Starting phenix.real_space_refine on Sat Jun 14 22:04:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9flu_50539/06_2025/9flu_50539.cif Found real_map, /net/cci-nas-00/data/ceres_data/9flu_50539/06_2025/9flu_50539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9flu_50539/06_2025/9flu_50539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9flu_50539/06_2025/9flu_50539.map" model { file = "/net/cci-nas-00/data/ceres_data/9flu_50539/06_2025/9flu_50539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9flu_50539/06_2025/9flu_50539.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.159 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 77 5.16 5 C 10171 2.51 5 N 2660 2.21 5 O 3612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16520 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2360 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 19, 'TRANS': 312} Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 6.30, per 1000 atoms: 0.38 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=21, 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 Simple disulfide: pdb=" SG CYS C3416 " - pdb=" SG CYS C3555 " distance=2.05 Simple disulfide: pdb=" SG CYS B3416 " - pdb=" SG CYS B3555 " distance=2.05 Simple disulfide: pdb=" SG CYS E3416 " - pdb=" SG CYS E3555 " distance=2.05 Simple disulfide: pdb=" SG CYS D3416 " - pdb=" SG CYS D3555 " distance=2.05 Simple disulfide: pdb=" SG CYS G3416 " - pdb=" SG CYS G3555 " distance=2.05 Simple disulfide: pdb=" SG CYS F3416 " - pdb=" SG CYS F3555 " distance=2.05 Simple disulfide: pdb=" SG CYS C3498 " - pdb=" SG CYS C3638 " distance=2.03 Simple disulfide: pdb=" SG CYS B3498 " - pdb=" SG CYS B3638 " distance=2.03 Simple disulfide: pdb=" SG CYS E3498 " - pdb=" SG CYS E3638 " distance=2.03 Simple disulfide: pdb=" SG CYS D3498 " - pdb=" SG CYS D3638 " distance=2.03 Simple disulfide: pdb=" SG CYS G3498 " - pdb=" SG CYS G3638 " distance=2.03 Simple disulfide: pdb=" SG CYS F3498 " - pdb=" SG CYS F3638 " distance=2.03 Simple disulfide: pdb=" SG CYS C3583 " - pdb=" SG CYS C3720 " distance=2.04 Simple disulfide: pdb=" SG CYS B3583 " - pdb=" SG CYS B3720 " distance=2.04 Simple disulfide: pdb=" SG CYS E3583 " - pdb=" SG CYS E3720 " distance=2.04 Simple disulfide: pdb=" SG CYS D3583 " - pdb=" SG CYS D3720 " distance=2.04 Simple disulfide: pdb=" SG CYS G3583 " - pdb=" SG CYS G3720 " distance=2.04 Simple disulfide: pdb=" SG CYS F3583 " - pdb=" SG CYS F3720 " 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: 4.37 Conformation dependent library (CDL) restraints added in 2.5 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: 3.49 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: 6.12 Time building geometry restraints manager: 5.14 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: 9331 12.59 - 25.18: 395 25.18 - 37.77: 137 37.77 - 50.36: 7 50.36 - 62.96: 14 Dihedral angle restraints: 9884 sinusoidal: 3227 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 9881 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: 2.21 - 2.75: 2730 2.75 - 3.29: 15564 3.29 - 3.82: 27218 3.82 - 4.36: 31675 4.36 - 4.90: 54524 Nonbonded interactions: 131711 Sorted by model distance: nonbonded pdb=" OE2 GLU E3515 " pdb=" CD ARG E3523 " model vdw 2.212 3.440 nonbonded pdb=" OE2 GLU D3515 " pdb=" CD ARG D3523 " model vdw 2.212 3.440 nonbonded pdb=" OE2 GLU G3515 " pdb=" CD ARG G3523 " model vdw 2.212 3.440 nonbonded pdb=" OE2 GLU B3515 " pdb=" CD ARG B3523 " model vdw 2.212 3.440 nonbonded pdb=" OE2 GLU A3515 " pdb=" CD ARG A3523 " model vdw 2.212 3.440 ... (remaining 131706 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 38.390 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.720 ------------------------------------------------------------------------------- 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 16870 Z= 0.896 Angle : 1.523 11.390 23366 Z= 1.019 Chirality : 0.077 0.265 2968 Planarity : 0.019 0.364 3024 Dihedral : 8.060 46.859 5551 Min Nonbonded Distance : 2.212 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 Details of bonding type rmsd hydrogen bonds : bond 0.18749 ( 504) hydrogen bonds : angle 9.06989 ( 1302) SS BOND : bond 0.01100 ( 21) SS BOND : angle 3.88376 ( 42) covalent geometry : bond 0.01786 (16849) covalent geometry : angle 1.51506 (23324) *********************** 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 : 1.676 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: 0.1965 time to fit residues: 117.6846 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 : 1.667 ------------------------------------------------------------------------------- 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: 0.8980 chunk 59 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 134 optimal weight: 6.9990 chunk 209 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3433 ASN A3687 ASN B3433 ASN B3687 ASN C3433 ASN C3687 