Starting phenix.real_space_refine on Mon Aug 25 08:37:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9flw_50541/08_2025/9flw_50541.cif Found real_map, /net/cci-nas-00/data/ceres_data/9flw_50541/08_2025/9flw_50541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9flw_50541/08_2025/9flw_50541.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9flw_50541/08_2025/9flw_50541.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9flw_50541/08_2025/9flw_50541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9flw_50541/08_2025/9flw_50541.map" } resolution = 3.7 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= 0.115 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 126 5.16 5 C 16478 2.51 5 N 4144 2.21 5 O 5432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26180 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3740 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 38, 'TRANS': 469} Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 3.10, per 1000 atoms: 0.12 Number of scatterers: 26180 At special positions: 0 Unit cell: (102.24, 100.11, 267.315, 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 126 16.00 O 5432 8.00 N 4144 7.00 C 16478 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A3583 " - pdb=" SG CYS A3720 " distance=2.04 Simple disulfide: pdb=" SG CYS A3665 " - pdb=" SG CYS A3817 " distance=2.03 Simple disulfide: pdb=" SG CYS A3747 " - pdb=" SG CYS A3898 " distance=2.04 Simple disulfide: pdb=" SG CYS A3760 " - pdb=" SG CYS A3810 " distance=2.03 Simple disulfide: pdb=" SG CYS A3843 " - pdb=" SG CYS A3980 " distance=2.03 Simple disulfide: pdb=" SG CYS A3924 " - pdb=" SG CYS A4065 " distance=2.04 Simple disulfide: pdb=" SG CYS B3583 " - pdb=" SG CYS B3720 " distance=2.04 Simple disulfide: pdb=" SG CYS C3583 " - pdb=" SG CYS C3720 " distance=2.03 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 Simple disulfide: pdb=" SG CYS B3665 " - pdb=" SG CYS B3817 " distance=2.03 Simple disulfide: pdb=" SG CYS C3665 " - pdb=" SG CYS C3817 " distance=2.03 Simple disulfide: pdb=" SG CYS D3665 " - pdb=" SG CYS D3817 " distance=2.03 Simple disulfide: pdb=" SG CYS E3665 " - pdb=" SG CYS E3817 " distance=2.03 Simple disulfide: pdb=" SG CYS F3665 " - pdb=" SG CYS F3817 " distance=2.03 Simple disulfide: pdb=" SG CYS G3665 " - pdb=" SG CYS G3817 " distance=2.03 Simple disulfide: pdb=" SG CYS B3747 " - pdb=" SG CYS B3898 " distance=2.04 Simple disulfide: pdb=" SG CYS C3747 " - pdb=" SG CYS C3898 " distance=2.04 Simple disulfide: pdb=" SG CYS D3747 " - pdb=" SG CYS D3898 " distance=2.04 Simple disulfide: pdb=" SG CYS E3747 " - pdb=" SG CYS E3898 " distance=2.04 Simple disulfide: pdb=" SG CYS F3747 " - pdb=" SG CYS F3898 " distance=2.04 Simple disulfide: pdb=" SG CYS G3747 " - pdb=" SG CYS G3898 " distance=2.04 Simple disulfide: pdb=" SG CYS B3760 " - pdb=" SG CYS B3810 " distance=2.03 Simple disulfide: pdb=" SG CYS C3760 " - pdb=" SG CYS C3810 " distance=2.03 Simple disulfide: pdb=" SG CYS D3760 " - pdb=" SG CYS D3810 " distance=2.03 Simple disulfide: pdb=" SG CYS E3760 " - pdb=" SG CYS E3810 " distance=2.03 Simple disulfide: pdb=" SG CYS F3760 " - pdb=" SG CYS F3810 " distance=2.03 Simple disulfide: pdb=" SG CYS G3760 " - pdb=" SG CYS G3810 " distance=2.03 Simple disulfide: pdb=" SG CYS B3843 " - pdb=" SG CYS B3980 " distance=2.03 Simple disulfide: pdb=" SG CYS C3843 " - pdb=" SG CYS C3980 " distance=2.03 Simple disulfide: pdb=" SG CYS D3843 " - pdb=" SG CYS D3980 " distance=2.03 Simple disulfide: pdb=" SG CYS E3843 " - pdb=" SG CYS E3980 " distance=2.03 Simple disulfide: pdb=" SG CYS F3843 " - pdb=" SG CYS F3980 " distance=2.03 Simple disulfide: pdb=" SG CYS G3843 " - pdb=" SG CYS G3980 " distance=2.03 Simple disulfide: pdb=" SG CYS B3924 " - pdb=" SG CYS B4065 " distance=2.04 Simple disulfide: pdb=" SG CYS C3924 " - pdb=" SG CYS C4065 " distance=2.04 Simple disulfide: pdb=" SG CYS D3924 " - pdb=" SG CYS D4065 " distance=2.04 Simple disulfide: pdb=" SG CYS E3924 " - pdb=" SG CYS E4065 " distance=2.04 Simple disulfide: pdb=" SG CYS F3924 " - pdb=" SG CYS F4065 " distance=2.04 Simple disulfide: pdb=" SG CYS G3924 " - pdb=" SG CYS G4065 " 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: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6538 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 126 sheets defined 2.6% alpha, 44.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... 