Starting phenix.real_space_refine on Thu Sep 18 12:03:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9flu_50539/09_2025/9flu_50539.cif Found real_map, /net/cci-nas-00/data/ceres_data/9flu_50539/09_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_50539/09_2025/9flu_50539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9flu_50539/09_2025/9flu_50539.map" model { file = "/net/cci-nas-00/data/ceres_data/9flu_50539/09_2025/9flu_50539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9flu_50539/09_2025/9flu_50539.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.159 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C, D, E, F, G Time building chain proxies: 2.33, per 1000 atoms: 0.14 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 B3416 " - pdb=" SG CYS B3555 " distance=2.05 Simple disulfide: pdb=" SG CYS C3416 " - pdb=" SG CYS C3555 " distance=2.05 Simple disulfide: pdb=" SG CYS D3416 " - pdb=" SG CYS D3555 " distance=2.05 Simple disulfide: pdb=" SG CYS E3416 " - pdb=" SG CYS E3555 " distance=2.05 Simple disulfide: pdb=" SG CYS F3416 " - pdb=" SG CYS F3555 " distance=2.05 Simple disulfide: pdb=" SG CYS G3416 " - pdb=" SG CYS G3555 " distance=2.05 Simple disulfide: pdb=" SG CYS B3498 " - pdb=" SG CYS B3638 " distance=2.03 Simple disulfide: pdb=" SG CYS C3498 " - pdb=" SG CYS C3638 " distance=2.03 Simple disulfide: pdb=" SG CYS D3498 " - pdb=" SG CYS D3638 " distance=2.03 Simple disulfide: pdb=" SG CYS E3498 " - pdb=" SG CYS E3638 " distance=2.03 Simple disulfide: pdb=" SG CYS F3498 " - pdb=" SG CYS F3638 " distance=2.03 Simple disulfide: pdb=" SG CYS G3498 " - pdb=" SG CYS G3638 " distance=2.03 Simple disulfide: pdb=" SG CYS B3583 " - pdb=" SG CYS B3720 " distance=2.04 Simple disulfide: pdb=" SG CYS C3583 " - pdb=" SG CYS C3720 " distance=2.04 Simple disulfide: pdb=" SG CYS D3583 " - pdb=" SG CYS D3720 " distance=2.04 Simple disulfide: pdb=" SG CYS E3583 " - pdb=" SG CYS E3720 " distance=2.04 Simple disulfide: pdb=" SG CYS F3583 " - pdb=" SG CYS F3720 " distance=2.04 Simple disulfide: pdb=" SG CYS G3583 " - pdb=" SG CYS G3720 " 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: 1.32 Conformation dependent library (CDL) restraints added in 775.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.85 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: 3.59 Time building geometry restraints manager: 1.77 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 15.650 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.800 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (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 ARG 0.004 0.002 ARG E3523 TYR 0.037 0.006 TYR B3540 PHE 0.056 0.009 PHE B3413 TRP 0.031 0.007 TRP B3683 Details of bonding type rmsd covalent geometry : bond 0.01786 (16849) covalent geometry : angle 1.51506 (23324) SS BOND : bond 0.01100 ( 21) SS BOND : angle 3.88376 ( 42) hydrogen bonds : bond 0.18749 ( 504) hydrogen bonds : angle 9.06989 ( 1302) *********************** 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 : 0.600 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: 0.0825 time to fit residues: 49.6265 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 : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3326 r_free = 0.3326 target = 0.127247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.102576 restraints weight = 17909.449| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.63 r_work: 0.2990 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2342 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= 0.129 Angle : 0.508 3.700 23366 Z= 0.287 Chirality : 0.047 0.146 2968 Planarity : 0.005 0.033 3024 Dihedral : 4.378 14.754 2394 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.97 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.86 (0.16), residues: 868 loop : 1.70 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F3523 TYR 0.011 0.001 TYR F3650 PHE 0.011 0.001 PHE B3413 TRP 0.020 0.002 TRP C3683 Details of bonding type rmsd covalent geometry : bond 0.00294 (16849) covalent geometry : angle 0.50558 (23324) SS BOND : bond 0.00437 ( 21) SS BOND : angle 1.33952 ( 42) hydrogen bonds : bond 0.04180 ( 504) hydrogen bonds : angle 6.54233 ( 1302) *********************** 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 317 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 265 time to evaluate : 0.687 Fit side-chains REVERT: A 3416 CYS cc_start: 0.8251 (m) cc_final: 0.8003 (m) REVERT: A 3467 ASP cc_start: 0.7991 (t0) cc_final: 0.7619 (t0) REVERT: B 3467 ASP cc_start: 0.7902 (t70) cc_final: 0.7497 (t0) REVERT: B 3687 ASN cc_start: 0.9091 (OUTLIER) cc_final: 0.8757 (t0) REVERT: C 3649 VAL cc_start: 0.8618 (t) cc_final: 0.8362 (m) REVERT: D 3649 VAL cc_start: 0.8485 (t) cc_final: 0.8236 (m) REVERT: E 3416 CYS cc_start: 0.8020 (m) cc_final: 0.7750 (m) REVERT: E 3467 ASP cc_start: 0.8090 (t0) cc_final: 0.7673 (p0) REVERT: E 3523 ARG cc_start: 0.8383 (mtt-85) cc_final: 0.8120 (mtt90) REVERT: F 3530 ILE cc_start: 0.8848 (mt) cc_final: 