ASN D3682 ASN D3687 ASN E3433 ASN E3687 ASN F3433 ASN F3687 ASN G3687 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.125930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.101225 restraints weight = 18208.990| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.64 r_work: 0.2945 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16870 Z= 0.134 Angle : 0.516 3.764 23366 Z= 0.290 Chirality : 0.047 0.147 2968 Planarity : 0.005 0.033 3024 Dihedral : 4.388 14.669 2394 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.67 % Allowed : 7.09 % Favored : 90.24 % 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 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.75 (0.16), residues: 931 loop : 1.76 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C3683 PHE 0.011 0.001 PHE F3413 TYR 0.011 0.001 TYR F3650 ARG 0.003 0.001 ARG G3523 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 504) hydrogen bonds : angle 6.51378 ( 1302) SS BOND : bond 0.00208 ( 21) SS BOND : angle 1.45137 ( 42) covalent geometry : bond 0.00308 (16849) covalent geometry : angle 0.51244 (23324) *********************** 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 315 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 263 time to evaluate : 1.838 Fit side-chains REVERT: A 3416 CYS cc_start: 0.8278 (m) cc_final: 0.8040 (m) REVERT: A 3467 ASP cc_start: 0.7972 (t0) cc_final: 0.7617 (t0) REVERT: B 3467 ASP cc_start: 0.7902 (t70) cc_final: 0.7504 (t0) REVERT: B 3687 ASN cc_start: 0.9114 (OUTLIER) cc_final: 0.8784 (t0) REVERT: C 3649 VAL cc_start: 0.8632 (t) cc_final: 0.8374 (m) REVERT: D 3649 VAL cc_start: 0.8490 (t) cc_final: 0.8245 (m) REVERT: E 3416 CYS cc_start: 0.8051 (m) cc_final: 0.7779 (m) REVERT: E 3467 ASP cc_start: 0.8075 (t0) cc_final: 0.7685 (p0) REVERT: E 3523 ARG cc_start: 0.8366 (mtt-85) cc_final: 0.8093 (mtt90) REVERT: F 3530 ILE cc_start: 0.8864 (mt) cc_final: 0.8528 (pt) REVERT: G 3467 ASP cc_start: 0.8091 (t0) cc_final: 0.7572 (p0) outliers start: 52 outliers final: 34 residues processed: 285 average time/residue: 0.2071 time to fit residues: 100.3820 Evaluate side-chains 210 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 1.671 ------------------------------------------------------------------------------- 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 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 E residue 3718 ASN Chi-restraints excluded: chain F residue 3561 SER Chi-restraints excluded: chain F residue 3709 VAL Chi-restraints excluded: chain F residue 3718 ASN 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 82 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 186 optimal weight: 0.4980 chunk 7 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 190 optimal weight: 0.3980 chunk 91 optimal weight: 0.1980 chunk 112 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 G3636 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.123454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.099396 restraints weight = 18157.477| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.55 r_work: 0.2915 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16870 Z= 0.125 Angle : 0.466 3.548 23366 Z= 0.260 Chirality : 0.046 0.141 2968 Planarity : 0.005 0.047 3024 Dihedral : 4.016 15.058 2394 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.57 % Allowed : 9.66 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.80 (0.16), residues: 917 loop : 1.72 (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 0.010 0.001 TYR E3650 ARG 0.005 0.001 ARG C3523 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 504) hydrogen bonds : angle 5.90869 ( 1302) SS BOND : bond 0.00094 ( 21) SS BOND : angle 0.90871 ( 42) covalent geometry : bond 0.00297 (16849) covalent geometry : angle 0.46443 (23324) *********************** 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 248 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 198 time to evaluate : 2.257 Fit side-chains REVERT: A 3416 CYS cc_start: 0.8157 (m) cc_final: 0.7920 (m) REVERT: A 3467 ASP cc_start: 0.7915 (t70) cc_final: 0.7451 (t70) REVERT: B 3467 ASP cc_start: 0.7862 (t70) cc_final: 0.7426 (t70) REVERT: B 3551 ASN cc_start: 0.8240 (p0) cc_final: 0.7926 (p0) REVERT: C 3506 SER cc_start: 0.8973 (p) cc_final: 0.8696 (t) REVERT: D 3443 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8325 (p0) REVERT: E 3416 CYS cc_start: 0.7988 (m) cc_final: 0.7718 (m) REVERT: E 3467 ASP cc_start: 0.7932 (t0) cc_final: 0.7558 (p0) REVERT: E 3506 SER cc_start: 0.8903 (p) cc_final: 0.8647 (t) REVERT: E 3523 ARG cc_start: 0.8516 (mtt-85) cc_final: 0.8196 (mtt90) REVERT: E 3716 ASP cc_start: 0.8355 (t0) cc_final: 0.8147 (m-30) REVERT: F 3530 ILE cc_start: 0.8970 (mt) cc_final: 0.8581 (pt) REVERT: G 3467 ASP cc_start: 0.7930 (t0) cc_final: 0.7554 (p0) outliers start: 50 outliers final: 40 residues processed: 223 average