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 'A' and resid 4049 through 4053 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 'B' and resid 4049 through 4053 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 'C' and resid 4049 through 4053 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 'D' and resid 4049 through 4053 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 'E' and resid 4049 through 4053 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 'F' and resid 4049 through 4053 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 helix chain 'G' and resid 4049 through 4053 Processing sheet with id=AA1, first strand: chain 'A' and resid 3576 through 3577 Processing sheet with id=AA2, first strand: chain 'A' and resid 3586 through 3589 removed outlier: 6.007A pdb=" N GLY A3586 " --> pdb=" O ASN A3622 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 3611 through 3613 Processing sheet with id=AA4, first strand: chain 'A' and resid 3611 through 3613 Processing sheet with id=AA5, first strand: chain 'A' and resid 3662 through 3665 removed outlier: 6.794A pdb=" N PHE A3662 " --> pdb=" O THR A3730 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ASN A3732 " --> pdb=" O PHE A3662 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL A3664 " --> pdb=" O ASN A3732 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY A3680 " --> pdb=" O VAL A3715 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 3740 through 3742 Processing sheet with id=AA7, first strand: chain 'A' and resid 3745 through 3747 removed outlier: 7.044A pdb=" N ILE A3746 " --> pdb=" O ASN A3829 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A3811 " --> pdb=" O GLN A3762 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 3745 through 3747 removed outlier: 7.044A pdb=" N ILE A3746 " --> pdb=" O ASN A3829 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 3836 through 3838 Processing sheet with id=AB1, first strand: chain 'A' and resid 3842 through 3843 removed outlier: 6.880A pdb=" N ILE A3842 " --> pdb=" O ASN A3910 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 3871 through 3873 removed outlier: 6.898A pdb=" N TRP A3862 " --> pdb=" O ILE A3872 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3871 through 3873 removed outlier: 6.898A pdb=" N TRP A3862 " --> pdb=" O ILE A3872 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3923 through 3924 removed outlier: 7.025A pdb=" N LEU A3923 " --> pdb=" O TYR A3991 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 3927 through 3930 removed outlier: 4.083A pdb=" N ASP A3927 " --> pdb=" O ILE A3962 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU A3929 " --> pdb=" O PRO A3960 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3951 through 3952 Processing sheet with id=AB7, first strand: chain 'A' and resid 4011 through 4015 Processing sheet with id=AB8, first strand: chain 'A' and resid 4037 through 4038 Processing sheet with id=AB9, first strand: chain 'A' and resid 4037 through 4038 Processing sheet with id=AC1, first strand: chain 'B' and resid 3576 through 3577 Processing sheet with id=AC2, first strand: chain 'B' and resid 3586 through 3589 removed outlier: 6.007A pdb=" N GLY B3586 " --> pdb=" O ASN B3622 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 3611 through 3613 Processing sheet with id=AC4, first strand: chain 'B' and resid 3611 through 3613 Processing sheet with id=AC5, first strand: chain 'B' and resid 3662 through 3665 removed outlier: 6.794A pdb=" N PHE B3662 " --> pdb=" O THR B3730 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ASN B3732 " --> pdb=" O PHE B3662 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B3664 " --> pdb=" O ASN B3732 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY B3680 " --> pdb=" O VAL B3715 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 3740 through 3742 Processing sheet with id=AC7, first strand: chain 'B' and resid 3745 through 3747 removed outlier: 7.044A pdb=" N ILE B3746 " --> pdb=" O ASN B3829 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B3811 " --> pdb=" O GLN B3762 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 3745 through 3747 removed outlier: 7.044A pdb=" N ILE B3746 " --> pdb=" O ASN B3829 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 3836 through 3838 Processing sheet with id=AD1, first strand: chain 'B' and resid 3842 through 3843 removed outlier: 6.879A pdb=" N ILE B3842 " --> pdb=" O ASN B3910 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 3871 through 3873 removed outlier: 6.898A pdb=" N TRP B3862 " --> pdb=" O