0.8520 (pt) REVERT: G 3467 ASP cc_start: 0.8100 (t0) cc_final: 0.7556 (p0) outliers start: 52 outliers final: 35 residues processed: 288 average time/residue: 0.0819 time to fit residues: 40.5005 Evaluate side-chains 212 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3428 VAL Chi-restraints excluded: chain A residue 3530 ILE Chi-restraints excluded: chain A residue 3561 SER Chi-restraints excluded: chain A residue 3709 VAL Chi-restraints excluded: chain A residue 3718 ASN Chi-restraints excluded: chain B residue 3406 THR Chi-restraints excluded: chain B residue 3530 ILE Chi-restraints excluded: chain B residue 3561 SER Chi-restraints excluded: chain B residue 3687 ASN Chi-restraints excluded: chain B residue 3709 VAL Chi-restraints excluded: chain B residue 3718 ASN Chi-restraints excluded: chain C residue 3530 ILE Chi-restraints excluded: chain C residue 3561 SER Chi-restraints excluded: chain C residue 3709 VAL Chi-restraints excluded: chain C residue 3718 ASN Chi-restraints excluded: chain D residue 3419 ASP Chi-restraints excluded: chain D residue 3443 ASN Chi-restraints excluded: chain D residue 3530 ILE Chi-restraints excluded: chain D residue 3561 SER Chi-restraints excluded: chain D residue 3687 ASN Chi-restraints excluded: chain D residue 3709 VAL Chi-restraints excluded: chain D residue 3718 ASN Chi-restraints excluded: chain E residue 3419 ASP Chi-restraints excluded: chain E residue 3443 ASN Chi-restraints excluded: chain E residue 3530 ILE Chi-restraints excluded: chain E residue 3561 SER Chi-restraints excluded: chain E residue 3709 VAL Chi-restraints excluded: chain 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 60 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 153 optimal weight: 0.0060 chunk 121 optimal weight: 0.7980 chunk 211 optimal weight: 0.0970 chunk 126 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 157 optimal weight: 0.3980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3636 ASN A3687 ASN B3687 ASN C3687 ASN D3687 ASN E3636 ASN G3636 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.126780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.103121 restraints weight = 18264.571| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.54 r_work: 0.2978 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 16870 Z= 0.091 Angle : 0.442 3.473 23366 Z= 0.247 Chirality : 0.045 0.142 2968 Planarity : 0.004 0.043 3024 Dihedral : 3.800 14.681 2394 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.21 % Allowed : 10.07 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 1.22 (0.16), residues: 819 loop : 1.62 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C3523 TYR 0.009 0.001 TYR G3650 PHE 0.006 0.001 PHE F3413 TRP 0.013 0.001 TRP E3434 Details of bonding type rmsd covalent geometry : bond 0.00201 (16849) covalent geometry : angle 0.44090 (23324) SS BOND : bond 0.00071 ( 21) SS BOND : angle 0.75936 ( 42) hydrogen bonds : bond 0.03395 ( 504) hydrogen bonds : angle 5.88902 ( 1302) *********************** 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 266 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 0.395 Fit side-chains REVERT: A 3416 CYS cc_start: 0.8091 (m) cc_final: 0.7845 (m) REVERT: A 3467 ASP cc_start: 0.7856 (t70) cc_final: 0.7531 (t70) REVERT: A 3506 SER cc_start: 0.8812 (p) cc_final: 0.8541 (t) REVERT: A 3716 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7995 (m-30) REVERT: B 3467 ASP cc_start: 0.7811 (t70) cc_final: 0.7394 (t70) REVERT: B 3506 SER cc_start: 0.8967 (p) cc_final: 0.8675 (t) REVERT: B 3551 ASN cc_start: 0.7972 (p0) cc_final: 0.7687 (p0) REVERT: B 3716 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7830 (m-30) REVERT: C 3506 SER cc_start: 0.8824 (p) cc_final: 0.8606 (t) REVERT: D 3443 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8263 (p0) REVERT: D 3716 ASP cc_start: 0.8032 (t0) cc_final: 0.7817 (m-30) REVERT: E 3416 CYS cc_start: 0.7888 (m) cc_final: 0.7619 (m) REVERT: E 3467 ASP cc_start: 0.7926 (t0) cc_final: 0.7483 (p0) REVERT: E 3506 SER cc_start: 0.8801 (p) cc_final: 0.8594 (t) REVERT: E 3523 ARG cc_start: 0.8448 (mtt-85) cc_final: 0.8120 (mtt90) REVERT: F 3530 ILE cc_start: 0.8946 (mt) cc_final: 0.8611 (pt) REVERT: F 3716 ASP cc_start: 0.8042 (t0) cc_final: 0.7714 (m-30) REVERT: G 3467 ASP cc_start: 0.7862 (t0) cc_final: 0.7481 (p0) outliers start: 43 outliers final: 30 residues processed: 241 average time/residue: 0.0853 time to fit residues: 34.7238 Evaluate side-chains 202 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3428 VAL Chi-restraints excluded: chain A residue 3431 SER Chi-restraints excluded: chain A residue 3530 ILE Chi-restraints excluded: chain A residue 3596 SER Chi-restraints excluded: chain A residue 3687 ASN Chi-restraints excluded: chain A residue 3709 VAL Chi-restraints excluded: chain A residue 3716 ASP Chi-restraints excluded: chain B residue 3535 SER Chi-restraints excluded: chain B residue 3596 SER Chi-restraints excluded: chain B residue 3716 ASP Chi-restraints