time/residue: 0.2571 time to fit residues: 95.5514 Evaluate side-chains 198 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3428 VAL Chi-restraints excluded: chain A residue 3431 SER Chi-restraints excluded: chain A residue 3530 ILE Chi-restraints excluded: chain A residue 3561 SER Chi-restraints excluded: chain A residue 3596 SER Chi-restraints excluded: chain A residue 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 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 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 3443 ASN Chi-restraints excluded: chain D residue 3535 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 3677 VAL Chi-restraints excluded: chain E residue 3709 VAL Chi-restraints excluded: chain F residue 3535 SER Chi-restraints excluded: chain F residue 3596 SER Chi-restraints excluded: chain F residue 3709 VAL Chi-restraints excluded: chain F residue 3718 ASN 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 3709 VAL Chi-restraints excluded: chain G residue 3718 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 147 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 173 optimal weight: 0.3980 chunk 169 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 223 optimal weight: 1.9990 chunk 221 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3687 ASN B3687 ASN C3687 ASN D3687 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.126227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.100387 restraints weight = 18136.463| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.92 r_work: 0.2898 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16870 Z= 0.113 Angle : 0.438 3.624 23366 Z= 0.242 Chirality : 0.046 0.144 2968 Planarity : 0.004 0.037 3024 Dihedral : 3.842 16.096 2394 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.03 % Allowed : 9.97 % Favored : 87.00 % 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: 1.91 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 1.05 (0.16), residues: 889 loop : 1.65 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G3683 PHE 0.008 0.001 PHE C3689 TYR 0.010 0.001 TYR G3650 ARG 0.006 0.001 ARG C3523 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 504) hydrogen bonds : angle 5.67845 ( 1302) SS BOND : bond 0.00080 ( 21) SS BOND : angle 0.79764 ( 42) covalent geometry : bond 0.00270 (16849) covalent geometry : angle 0.43746 (23324) *********************** 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 257 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 198 time to evaluate : 1.653 Fit side-chains REVERT: A 3416 CYS cc_start: 0.8420 (m) cc_final: 0.8188 (m) REVERT: A 3467 ASP cc_start: 0.7914 (t70) cc_final: 0.7416 (t0) REVERT: B 3467 ASP cc_start: 0.7836 (t70) cc_final: 0.7317 (t70) REVERT: B 3551 ASN cc_start: 0.8107 (p0) cc_final: 0.7750 (p0) REVERT: B 3716 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7728 (m-30) REVERT: C 3506 SER cc_start: 0.8953 (p) cc_final: 0.8620 (t) REVERT: E 3416 CYS cc_start: 0.8229 (m) cc_final: 0.7988 (m) REVERT: E 3467 ASP cc_start: 0.7967 (t0) cc_final: 0.7478 (p0) REVERT: E 3506 SER cc_start: 0.8930 (p) cc_final: 0.8640 (t) REVERT: F 3443 ASN cc_start: 0.8575 (m-40) cc_final: 0.8284 (p0) REVERT: F 3530 ILE cc_start: 0.8965 (mt) cc_final: 0.8563 (pt) REVERT: G 3443 ASN cc_start: 0.8638 (m-40) cc_final: 0.8429 (p0) REVERT: G 3467 ASP cc_start: 0.7874 (t0) cc_final: 0.7585 (p0) REVERT: G 3716 ASP cc_start: 0.8211 (t0) cc_final: 0.7774 (m-30) outliers start: 59 outliers final: 42 residues processed: 226 average time/residue: 0.2011 time to fit residues: 76.7341 Evaluate side-chains 219 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 1.762 ------------------------------------------------------------------------------- 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 3535 SER 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 3709 VAL Chi-restraints excluded: chain B residue 3716 ASP Chi-restraints excluded: chain B residue 3718 ASN Chi-restraints excluded: chain C residue 3530 ILE Chi-restraints excluded: chain C residue 3535 SER Chi-restraints excluded: chain C residue 3561 SER Chi-restraints excluded: chain C residue 3596 SER Chi-restraints excluded: chain C residue 3626 ASP 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 D residue 3535 SER Chi-restraints excluded: chain D residue 3561 SER Chi-restraints excluded: chain D residue 3596 SER Chi-restraints excluded: chain D residue 3658 VAL Chi-restraints excluded: chain D residue 3687 ASN Chi-restraints excluded: chain D residue 3709 VAL Chi-restraints excluded: chain D residue 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 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 3718 ASN Chi-restraints excluded: chain G residue 3406 THR Chi-restraints excluded: chain G residue 3709 VAL Chi-restraints excluded: chain G residue 3718 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 