ILE B3872 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 3871 through 3873 removed outlier: 6.898A pdb=" N TRP B3862 " --> pdb=" O ILE B3872 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 3923 through 3924 removed outlier: 7.024A pdb=" N LEU B3923 " --> pdb=" O TYR B3991 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 3927 through 3930 removed outlier: 4.083A pdb=" N ASP B3927 " --> pdb=" O ILE B3962 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU B3929 " --> pdb=" O PRO B3960 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 3951 through 3952 Processing sheet with id=AD7, first strand: chain 'B' and resid 4011 through 4015 Processing sheet with id=AD8, first strand: chain 'B' and resid 4037 through 4038 Processing sheet with id=AD9, first strand: chain 'B' and resid 4037 through 4038 Processing sheet with id=AE1, first strand: chain 'C' and resid 3576 through 3577 Processing sheet with id=AE2, first strand: chain 'C' and resid 3586 through 3589 removed outlier: 6.007A pdb=" N GLY C3586 " --> pdb=" O ASN C3622 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 3611 through 3613 Processing sheet with id=AE4, first strand: chain 'C' and resid 3611 through 3613 Processing sheet with id=AE5, first strand: chain 'C' and resid 3662 through 3665 removed outlier: 6.794A pdb=" N PHE C3662 " --> pdb=" O THR C3730 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ASN C3732 " --> pdb=" O PHE C3662 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL C3664 " --> pdb=" O ASN C3732 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY C3680 " --> pdb=" O VAL C3715 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 3740 through 3742 Processing sheet with id=AE7, first strand: chain 'C' and resid 3745 through 3747 removed outlier: 7.045A pdb=" N ILE C3746 " --> pdb=" O ASN C3829 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C3811 " --> pdb=" O GLN C3762 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 3745 through 3747 removed outlier: 7.045A pdb=" N ILE C3746 " --> pdb=" O ASN C3829 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 3836 through 3838 Processing sheet with id=AF1, first strand: chain 'C' and resid 3842 through 3843 removed outlier: 6.880A pdb=" N ILE C3842 " --> pdb=" O ASN C3910 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 3871 through 3873 removed outlier: 6.898A pdb=" N TRP C3862 " --> pdb=" O ILE C3872 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 3871 through 3873 removed outlier: 6.898A pdb=" N TRP C3862 " --> pdb=" O ILE C3872 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 3923 through 3924 removed outlier: 7.024A pdb=" N LEU C3923 " --> pdb=" O TYR C3991 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'C' and resid 3927 through 3930 removed outlier: 4.083A pdb=" N ASP C3927 " --> pdb=" O ILE C3962 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU C3929 " --> pdb=" O PRO C3960 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 3951 through 3952 Processing sheet with id=AF7, first strand: chain 'C' and resid 4011 through 4015 Processing sheet with id=AF8, first strand: chain 'C' and resid 4037 through 4038 Processing sheet with id=AF9, first strand: chain 'C' and resid 4037 through 4038 Processing sheet with id=AG1, first strand: chain 'D' and resid 3576 through 3577 Processing sheet with id=AG2, first strand: chain 'D' and resid 3586 through 3589 removed outlier: 6.008A pdb=" N GLY D3586 " --> pdb=" O ASN D3622 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 3611 through 3613 Processing sheet with id=AG4, first strand: chain 'D' and resid 3611 through 3613 Processing sheet with id=AG5, first strand: chain 'D' and resid 3662 through 3665 removed outlier: 6.794A pdb=" N PHE D3662 " --> pdb=" O THR D3730 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ASN D3732 " --> pdb=" O PHE D3662 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL D3664 " --> pdb=" O ASN D3732 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY D3680 " --> pdb=" O VAL D3715 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 3740 through 3742 Processing sheet with id=AG7, first strand: chain 'D' and resid 3745 through 3747 removed outlier: 7.044A pdb=" N ILE D3746 " --> pdb=" O ASN D3829 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D3811 " --> pdb=" O GLN D3762 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 3745 through 3747 removed outlier: 7.044A pdb=" N ILE D3746 " --> pdb=" O ASN D3829 