excluded: chain B residue 3718 ASN Chi-restraints excluded: chain C residue 3535 SER Chi-restraints excluded: chain C residue 3596 SER Chi-restraints excluded: chain C residue 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 3718 ASN Chi-restraints excluded: chain E residue 3443 ASN Chi-restraints excluded: chain E residue 3535 SER Chi-restraints excluded: chain E residue 3596 SER Chi-restraints excluded: chain E residue 3677 VAL Chi-restraints excluded: chain E residue 3709 VAL Chi-restraints excluded: chain E residue 3718 ASN Chi-restraints excluded: chain F residue 3535 SER Chi-restraints excluded: chain F residue 3596 SER Chi-restraints excluded: chain F residue 3624 SER Chi-restraints excluded: chain F residue 3718 ASN Chi-restraints excluded: chain G residue 3406 THR Chi-restraints excluded: chain G residue 3596 SER 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 197 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 177 optimal weight: 0.0170 overall best weight: 0.8220 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.125787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.100573 restraints weight = 18193.873| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.79 r_work: 0.2918 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16870 Z= 0.124 Angle : 0.447 3.578 23366 Z= 0.247 Chirality : 0.046 0.143 2968 Planarity : 0.004 0.038 3024 Dihedral : 3.877 15.850 2394 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.13 % Allowed : 10.53 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 1.06 (0.16), residues: 889 loop : 1.65 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C3523 TYR 0.009 0.001 TYR G3650 PHE 0.008 0.001 PHE E3413 TRP 0.016 0.002 TRP B3434 Details of bonding type rmsd covalent geometry : bond 0.00299 (16849) covalent geometry : angle 0.44565 (23324) SS BOND : bond 0.00087 ( 21) SS BOND : angle 0.80885 ( 42) hydrogen bonds : bond 0.03480 ( 504) hydrogen bonds : angle 5.69912 ( 1302) *********************** 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 252 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 191 time to evaluate : 0.568 Fit side-chains REVERT: A 3416 CYS cc_start: 0.8372 (m) cc_final: 0.8135 (m) REVERT: A 3467 ASP cc_start: 0.7921 (t70) cc_final: 0.7455 (t70) REVERT: B 3467 ASP cc_start: 0.7851 (t70) cc_final: 0.7355 (t70) REVERT: B 3506 SER cc_start: 0.9002 (p) cc_final: 0.8735 (t) REVERT: B 3551 ASN cc_start: 0.8158 (p0) cc_final: 0.7788 (p0) REVERT: B 3687 ASN cc_start: 0.9011 (OUTLIER) cc_final: 0.8666 (t0) REVERT: C 3506 SER cc_start: 0.8968 (p) cc_final: 0.8649 (t) REVERT: D 3443 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8375 (p0) REVERT: E 3416 CYS cc_start: 0.8234 (m) cc_final: 0.7974 (m) REVERT: E 3467 ASP cc_start: 0.7868 (t0) cc_final: 0.7542 (p0) REVERT: E 3506 SER cc_start: 0.8943 (p) cc_final: 0.8652 (t) REVERT: F 3443 ASN cc_start: 0.8446 (m-40) cc_final: 0.8186 (p0) REVERT: F 3530 ILE cc_start: 0.8983 (mt) cc_final: 0.8546 (pt) REVERT: F 3716 ASP cc_start: 0.8191 (t0) cc_final: 0.7979 (m-30) REVERT: G 3443 ASN cc_start: 0.8627 (m-40) cc_final: 0.8420 (p0) REVERT: G 3467 ASP cc_start: 0.7814 (t0) cc_final: 0.7613 (p0) REVERT: G 3540 TYR cc_start: 0.9100 (t80) cc_final: 0.8707 (t80) REVERT: G 3716 ASP cc_start: 0.8209 (t0) cc_final: 0.7751 (m-30) outliers start: 61 outliers final: 45 residues processed: 222 average time/residue: 0.0875 time to fit residues: 32.9523 Evaluate side-chains 212 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 3709 VAL Chi-restraints excluded: chain A residue 3718 ASN Chi-restraints excluded: chain B residue 3406 THR Chi-restraints excluded: chain B residue 3535 SER Chi-restraints excluded: chain B residue 3561 SER Chi-restraints excluded: chain B residue 3596 SER Chi-restraints excluded: chain B residue 3687 ASN Chi-restraints excluded: chain B residue 3709 VAL Chi-restraints excluded: chain B residue 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 3443 ASN Chi-restraints excluded: chain D residue 3535 SER Chi-restraints excluded: chain D residue 3561 SER Chi-restraints excluded: chain D residue 3596 SER Chi-restraints excluded: chain D residue 3658 VAL Chi-restraints excluded: chain D residue 3687 ASN Chi-restraints excluded: chain D residue 3709 VAL Chi-restraints excluded: chain D residue 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 176 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D3687 ASN E3687 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.115399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.093536 restraints weight = 18938.726| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.38 r_work: 0.2816 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 16870 Z= 0.271 Angle : 0.556 5.012 23366 Z= 0.307 Chirality : 0.050 0.146 2968 Planarity : 0.005 0.047 3024 Dihedral : 4.677 18.297 2394 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.80 % Allowed : 10.07 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.37 (0.16), residues: 931 loop : 1.40 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C3523 TYR 0.014 0.002 TYR G3650 PHE 0.014 0.002 PHE E3413 TRP 0.013 0.002 TRP B3434 Details of bonding type rmsd covalent geometry : bond 0.00680 (16849) covalent geometry : angle 0.55393 (23324) SS BOND : bond 0.00165 ( 21) SS BOND : angle 1.25592 ( 42) hydrogen bonds : bond 0.04536 ( 504) hydrogen bonds : angle 6.14436 ( 1302) *********************** 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 225 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 151 time to evaluate : 0.426 Fit side-chains REVERT: A 3467 ASP cc_start: 0.7958 (t70) cc_final: 0.7469 (t0) REVERT: B 3467 ASP cc_start: 0.7992 (t70) cc_final: 0.7432 (t70) REVERT: B 3716 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: C 3454 THR cc_start: 0.8771 (t) cc_final: 0.8500 (p) REVERT: C 3475 ASP cc_start: 0.7987 (m-30) cc_final: 0.7784 (m-30) REVERT: D 3716 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7765 (m-30) REVERT: E 3454 THR cc_start: 0.8773 (t) cc_final: 0.8415 (p) REVERT: E 3467 ASP cc_start: 0.8007 (t0) cc_final: 0.7576 (p0) REVERT: E 3718 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8206 (p0) REVERT: F 3409 VAL cc_start: 0.9035 (t) cc_final: 0.8782 (m) REVERT: F 3530 ILE cc_start: 0.8933 (mt) cc_final: 0.8600 (pt) REVERT: F 3579 ASP cc_start: 0.7665 (p0) cc_final: 0.7344 (t0) REVERT: F 3716 ASP cc_start: 0.8165 (t0) cc_final: 0.7654 (m-30) REVERT: G 3443 ASN cc_start: 0.8627 (m-40) cc_final: 0.8380 (p0) REVERT: G 3467 ASP cc_start: 0.7865 (t0) cc_final: 0.7571 (p0) outliers start: 74 outliers final: 59 residues processed: 204 average time/residue: 0.0912 time to fit residues: 31.2888 Evaluate side-chains 191 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 129 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3406 THR Chi-restraints excluded: chain A residue 3428 VAL Chi-restraints excluded: chain A residue 3431 SER Chi-restraints excluded: chain A residue 3443 ASN Chi-restraints excluded: chain A residue 3478 VAL Chi-restraints excluded: chain A residue 3530 ILE Chi-restraints excluded: chain A residue 3561 SER Chi-restraints excluded: chain A residue 3676 THR Chi-restraints excluded: chain A residue 3709 VAL Chi-restraints excluded: chain A residue 3718 ASN Chi-restraints excluded: chain B residue 3406 THR Chi-restraints excluded: chain B residue 3478 VAL Chi-restraints excluded: chain B residue 3530 ILE Chi-restraints excluded: chain B residue 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 3676 THR Chi-restraints excluded: chain B residue 3709 VAL Chi-restraints excluded: chain B residue 3716 ASP 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 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 3711 THR Chi-restraints excluded: chain D residue 3716 ASP Chi-restraints excluded: chain D residue 3718 ASN Chi-restraints excluded: chain E residue 3442 SER 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 3687 ASN 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 3718 ASN Chi-restraints excluded: chain G residue 3406 THR Chi-restraints excluded: chain G residue 3530 ILE Chi-restraints excluded: chain G residue 3533 ILE Chi-restraints excluded: chain G residue 3561 SER Chi-restraints excluded: chain G residue 3596 SER Chi-restraints excluded: chain G residue 3658 VAL Chi-restraints excluded: chain G residue 3676 THR Chi-restraints excluded: chain G residue 3709 VAL Chi-restraints excluded: chain G residue 3718 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 147 optimal weight: 0.0070 chunk 1 optimal weight: 5.9990 chunk 153 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3687 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 = 0.3228 r_free = 0.3228 target = 0.119139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.097508 restraints weight = 18646.302| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.47 r_work: 0.2854 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16870 Z= 0.120 Angle : 0.439 3.382 23366 Z= 0.242 Chirality : 0.046 0.151 2968 Planarity : 0.005 0.044 3024 Dihedral : 3.901 16.860 2394 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.24 % Allowed : 11.15 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.77 (0.16), residues: 882 loop : 1.41 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C3523 TYR 0.009 0.001 TYR G3650 PHE 0.007 0.001 PHE F3413 TRP 0.015 0.002 TRP B3434 Details of bonding type rmsd covalent geometry : bond 0.00291 (16849) covalent geometry : angle 0.43793 (23324) SS BOND : bond 0.00177 ( 21) SS BOND : angle 0.74163 ( 42) hydrogen bonds : bond 0.03482 ( 504) hydrogen bonds : angle 5.77868 ( 1302) *********************** 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 243 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 180 time to evaluate : 0.606 Fit side-chains REVERT: A 3467 ASP cc_start: 0.7905 (t70) cc_final: 0.7492 (t0) REVERT: B 3467 ASP cc_start: 0.7964 (t70) cc_final: 0.7456 (t70) REVERT: B 3687 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8814 (t0) REVERT: B 3716 ASP cc_start: 0.8172 (m-30) cc_final: 0.7625 (m-30) REVERT: C 3454 THR cc_start: 0.8683 (t) cc_final: 0.8391 (p) REVERT: C 3619 MET cc_start: 0.8475 (ttm) cc_final: 0.8247 (ttp) REVERT: D 3716 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7705 (m-30) REVERT: E 3454 THR cc_start: 0.8694 (t) cc_final: 0.8452 (m) REVERT: E 3467 ASP cc_start: 0.7849 (t0) cc_final: 0.7590 (p0) REVERT: F 3454 THR cc_start: 0.8738 (t) cc_final: 0.8458 (m) REVERT: F 3530 ILE cc_start: 0.8968 (mt) cc_final: 0.8597 (pt) REVERT: F 3579 ASP cc_start: 0.7484 (p0) cc_final: 0.7256 (t0) REVERT: F 3716 ASP cc_start: 0.8121 (t0) cc_final: 0.7660 (m-30) outliers start: 63 outliers final: 49 residues processed: 220 average time/residue: 0.0821 time to fit residues: 30.8097 Evaluate side-chains 218 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 167 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3428 VAL Chi-restraints excluded: chain A residue 3431 SER Chi-restraints excluded: chain A residue 3530 ILE Chi-restraints excluded: chain A residue 3561 SER Chi-restraints excluded: chain A residue 3596 SER Chi-restraints excluded: chain A residue 3676 THR Chi-restraints excluded: chain A residue 3709 VAL Chi-restraints excluded: chain B residue 3406 THR Chi-restraints excluded: chain B residue 3561 SER Chi-restraints excluded: chain B residue 3596 SER Chi-restraints excluded: chain B residue 3658 VAL Chi-restraints excluded: chain B residue 3676 THR Chi-restraints excluded: chain B residue 3687 ASN Chi-restraints excluded: chain B residue 3709 VAL Chi-restraints excluded: chain B residue 3727 VAL Chi-restraints excluded: chain C residue 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 D residue 3535 SER Chi-restraints excluded: chain D residue 3561 SER Chi-restraints excluded: chain D residue 3596 SER Chi-restraints excluded: chain D residue 3658 VAL Chi-restraints excluded: chain D residue 3676 THR Chi-restraints excluded: chain D residue 3687 ASN Chi-restraints excluded: chain D residue 3709 VAL Chi-restraints excluded: chain D residue 3716 ASP Chi-restraints excluded: chain D residue 3718 ASN Chi-restraints excluded: chain E residue 3443 ASN Chi-restraints excluded: chain E residue 3478 VAL Chi-restraints excluded: chain E residue 3530 ILE Chi-restraints excluded: chain E residue 3535 SER Chi-restraints excluded: chain E residue 3561 SER Chi-restraints excluded: chain E residue 3596 SER Chi-restraints excluded: chain E residue 3676 THR Chi-restraints excluded: chain E residue 3709 VAL 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 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 3727 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 65 optimal weight: 6.9990 chunk 217 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 202 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3687 ASN C3687 ASN D3687 ASN G3687 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.113335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.090073 restraints weight = 19085.634| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.43 r_work: 0.2777 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 16870 Z= 0.313 Angle : 0.577 5.276 23366 Z= 0.318 Chirality : 0.052 0.160 2968 Planarity : 0.005 0.052 3024 Dihedral : 4.714 19.018 2394 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.96 % Allowed : 11.82 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.23 (0.16), residues: 896 loop : 0.99 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C3523 TYR 0.015 0.002 TYR G3650 PHE 0.015 0.002 PHE E3413 TRP 0.015 0.002 TRP B3434 Details of bonding type rmsd covalent geometry : bond 0.00789 (16849) covalent geometry : angle 0.57537 (23324) SS BOND : bond 0.00187 ( 21) SS BOND : angle 1.08553 ( 42) hydrogen bonds : bond 0.04766 ( 504) hydrogen bonds : angle 6.17815 ( 1302) *********************** 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 209 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 132 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 3467 ASP cc_start: 0.7975 (t70) cc_final: 0.7551 (t70) REVERT: B 3467 ASP cc_start: 0.8094 (t70) cc_final: 0.7625 (t70) REVERT: B 3716 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7658 (m-30) REVERT: C 3454 THR cc_start: 0.8813 (t) cc_final: 0.8522 (p) REVERT: D 3716 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7695 (m-30) REVERT: E 3467 ASP cc_start: 0.8151 (t0) cc_final: 0.7494 (p0) REVERT: F 3454 THR cc_start: 0.8742 (t) cc_final: 0.8539 (p) REVERT: F 3530 ILE cc_start: 0.8937 (mt) cc_final: 0.8264 (tt) outliers start: 77 outliers final: 67 residues processed: 195 average time/residue: 0.0845 time to fit residues: 27.6885 Evaluate side-chains 193 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 124 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 A residue 3727 VAL Chi-restraints excluded: chain B residue 3406 THR Chi-restraints excluded: chain B residue 3478 VAL Chi-restraints excluded: chain B residue 3530 ILE