187 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 78 optimal weight: 0.5980 chunk 108 optimal weight: 0.0070 chunk 39 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.121117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.098572 restraints weight = 18495.767| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.52 r_work: 0.2894 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16870 Z= 0.109 Angle : 0.428 3.416 23366 Z= 0.235 Chirality : 0.046 0.138 2968 Planarity : 0.004 0.038 3024 Dihedral : 3.708 15.790 2394 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.34 % Allowed : 9.87 % Favored : 86.79 % 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: 1.95 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 1.14 (0.16), residues: 882 loop : 1.63 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C3683 PHE 0.007 0.001 PHE D3689 TYR 0.009 0.001 TYR E3650 ARG 0.006 0.001 ARG C3523 Details of bonding type rmsd hydrogen bonds : bond 0.03294 ( 504) hydrogen bonds : angle 5.56318 ( 1302) SS BOND : bond 0.00071 ( 21) SS BOND : angle 0.69882 ( 42) covalent geometry : bond 0.00262 (16849) covalent geometry : angle 0.42736 (23324) *********************** 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 261 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 196 time to evaluate : 3.307 Fit side-chains REVERT: A 3467 ASP cc_start: 0.7870 (t70) cc_final: 0.7468 (t0) REVERT: B 3416 CYS cc_start: 0.7947 (m) cc_final: 0.7745 (m) REVERT: B 3467 ASP cc_start: 0.7877 (t70) cc_final: 0.7431 (t70) REVERT: B 3687 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8657 (t0) REVERT: B 3716 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7631 (m-30) REVERT: C 3443 ASN cc_start: 0.8508 (m110) cc_final: 0.8283 (p0) REVERT: C 3475 ASP cc_start: 0.7772 (m-30) cc_final: 0.7563 (m-30) REVERT: C 3506 SER cc_start: 0.8944 (p) cc_final: 0.8598 (t) REVERT: E 3467 ASP cc_start: 0.7836 (t0) cc_final: 0.7613 (p0) REVERT: E 3506 SER cc_start: 0.8926 (p) cc_final: 0.8604 (t) REVERT: F 3530 ILE cc_start: 0.8980 (mt) cc_final: 0.8559 (pt) REVERT: F 3676 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8078 (p) REVERT: F 3716 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7674 (m-30) REVERT: G 3716 ASP cc_start: 0.8121 (t0) cc_final: 0.7696 (m-30) outliers start: 65 outliers final: 52 residues processed: 229 average time/residue: 0.2603 time to fit residues: 102.4401 Evaluate side-chains 226 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 170 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3406 THR Chi-restraints excluded: chain A residue 3428 VAL Chi-restraints excluded: chain A residue 3431 SER Chi-restraints excluded: chain A residue 3530 ILE Chi-restraints excluded: chain A residue 3561 SER Chi-restraints excluded: chain A residue 3596 SER Chi-restraints excluded: chain A residue 3676 THR Chi-restraints excluded: chain A residue 3687 ASN Chi-restraints excluded: chain A residue 3709 VAL Chi-restraints excluded: chain A residue 3718 ASN Chi-restraints excluded: chain B residue 3406 THR 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 3716 ASP Chi-restraints excluded: chain B residue 3718 ASN Chi-restraints excluded: chain C residue 3530 ILE Chi-restraints excluded: chain C residue 3535 SER Chi-restraints excluded: chain C residue 3561 SER Chi-restraints excluded: chain C residue 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 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 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 E residue 3718 ASN 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 3716 ASP Chi-restraints excluded: chain F residue 3718 ASN 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 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 148 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 215 optimal weight: 0.7980 chunk 199 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 202 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3222 r_free = 0.3222 target = 0.118930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.095440 restraints weight = 18618.923| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.48 r_work: 0.2850 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16870 Z= 0.149 Angle : 0.452 3.512 23366 Z= 0.248 Chirality : 0.047 0.150 2968 Planarity : 0.005 0.038 3024 Dihedral : 3.837 15.696 2394 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.44 % Allowed : 10.79 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.99 (0.16), residues: 882 loop : 1.56 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G3683 PHE 0.008 0.001 PHE E3413 TYR 0.010 0.001 TYR G3650 ARG 0.006 0.001 ARG C3523 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 504) hydrogen bonds : angle 5.59571 ( 1302) SS BOND : bond 0.00097 ( 21) SS BOND : angle 0.85065 ( 42) covalent geometry : bond 0.00369 (16849) covalent geometry : angle 0.45146 (23324) *********************** 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 242 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 175 time to evaluate : 1.769 Fit side-chains REVERT: A 3443 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8212 (p0) REVERT: A 3467 ASP cc_start: 0.7913 (t70) cc_final: 0.7512 (t70) REVERT: B 3467 ASP cc_start: 0.7884 (t70) cc_final: 0.7474 (t70) REVERT: B 3716 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7704 (m-30) REVERT: C 3443 ASN cc_start: 0.8497 (m110) cc_final: 0.8296 (p0) REVERT: C 3506 SER cc_start: 0.8945 (p) cc_final: 0.8550 (t) REVERT: C 3668 ASP cc_start: 0.7832 (m-30) cc_final: 0.7510 (m-30) REVERT: C 3684 SER cc_start: 0.8788 (p) cc_final: 0.8581 (m) REVERT: D 3716 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7585 (m-30) REVERT: E 3454 THR cc_start: 0.8719 (t) cc_final: 0.8475 (m) REVERT: E 3467 ASP cc_start: 0.7865 (t0) cc_final: 0.7606 (p0) REVERT: F 3530 ILE cc_start: 0.9009 (mt) cc_final: 0.8613 (pt) REVERT: F 3716 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7667 (m-30) REVERT: G 3716 ASP cc_start: 0.8137 (t0) cc_final: 0.7743 (m-30) outliers start: 67 outliers final: 59 residues processed: 213 average time/residue: 0.2144 time to fit residues: 77.3884 Evaluate side-chains 234 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 171 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3406 THR Chi-restraints excluded: chain A residue 3428 VAL Chi-restraints excluded: chain A residue 3431 SER Chi-restraints excluded: chain A residue 3443 ASN Chi-restraints excluded: chain A residue 3478 VAL Chi-restraints excluded: chain A residue 3530 ILE Chi-restraints excluded: chain A residue 3561 SER Chi-restraints excluded: chain A residue 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 3530 ILE Chi-restraints excluded: chain B residue 3561 SER Chi-restraints excluded: chain B residue 3596 SER Chi-restraints excluded: chain B residue 3658 VAL Chi-restraints excluded: chain B residue 3676 THR Chi-restraints excluded: chain B residue 3709 VAL Chi-restraints excluded: chain B residue 3716 ASP Chi-restraints excluded: chain B residue 3718 ASN 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 3561 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 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 3478 VAL Chi-restraints excluded: chain F residue 3561 SER Chi-restraints excluded: chain F residue 3676 THR Chi-restraints excluded: chain F residue 3709 VAL Chi-restraints excluded: chain F residue 3716 ASP Chi-restraints excluded: chain F residue 3718 ASN 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 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 23 optimal weight: 0.6980 chunk 210 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 202 optimal weight: 0.0270 chunk 0 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 chunk 171 optimal weight: 7.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 = 0.3251 r_free = 0.3251 target = 0.121135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.097832 restraints weight = 18504.994| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.47 r_work: 0.2874 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16870 Z= 0.103 Angle : 0.422 3.297 23366 Z= 0.231 Chirality : 0.045 0.142 2968 Planarity : 0.004 0.040 3024 Dihedral : 3.614 15.193 2394 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.65 % Allowed : 11.00 % Favored : 85.35 % 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: 1.90 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 1.09 (0.16), residues: 882 loop : 1.60 (0.17), residues: 1428 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 G3650 ARG 0.005 0.001 ARG C3523 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 504) hydrogen bonds : angle 5.50193 ( 1302) SS BOND : bond 0.00067 ( 21) SS BOND : angle 0.72479 ( 42) covalent geometry : bond 0.00245 (16849) covalent geometry : angle 0.42077 (23324) *********************** 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 257 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 186 time to evaluate : 1.771 Fit side-chains REVERT: A 3443 ASN cc_start: 0.8478 (m-40) cc_final: 0.8214 (p0) REVERT: A 3467 ASP cc_start: 0.7886 (t70) cc_final: 0.7501 (t70) REVERT: B 3467 ASP cc_start: 0.7890 (t70) cc_final: 0.7477 (t70) REVERT: B 3716 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7681 (m-30) REVERT: C 3506 SER cc_start: 0.8968 (p) cc_final: 0.8564 (t) REVERT: C 3668 ASP cc_start: 0.7761 (m-30) cc_final: 0.7444 (m-30) REVERT: C 3684 SER cc_start: 0.8814 (p) cc_final: 0.8606 (m) REVERT: D 3716 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7578 (m-30) REVERT: F 3530 ILE cc_start: 0.8992 (mt) cc_final: 0.8606 (pt) REVERT: F 3676 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8169 (p) REVERT: F 3716 