1.893 ------------------------------------------------------------------------------- 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 3443 ASN 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 A residue 3718 ASN 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 C residue 3530 ILE Chi-restraints excluded: chain C residue 3534 SER Chi-restraints excluded: chain C residue 3535 SER Chi-restraints excluded: chain C residue 3561 SER Chi-restraints excluded: chain C residue 3591 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 3718 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 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 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 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 3676 THR Chi-restraints excluded: chain F residue 3709 VAL Chi-restraints excluded: chain G residue 3406 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 223 optimal weight: 0.9990 chunk 185 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3687 ASN C3687 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16849 Z= 0.205 Angle : 0.440 3.336 23324 Z= 0.242 Chirality : 0.046 0.149 2968 Planarity : 0.005 0.040 3024 Dihedral : 3.814 15.660 2394 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.49 % Allowed : 10.89 % Favored : 85.61 % 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: 1.77 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 1.00 (0.16), residues: 882 loop : 1.51 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A3683 PHE 0.007 0.001 PHE E3413 TYR 0.009 0.001 TYR E3650 ARG 0.006 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 244 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 176 time to evaluate : 1.791 Fit side-chains REVERT: B 3409 VAL cc_start: 0.8719 (t) cc_final: 0.8425 (m) REVERT: B 3551 ASN cc_start: 0.8425 (p0) cc_final: 0.8170 (p0) REVERT: C 3506 SER cc_start: 0.8859 (p) cc_final: 0.8523 (t) REVERT: C 3684 SER cc_start: 0.8612 (p) cc_final: 0.8347 (m) REVERT: F 3409 VAL cc_start: 0.8738 (t) cc_final: 0.8480 (m) REVERT: F 3530 ILE cc_start: 0.8805 (mt) cc_final: 0.8528 (pt) outliers start: 68 outliers final: 61 residues processed: 215 average time/residue: 0.2068 time to fit residues: 75.2067 Evaluate side-chains 227 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 166 time to evaluate : 1.975 ------------------------------------------------------------------------------- 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 3718 ASN 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 3709 VAL Chi-restraints excluded: chain B residue 3727 VAL Chi-restraints excluded: chain C residue 3530 ILE Chi-restraints excluded: chain C residue 3534 SER Chi-restraints excluded: chain C residue 3535 SER Chi-restraints excluded: chain C residue 3591 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 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 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 3677 VAL 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 3596 SER Chi-restraints excluded: chain F residue 3676 THR Chi-restraints excluded: chain F residue 3709 VAL 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 3561 SER Chi-restraints excluded: chain G residue 3596 SER Chi-restraints excluded: chain G residue 3649 VAL 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 3727 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 126 optimal weight: 0.4980 chunk 188 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16849 Z= 0.282 Angle : 0.468 3.716 23324 Z= 0.257 Chirality : 0.047 0.147 2968 Planarity : 0.005 0.044 3024 Dihedral : 3.995 16.014 2394 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.96 % Allowed : 11.15 % Favored : 84.89 % 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: 0.69 (0.16), residues: 917 loop : 1.48 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A3683 PHE 0.009 0.001 PHE E3413 TYR 0.010 0.001 TYR E3650 ARG 0.005 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 236 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 159 time to evaluate : 2.078 Fit side-chains REVERT: B 3409 VAL cc_start: 0.8830 (t) cc_final: 0.8549 (m) REVERT: C 3684 SER cc_start: 0.8662 (p) cc_final: 0.8404 (m) REVERT: E 3454 THR cc_start: 0.8846 (p) cc_final: 0.8383 (m) REVERT: F 3409 VAL cc_start: 0.8798 (t) cc_final: 0.8553 (m) REVERT: F 3530 ILE cc_start: 0.8776 (mt) cc_final: 0.8495 (pt) outliers start: 77 outliers final: 67 residues processed: 211 average time/residue: 0.2127 time to fit residues: 75.4431 Evaluate side-chains 219 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 152 time to evaluate : 1.782 ------------------------------------------------------------------------------- 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 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 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 3534 SER 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 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 3442 SER 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 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 3676 THR Chi-restraints excluded: chain F residue 3709 VAL 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 3649 VAL 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 3727 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 67 optimal weight: 0.0470 chunk 43 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16849 Z= 0.175 Angle : 0.433 5.769 23324 Z= 0.238 Chirality : 0.046 0.141 2968 Planarity : 0.005 0.041 3024 Dihedral : 3.728 15.599 2394 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.29 % Allowed : 11.92 % Favored : 84.79 % 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: 1.72 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 1.06 (0.16), residues: 819 loop : 1.39 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D3683 PHE 0.006 0.001 PHE E3413 TYR 0.008 0.001 TYR E3650 ARG 0.005 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 238 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 174 time to evaluate : 1.907 Fit side-chains revert: symmetry clash REVERT: B 3409 VAL cc_start: 0.8807 (t) cc_final: 0.8540 (m) REVERT: B 3551 ASN cc_start: 0.8583 (p0) cc_final: 0.8324 (p0) REVERT: B 3687 ASN cc_start: 0.9003 (OUTLIER) cc_final: 0.8679 (t0) REVERT: C 3684 SER cc_start: 0.8564 (p) cc_final: 0.8333 (m) REVERT: F 3409 VAL cc_start: 0.8781 (t) cc_final: 0.8567 (m) REVERT: F 3530 ILE cc_start: 0.8805 (mt) cc_final: 0.8532 (pt) REVERT: F 3676 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8342 (p) outliers start: 64 outliers final: 60 residues processed: 218 average time/residue: 0.2140 time to fit residues: 78.2316 Evaluate side-chains 224 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 162 time to evaluate : 1.846 ------------------------------------------------------------------------------- 