Chi-restraints excluded: chain B residue 3561 SER Chi-restraints excluded: chain B residue 3658 VAL Chi-restraints excluded: chain B residue 3676 THR Chi-restraints excluded: chain B residue 3709 VAL Chi-restraints excluded: chain B residue 3716 ASP Chi-restraints excluded: chain B residue 3727 VAL Chi-restraints excluded: chain C residue 3478 VAL Chi-restraints excluded: chain C residue 3530 ILE Chi-restraints excluded: chain C residue 3535 SER Chi-restraints excluded: chain C residue 3561 SER Chi-restraints excluded: chain C residue 3596 SER Chi-restraints excluded: chain C residue 3626 ASP Chi-restraints excluded: chain C residue 3687 ASN Chi-restraints excluded: chain C residue 3709 VAL Chi-restraints excluded: chain C residue 3711 THR Chi-restraints excluded: chain C residue 3716 ASP Chi-restraints excluded: chain C residue 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 3711 THR 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 3711 THR 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 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 3658 VAL Chi-restraints excluded: chain G residue 3676 THR Chi-restraints excluded: chain G residue 3709 VAL Chi-restraints excluded: chain G residue 3711 THR Chi-restraints excluded: chain G residue 3727 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 106 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 209 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 G3687 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.115124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.093340 restraints weight = 18984.499| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.41 r_work: 0.2801 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16870 Z= 0.202 Angle : 0.493 4.286 23366 Z= 0.272 Chirality : 0.048 0.149 2968 Planarity : 0.005 0.048 3024 Dihedral : 4.346 17.665 2394 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.01 % Allowed : 12.23 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.24 (0.16), residues: 917 loop : 1.08 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C3523 TYR 0.012 0.001 TYR G3650 PHE 0.011 0.002 PHE E3413 TRP 0.016 0.002 TRP B3434 Details of bonding type rmsd covalent geometry : bond 0.00506 (16849) covalent geometry : angle 0.49228 (23324) SS BOND : bond 0.00142 ( 21) SS BOND : angle 0.85784 ( 42) hydrogen bonds : bond 0.04072 ( 504) hydrogen bonds : angle 5.95299 ( 1302) *********************** 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 216 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 138 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 3467 ASP cc_start: 0.7996 (t70) cc_final: 0.7551 (t70) REVERT: B 3467 ASP cc_start: 0.8098 (t70) cc_final: 0.7622 (t70) REVERT: B 3716 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: C 3454 THR cc_start: 0.8766 (t) cc_final: 0.8447 (p) REVERT: C 3619 MET cc_start: 0.8500 (ttm) cc_final: 0.8261 (ttp) REVERT: D 3716 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7693 (m-30) REVERT: E 3467 ASP cc_start: 0.8111 (t0) cc_final: 0.7778 (t0) REVERT: F 3454 THR cc_start: 0.8738 (t) cc_final: 0.8486 (m) REVERT: F 3530 ILE cc_start: 0.8954 (mt) cc_final: 0.8636 (pt) REVERT: F 3579 ASP cc_start: 0.7607 (p0) cc_final: 0.7327 (t0) REVERT: G 3454 THR cc_start: 0.8780 (t) cc_final: 0.8447 (p) outliers start: 78 outliers final: 72 residues processed: 197 average time/residue: 0.0837 time to fit residues: 27.8785 Evaluate side-chains 210 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 136 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 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 3684 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 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 3711 THR Chi-restraints excluded: chain B residue 3716 ASP Chi-restraints excluded: chain B residue 3727 VAL Chi-restraints excluded: chain C residue 3478 VAL Chi-restraints excluded: chain C residue 3530 ILE Chi-restraints excluded: chain C residue 3535 SER Chi-restraints excluded: chain C residue 3561 SER Chi-restraints excluded: chain C residue 3596 SER Chi-restraints excluded: chain C residue 3626 ASP Chi-restraints excluded: chain C residue 3687 ASN Chi-restraints excluded: chain C residue 3709 VAL Chi-restraints excluded: chain C residue 3711 THR Chi-restraints excluded: chain C residue 3716 ASP Chi-restraints excluded: chain D residue 3478 VAL Chi-restraints excluded: chain D residue 3530 ILE 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 3627 THR 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 3711 THR Chi-restraints excluded: chain D residue 3716 ASP Chi-restraints excluded: chain D residue 3718 ASN Chi-restraints excluded: chain D residue 3727 VAL Chi-restraints excluded: chain E residue 3443 ASN Chi-restraints excluded: chain E residue 3478 VAL Chi-restraints excluded: chain E residue 3530 ILE Chi-restraints excluded: chain E residue 3535 SER Chi-restraints excluded: chain E residue 3561 SER Chi-restraints excluded: chain E residue 