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7685 (m-30) REVERT: G 3716 ASP cc_start: 0.8140 (t0) cc_final: 0.7728 (m-30) outliers start: 71 outliers final: 62 residues processed: 229 average time/residue: 0.2143 time to fit residues: 82.8728 Evaluate side-chains 238 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 172 time to evaluate : 1.816 ------------------------------------------------------------------------------- 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 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 3716 ASP 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 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 3687 ASN Chi-restraints excluded: chain D residue 3709 VAL Chi-restraints excluded: chain D residue 3716 ASP Chi-restraints excluded: chain D residue 3718 ASN Chi-restraints excluded: chain D residue 3727 VAL Chi-restraints excluded: chain E residue 3443 ASN Chi-restraints excluded: chain E residue 3478 VAL Chi-restraints excluded: chain E residue 3530 ILE Chi-restraints excluded: chain E residue 3535 SER Chi-restraints excluded: chain E residue 3561 SER Chi-restraints excluded: chain E residue 3596 SER Chi-restraints excluded: chain E residue 3676 THR Chi-restraints excluded: chain E residue 3709 VAL Chi-restraints excluded: chain E residue 3718 ASN Chi-restraints excluded: chain F residue 3478 VAL Chi-restraints excluded: chain F residue 3561 SER Chi-restraints excluded: chain F residue 3676 THR Chi-restraints excluded: chain F residue 3709 VAL Chi-restraints excluded: chain F residue 3716 ASP Chi-restraints excluded: chain F residue 3718 ASN 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 3658 VAL Chi-restraints excluded: chain G residue 3676 THR Chi-restraints excluded: chain G residue 3709 VAL Chi-restraints excluded: chain G residue 3718 ASN Chi-restraints excluded: chain G residue 3727 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 113 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 201 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.117632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.095235 restraints weight = 18659.819| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.47 r_work: 0.2834 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16870 Z= 0.168 Angle : 0.462 3.671 23366 Z= 0.253 Chirality : 0.047 0.143 2968 Planarity : 0.005 0.040 3024 Dihedral : 3.890 15.779 2394 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.01 % Allowed : 10.89 % Favored : 85.10 % 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: 1.67 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.74 (0.16), residues: 917 loop : 1.61 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A3683 PHE 0.009 0.001 PHE E3413 TYR 0.010 0.001 TYR G3650 ARG 0.006 0.001 ARG C3523 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 504) hydrogen bonds : angle 5.62036 ( 1302) SS BOND : bond 0.00164 ( 21) SS BOND : angle 0.86965 ( 42) covalent geometry : bond 0.00418 (16849) covalent geometry : angle 0.46136 (23324) *********************** 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 245 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 167 time to evaluate : 2.031 Fit side-chains REVERT: A 3443 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8217 (p0) REVERT: A 3467 ASP cc_start: 0.7889 (t70) cc_final: 0.7482 (t70) REVERT: B 3467 ASP cc_start: 0.7933 (t70) cc_final: 0.7488 (t70) REVERT: B 3716 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7651 (m-30) REVERT: C 3668 ASP cc_start: 0.7676 (m-30) cc_final: 0.7445 (m-30) REVERT: D 3716 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7555 (m-30) REVERT: E 3454 THR cc_start: 0.8694 (t) cc_final: 0.8445 (m) REVERT: F 3454 THR cc_start: 0.8747 (t) cc_final: 0.8461 (m) REVERT: F 3530 ILE cc_start: 0.8991 (mt) cc_final: 0.8616 (pt) REVERT: F 3579 ASP cc_start: 0.7676 (p0) cc_final: 0.7255 (t0) REVERT: F 3716 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7633 (m-30) outliers start: 78 outliers final: 68 residues processed: 217 average time/residue: 0.2245 time to fit residues: 82.2082 Evaluate side-chains 236 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 164 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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 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 3530 ILE Chi-restraints excluded: chain B residue 3561 SER Chi-restraints excluded: chain B residue 3596 SER Chi-restraints excluded: chain B residue 3658 VAL Chi-restraints excluded: chain B residue 3676 THR Chi-restraints excluded: chain B residue 3709 VAL Chi-restraints excluded: chain B residue 3716 ASP 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 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 D residue 3727 VAL Chi-restraints excluded: chain E residue 3443 ASN Chi-restraints excluded: chain E residue 3478 VAL Chi-restraints excluded: chain E residue 3530 ILE Chi-restraints excluded: chain E residue 3535 SER Chi-restraints excluded: chain E residue 3561 SER Chi-restraints excluded: chain E residue 3596 SER Chi-restraints excluded: chain E residue 3676 THR Chi-restraints excluded: chain E residue 3709 VAL Chi-restraints excluded: chain E residue 3716 ASP Chi-restraints excluded: chain F residue 3478 VAL Chi-restraints excluded: chain F residue 3561 SER Chi-restraints excluded: chain F residue 3676 THR Chi-restraints excluded: chain F residue 3709 VAL Chi-restraints excluded: chain F residue 3716 ASP Chi-restraints excluded: chain F residue 3718 ASN Chi-restraints excluded: chain F residue 3727 VAL Chi-restraints excluded: chain G residue 3406 THR Chi-restraints excluded: chain G residue 3478 VAL Chi-restraints excluded: chain G residue 3530 ILE Chi-restraints excluded: chain G residue 3533 ILE Chi-restraints excluded: chain G residue 3561 SER Chi-restraints excluded: chain G residue 3596 SER Chi-restraints excluded: chain G residue 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 3718 ASN Chi-restraints excluded: chain G residue 3727 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 66 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 191 optimal weight: 6.9990 chunk 152 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.3206 r_free = 0.3206 target = 0.117460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.095706 restraints weight = 18693.837| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.43 r_work: 0.2841 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16870 Z= 0.159 Angle : 0.456 3.688 23366 Z= 0.250 Chirality : 0.047 0.149 2968 Planarity : 0.005 0.042 3024 Dihedral : 3.897 15.602 2394 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.80 % Allowed : 11.36 % Favored : 84.84 % 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: 1.58 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.69 (0.16), residues: 917 loop : 1.53 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G3683 PHE 0.009 0.001 PHE E3413 TYR 0.010 0.001 TYR G3650 ARG 0.006 0.001 ARG C3523 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 504) hydrogen bonds : angle 5.61832 ( 1302) SS BOND : bond 0.00152 ( 21) SS BOND : angle 0.79847 ( 42) covalent geometry : bond 0.00395 (16849) covalent geometry : angle 0.45530 (23324) *********************** 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 240 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 166 time to evaluate : 1.815 Fit side-chains revert: symmetry clash REVERT: A 3443 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8272 (p0) REVERT: B 3467 ASP cc_start: 0.7957 (t70) cc_final: 0.7510 (t70) REVERT: B 3716 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7610 (m-30) REVERT: C 3668 ASP cc_start: 0.7705 (m-30) cc_final: 0.7424 (m-30) REVERT: D 3716 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7564 (m-30) REVERT: E 3454 THR cc_start: 0.8714 (t) cc_final: 0.8465 (m) REVERT: F 3454 THR cc_start: 0.8772 (t) cc_final: 0.8496 (m) REVERT: F 3530 ILE cc_start: 0.8998 (mt) cc_final: 0.8625 (pt) REVERT: F 3579 ASP cc_start: 0.7577 (p0) cc_final: 0.7194 (t0) REVERT: F 3716 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7616 (m-30) outliers start: 74 outliers final: 67 residues processed: 215 average time/residue: 0.2128 time to fit residues: 77.5399 Evaluate side-chains 232 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 161 time to evaluate : 1.793 ------------------------------------------------------------------------------- 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 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 3709 VAL Chi-restraints excluded: chain B residue 3716 ASP 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 3561 SER Chi-restraints excluded: chain D residue 3596 SER Chi-restraints excluded: chain D residue 3658 VAL Chi-restraints excluded: chain D residue 3676 THR Chi-restraints excluded: chain D residue 3687 ASN Chi-restraints excluded: chain D residue 3709 VAL Chi-restraints excluded: chain D residue 3716 ASP Chi-restraints excluded: chain D residue 3718 ASN Chi-restraints excluded: chain D residue 3727 VAL Chi-restraints excluded: chain E residue 3443 ASN Chi-restraints excluded: chain E residue 3478 VAL Chi-restraints excluded: chain E residue 3530 ILE Chi-restraints excluded: chain E residue 3535 SER Chi-restraints excluded: chain E residue 3561 SER Chi-restraints excluded: chain E residue 3596 SER Chi-restraints excluded: chain E residue 3676 THR Chi-restraints excluded: chain E residue 3709 VAL Chi-restraints excluded: chain E residue 3716 ASP Chi-restraints excluded: chain 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 3716 ASP Chi-restraints excluded: chain F residue 3718 ASN 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 3718 ASN Chi-restraints excluded: chain G residue 3727 