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 3709 VAL Chi-restraints excluded: chain A residue 3718 ASN Chi-restraints excluded: chain A residue 3727 VAL 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 3718 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 3534 SER 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 3718 ASN Chi-restraints excluded: chain D residue 3478 VAL Chi-restraints excluded: chain D residue 3535 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 D residue 3727 VAL Chi-restraints excluded: chain E residue 3419 ASP 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 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 3676 THR Chi-restraints excluded: chain F residue 3709 VAL 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 3727 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 207 optimal weight: 0.4980 chunk 124 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 196 optimal weight: 0.6980 chunk 206 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3899 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= 0.181 Angle : 0.430 4.805 23324 Z= 0.236 Chirality : 0.046 0.142 2968 Planarity : 0.005 0.041 3024 Dihedral : 3.656 15.261 2394 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.34 % Allowed : 11.92 % Favored : 84.74 % 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: 1.74 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.94 (0.16), residues: 854 loop : 1.51 (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 E3413 TYR 0.008 0.001 TYR E3650 ARG 0.005 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 235 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 170 time to evaluate : 1.714 Fit side-chains revert: symmetry clash REVERT: A 3523 ARG cc_start: 0.7829 (mtt90) cc_final: 0.7601 (mtt-85) REVERT: B 3409 VAL cc_start: 0.8786 (t) cc_final: 0.8527 (m) REVERT: B 3551 ASN cc_start: 0.8543 (p0) cc_final: 0.8291 (p0) REVERT: B 3687 ASN cc_start: 0.9002 (OUTLIER) cc_final: 0.8743 (t0) REVERT: C 3684 SER cc_start: 0.8604 (p) cc_final: 0.8374 (m) REVERT: F 3409 VAL cc_start: 0.8775 (t) cc_final: 0.8571 (m) REVERT: F 3530 ILE cc_start: 0.8800 (mt) cc_final: 0.8505 (pt) REVERT: F 3676 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8244 (p) outliers start: 65 outliers final: 62 residues processed: 215 average time/residue: 0.2212 time to fit residues: 79.5319 Evaluate side-chains 227 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 163 time to evaluate : 1.846 ------------------------------------------------------------------------------- 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 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 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 3718 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 3534 SER Chi-restraints excluded: chain C residue 3535 SER Chi-restraints excluded: chain C residue 3561 SER Chi-restraints excluded: chain C residue 3591 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 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 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 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 3676 THR Chi-restraints excluded: chain F residue 3709 VAL 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 3649 VAL 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 3727 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 230 optimal weight: 7.9990 chunk 211 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16849 Z= 0.244 Angle : 0.450 4.467 23324 Z= 0.246 Chirality : 0.047 0.145 2968 Planarity : 0.005 0.043 3024 Dihedral : 3.781 15.324 2394 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.39 % Allowed : 12.18 % 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: 1.59 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.75 (0.16), residues: 917 loop : 1.51 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C3683 PHE 0.008 0.001 PHE E3413 TYR 0.009 0.001 TYR E3650 ARG 0.004 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: 66 poor density : 159 time to evaluate : 1.872 Fit side-chains revert: symmetry clash REVERT: B 3409 VAL cc_start: 0.8823 (t) cc_final: 0.8576 (m) REVERT: B 3551 ASN cc_start: 0.8574 (p0) cc_final: 0.8324 (p0) REVERT: B 3687 ASN cc_start: 0.9012 (OUTLIER) cc_final: 0.8754 (t0) REVERT: C 3684 SER cc_start: 0.8564 (p) cc_final: 0.8327 (m) REVERT: F 3409 VAL cc_start: 0.8807 (t) cc_final: 0.8606 (m) REVERT: F 3454 THR cc_start: 0.8751 (p) cc_final: 0.8441 (m) REVERT: F 3530 ILE cc_start: 0.8800 (mt) cc_final: 0.8519 (pt) REVERT: F 3676 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8233 (p) outliers start: 66 outliers final: 63 residues processed: 206 average time/residue: 0.2096 time to fit residues: 72.5236 Evaluate side-chains 223 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 158 time to evaluate : 1.831 ------------------------------------------------------------------------------- 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 3718 ASN 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 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 3718 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 3534 SER Chi-restraints excluded: chain C residue 3535 SER Chi-restraints excluded: chain C residue 3561 SER Chi-restraints excluded: chain C residue 3591 SER Chi-restraints excluded: chain C residue 3596 SER Chi-restraints excluded: chain C residue 3626 ASP Chi-restraints excluded: chain C residue 3709 VAL 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 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 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 3676 THR Chi-restraints excluded: chain F residue 3709 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 3649 VAL 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 3727 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 168 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 161 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.118051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.096552 restraints weight = 19181.774| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.45 r_work: 0.2867 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16849 Z= 0.175 Angle : 0.428 4.259 23324 Z= 0.234 Chirality : 0.046 0.141 2968 Planarity : 0.004 0.041 3024 Dihedral : 3.632 15.140 2394 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.39 % Allowed : 12.13 % 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: 1.74 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.97 (0.16), residues: 854 loop : 1.49 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C3683 PHE 0.008 0.001 PHE D3689 TYR 0.008 0.001 TYR E3650 ARG 0.005 0.001 ARG C3523 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3181.41 seconds wall clock time: 59 minutes 4.47 seconds (3544.47 seconds total)