3596 SER Chi-restraints excluded: chain E residue 3676 THR Chi-restraints excluded: chain E residue 3709 VAL Chi-restraints excluded: chain F residue 3478 VAL Chi-restraints excluded: chain F residue 3561 SER Chi-restraints excluded: chain F residue 3596 SER Chi-restraints excluded: chain F residue 3676 THR Chi-restraints excluded: chain F residue 3709 VAL Chi-restraints excluded: chain F residue 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 3658 VAL Chi-restraints excluded: chain G residue 3676 THR Chi-restraints excluded: chain G residue 3687 ASN 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 89 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 164 optimal weight: 0.3980 chunk 125 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 G3687 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.117724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.096473 restraints weight = 18750.372| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.47 r_work: 0.2841 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3883 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= 0.124 Angle : 0.443 3.588 23366 Z= 0.243 Chirality : 0.046 0.144 2968 Planarity : 0.005 0.044 3024 Dihedral : 3.945 16.927 2394 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.55 % Allowed : 12.49 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.56 (0.16), residues: 854 loop : 1.17 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C3523 TYR 0.009 0.001 TYR G3650 PHE 0.007 0.001 PHE F3413 TRP 0.018 0.002 TRP B3434 Details of bonding type rmsd covalent geometry : bond 0.00302 (16849) covalent geometry : angle 0.44207 (23324) SS BOND : bond 0.00102 ( 21) SS BOND : angle 0.70209 ( 42) hydrogen bonds : bond 0.03504 ( 504) hydrogen bonds : angle 5.71545 ( 1302) *********************** 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 236 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 167 time to evaluate : 0.617 Fit side-chains REVERT: A 3467 ASP cc_start: 0.7968 (t70) cc_final: 0.7242 (t70) REVERT: B 3467 ASP cc_start: 0.8088 (t70) cc_final: 0.7622 (t70) REVERT: B 3716 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7579 (m-30) REVERT: C 3454 THR cc_start: 0.8713 (t) cc_final: 0.8433 (m) REVERT: D 3716 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7690 (m-30) REVERT: F 3454 THR cc_start: 0.8814 (t) cc_final: 0.8564 (m) REVERT: F 3530 ILE cc_start: 0.8994 (mt) cc_final: 0.8615 (pt) REVERT: G 3454 THR cc_start: 0.8812 (t) cc_final: 0.8576 (m) REVERT: G 3687 ASN cc_start: 0.9059 (OUTLIER) cc_final: 0.8786 (t0) outliers start: 69 outliers final: 58 residues processed: 217 average time/residue: 0.0842 time to fit residues: 31.1110 Evaluate side-chains 209 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 148 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3428 VAL Chi-restraints excluded: chain A residue 3431 SER Chi-restraints excluded: chain A residue 3478 VAL Chi-restraints excluded: chain A residue 3530 ILE Chi-restraints excluded: chain A residue 3561 SER Chi-restraints excluded: chain A residue 3596 SER Chi-restraints excluded: chain A residue 3676 THR Chi-restraints excluded: chain A residue 3709 VAL Chi-restraints excluded: chain A residue 3718 ASN Chi-restraints excluded: chain A residue 3727 VAL Chi-restraints excluded: chain B residue 3478 VAL Chi-restraints excluded: chain B residue 3561 SER Chi-restraints excluded: chain B residue 3596 SER Chi-restraints excluded: chain B residue 3658 VAL Chi-restraints excluded: chain B residue 3676 THR Chi-restraints excluded: chain B residue 3709 VAL Chi-restraints excluded: chain B residue 3716 ASP Chi-restraints excluded: chain B residue 3727 VAL Chi-restraints excluded: chain C residue 3478 VAL Chi-restraints excluded: chain C residue 3530 ILE Chi-restraints excluded: chain C residue 3535 SER Chi-restraints excluded: chain C residue 3561 SER Chi-restraints excluded: chain C residue 3596 SER Chi-restraints excluded: chain C residue 3626 ASP Chi-restraints excluded: chain C residue 3709 VAL Chi-restraints excluded: chain C residue 3716 ASP Chi-restraints excluded: chain C residue 3718 ASN Chi-restraints excluded: chain D residue 3535 SER Chi-restraints excluded: chain D residue 3561 SER Chi-restraints excluded: chain D residue 3596 SER Chi-restraints excluded: chain D residue 3658 VAL Chi-restraints excluded: chain D residue 3676 THR Chi-restraints excluded: chain D residue 3687 ASN Chi-restraints excluded: chain D residue 3709 VAL Chi-restraints excluded: chain D residue 3716 ASP Chi-restraints excluded: chain D residue 3718 ASN Chi-restraints excluded: chain D residue 3727 VAL Chi-restraints excluded: chain E residue 3478 VAL Chi-restraints excluded: chain E residue 3530 ILE Chi-restraints excluded: chain E residue 3535 SER Chi-restraints excluded: chain E residue 3561 SER Chi-restraints excluded: chain E residue 3596 SER Chi-restraints excluded: chain E residue 3676 THR Chi-restraints excluded: chain E residue 3709 VAL Chi-restraints excluded: chain