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 136 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 200 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 213 optimal weight: 0.3980 chunk 114 optimal weight: 0.2980 chunk 201 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3199 r_free = 0.3199 target = 0.116984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.093572 restraints weight = 18825.415| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.46 r_work: 0.2834 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16870 Z= 0.164 Angle : 0.462 3.904 23366 Z= 0.253 Chirality : 0.047 0.171 2968 Planarity : 0.005 0.043 3024 Dihedral : 3.918 15.877 2394 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.85 % Allowed : 11.51 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.67 (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 C3683 PHE 0.009 0.001 PHE E3413 TYR 0.010 0.001 TYR G3650 ARG 0.006 0.001 ARG C3523 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 504) hydrogen bonds : angle 5.61824 ( 1302) SS BOND : bond 0.00155 ( 21) SS BOND : angle 0.79866 ( 42) covalent geometry : bond 0.00408 (16849) covalent geometry : angle 0.46147 (23324) ********************** 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 238 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 163 time to evaluate : 2.393 Fit side-chains REVERT: A 3443 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8276 (p0) REVERT: A 3467 ASP cc_start: 0.7898 (t70) cc_final: 0.7440 (t0) REVERT: B 3467 ASP cc_start: 0.7972 (t70) cc_final: 0.7527 (t70) REVERT: B 3716 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7667 (m-30) REVERT: C 3454 THR cc_start: 0.8693 (t) cc_final: 0.8391 (p) REVERT: C 3668 ASP cc_start: 0.7697 (m-30) cc_final: 0.7460 (m-30) REVERT: D 3716 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7607 (m-30) REVERT: E 3454 THR cc_start: 0.8749 (t) cc_final: 0.8495 (m) REVERT: F 3454 THR cc_start: 0.8813 (t) cc_final: 0.8536 (m) REVERT: F 3530 ILE cc_start: 0.9003 (mt) cc_final: 0.8641 (pt) REVERT: F 3579 ASP cc_start: 0.7596 (p0) cc_final: 0.7221 (t0) REVERT: F 3716 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7648 (m-30) outliers start: 75 outliers final: 67 residues processed: 215 average time/residue: 0.2415 time to fit residues: 88.4615 Evaluate side-chains 231 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 160 time to evaluate : 1.818 ------------------------------------------------------------------------------- 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 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 3506 SER 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 3716 ASP 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 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 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 3716 ASP Chi-restraints excluded: chain F residue 3718 ASN Chi-restraints excluded: chain F residue 3727 VAL Chi-restraints excluded: chain G residue 3406 THR Chi-restraints excluded: chain G residue 3478 VAL Chi-restraints excluded: chain G residue 3530 ILE Chi-restraints excluded: chain G residue 3533 ILE Chi-restraints excluded: chain G residue 3561 SER Chi-restraints excluded: chain G residue 3596 SER Chi-restraints excluded: chain G residue 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 3718 ASN Chi-restraints excluded: chain G residue 3727 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 0.3980 chunk 194 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 52 optimal weight: 0.0040 chunk 224 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 221 optimal weight: 0.6980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3687 ASN D3687 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.120244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.098530 restraints weight = 18565.751| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.54 r_work: 0.2868 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16870 Z= 0.099 Angle : 0.422 4.005 23366 Z= 0.230 Chirality : 0.045 0.147 2968 Planarity : 0.004 0.040 3024 Dihedral : 3.545 14.904 2394 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.34 % Allowed : 11.82 % Favored : 84.84 % 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 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.98 (0.16), residues: 854 loop : 1.54 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A3683 PHE 0.006 0.001 PHE E3413 TYR 0.008 0.001 TYR G3650 ARG 0.006 0.001 ARG C3523 Details of bonding type rmsd hydrogen bonds : bond 0.03093 ( 504) hydrogen bonds : angle 5.42406 ( 1302) SS BOND : bond 0.00083 ( 21) SS BOND : angle 0.63107 ( 42) covalent geometry : bond 0.00234 (16849) covalent geometry : angle 0.42130 (23324) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7536.85 seconds wall clock time: 132 minutes 14.03 seconds (7934.03 seconds total)