E residue 3727 VAL Chi-restraints excluded: chain F residue 3478 VAL Chi-restraints excluded: chain F residue 3561 SER Chi-restraints excluded: chain F residue 3596 SER Chi-restraints excluded: chain F residue 3676 THR Chi-restraints excluded: chain F residue 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 3687 ASN 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 65 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 218 optimal weight: 0.5980 chunk 102 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3687 ASN C3687 ASN D3687 ASN G3687 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.116539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.094917 restraints weight = 18760.484| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.51 r_work: 0.2838 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16870 Z= 0.147 Angle : 0.460 5.956 23366 Z= 0.253 Chirality : 0.047 0.148 2968 Planarity : 0.005 0.044 3024 Dihedral : 3.957 16.568 2394 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.49 % Allowed : 13.26 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.62 (0.16), residues: 854 loop : 1.17 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C3523 TYR 0.009 0.001 TYR G3650 PHE 0.008 0.001 PHE G3413 TRP 0.016 0.002 TRP B3434 Details of bonding type rmsd covalent geometry : bond 0.00364 (16849) covalent geometry : angle 0.45933 (23324) SS BOND : bond 0.00113 ( 21) SS BOND : angle 0.69930 ( 42) hydrogen bonds : bond 0.03619 ( 504) hydrogen bonds : angle 5.65006 ( 1302) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 157 time to evaluate : 0.504 Fit side-chains REVERT: A 3443 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.8189 (p0) REVERT: A 3467 ASP cc_start: 0.7872 (t70) cc_final: 0.7397 (t0) REVERT: B 3454 THR cc_start: 0.8722 (t) cc_final: 0.8458 (m) REVERT: B 3467 ASP cc_start: 0.8055 (t70) cc_final: 0.7622 (t70) REVERT: B 3716 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7563 (m-30) REVERT: C 3454 THR cc_start: 0.8697 (t) cc_final: 0.8423 (m) REVERT: D 3716 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7690 (m-30) REVERT: F 3454 THR cc_start: 0.8771 (t) cc_final: 0.8535 (m) REVERT: F 3530 ILE cc_start: 0.8998 (mt) cc_final: 0.8617 (pt) outliers start: 68 outliers final: 63 residues processed: 207 average time/residue: 0.0834 time to fit residues: 29.1940 Evaluate side-chains 219 residues out of total 1946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 153 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 3684 SER 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 3727 VAL Chi-restraints excluded: chain C residue 3478 VAL Chi-restraints excluded: chain C residue 3530 ILE Chi-restraints excluded: chain C residue 3535 SER Chi-restraints excluded: chain C residue 3561 SER Chi-restraints excluded: chain C residue 3596 SER Chi-restraints excluded: chain C residue 3626 ASP Chi-restraints excluded: chain C residue 3687 ASN Chi-restraints excluded: chain C residue 3709 VAL Chi-restraints excluded: chain C residue 3716 ASP Chi-restraints excluded: chain C residue 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 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 3727 VAL Chi-restraints excluded: chain F residue 3478 VAL Chi-restraints excluded: chain F residue 3561 SER Chi-restraints excluded: chain F residue 3596 SER Chi-restraints excluded: chain F residue 3676 THR Chi-restraints excluded: chain F residue 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 3687 ASN 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 46 optimal weight: 0.4980 chunk 92 optimal weight: 5.9990 chunk 168 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 58 optimal weight: 0.0170 chunk 129 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3687 ASN C3687 ASN D3687 ASN G3687 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.117893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.096787 restraints weight = 18654.282| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.44 r_work: 0.2844 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3989 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= 0.117 Angle : 0.440 4.654 23366 Z= 0.242 Chirality : 0.046 0.144 2968 Planarity : 0.005 0.042 3024 Dihedral : 3.772 15.998 2394 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.19 % Allowed : 13.62 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.17), residues: 2310 helix: None (None), residues: 0 sheet: 0.89 (0.17), residues: 819 loop : 1.15 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C3523 TYR 0.008 0.001 TYR G3650 PHE 0.006 0.001 PHE E3413 TRP 0.018 0.002 TRP B3434 Details of bonding type rmsd covalent geometry : bond 0.00283 (16849) covalent geometry : angle 0.43938 (23324) SS BOND : bond 0.00088 ( 21) SS BOND : angle 0.62582 ( 42) hydrogen bonds : bond 0.03376 ( 504) hydrogen bonds : angle 5.54967 ( 1302) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3064.81 seconds wall clock time: 53 minutes 23.70 seconds (3203.70 seconds total)