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 3836 through 3838 Processing sheet with id=AH1, first strand: chain 'D' and resid 3842 through 3843 removed outlier: 6.880A pdb=" N ILE D3842 " --> pdb=" O ASN D3910 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'D' and resid 3871 through 3873 removed outlier: 6.898A pdb=" N TRP D3862 " --> pdb=" O ILE D3872 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 3871 through 3873 removed outlier: 6.898A pdb=" N TRP D3862 " --> pdb=" O ILE D3872 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 3923 through 3924 removed outlier: 7.024A pdb=" N LEU D3923 " --> pdb=" O TYR D3991 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'D' and resid 3927 through 3930 removed outlier: 4.082A pdb=" N ASP D3927 " --> pdb=" O ILE D3962 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU D3929 " --> pdb=" O PRO D3960 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 3951 through 3952 Processing sheet with id=AH7, first strand: chain 'D' and resid 4011 through 4015 Processing sheet with id=AH8, first strand: chain 'D' and resid 4037 through 4038 Processing sheet with id=AH9, first strand: chain 'D' and resid 4037 through 4038 Processing sheet with id=AI1, first strand: chain 'E' and resid 3576 through 3577 Processing sheet with id=AI2, first strand: chain 'E' and resid 3586 through 3589 removed outlier: 6.007A pdb=" N GLY E3586 " --> pdb=" O ASN E3622 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 3611 through 3613 Processing sheet with id=AI4, first strand: chain 'E' and resid 3611 through 3613 Processing sheet with id=AI5, first strand: chain 'E' and resid 3662 through 3665 removed outlier: 6.793A pdb=" N PHE E3662 " --> pdb=" O THR E3730 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ASN E3732 " --> pdb=" O PHE E3662 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL E3664 " --> pdb=" O ASN E3732 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY E3680 " --> pdb=" O VAL E3715 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E' and resid 3740 through 3742 Processing sheet with id=AI7, first strand: chain 'E' and resid 3745 through 3747 removed outlier: 7.044A pdb=" N ILE E3746 " --> pdb=" O ASN E3829 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE E3811 " --> pdb=" O GLN E3762 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 3745 through 3747 removed outlier: 7.044A pdb=" N ILE E3746 " --> pdb=" O ASN E3829 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 3836 through 3838 Processing sheet with id=AJ1, first strand: chain 'E' and resid 3842 through 3843 removed outlier: 6.879A pdb=" N ILE E3842 " --> pdb=" O ASN E3910 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'E' and resid 3871 through 3873 removed outlier: 6.899A pdb=" N TRP E3862 " --> pdb=" O ILE E3872 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'E' and resid 3871 through 3873 removed outlier: 6.899A pdb=" N TRP E3862 " --> pdb=" O ILE E3872 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'E' and resid 3923 through 3924 removed outlier: 7.025A pdb=" N LEU E3923 " --> pdb=" O TYR E3991 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ4 Processing sheet with id=AJ5, first strand: chain 'E' and resid 3927 through 3930 removed outlier: 4.082A pdb=" N ASP E3927 " --> pdb=" O ILE E3962 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU E3929 " --> pdb=" O PRO E3960 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'E' and resid 3951 through 3952 Processing sheet with id=AJ7, first strand: chain 'E' and resid 4011 through 4015 Processing sheet with id=AJ8, first strand: chain 'E' and resid 4037 through 4038 Processing sheet with id=AJ9, first strand: chain 'E' and resid 4037 through 4038 Processing sheet with id=AK1, first strand: chain 'F' and resid 3576 through 3577 Processing sheet with id=AK2, first strand: chain 'F' and resid 3586 through 3589 removed outlier: 6.007A pdb=" N GLY F3586 " --> pdb=" O ASN F3622 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'F' and resid 3611 through 3613 Processing sheet with id=AK4, first strand: chain 'F' and resid 3611 through 3613 Processing sheet with id=AK5, first strand: chain 'F' and resid 3662 through 3665 removed outlier: 6.794A pdb=" N PHE F3662 " --> pdb=" O THR F3730 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ASN F3732 " --> pdb=" O PHE F3662 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL F3664 " --> pdb=" O ASN F3732 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY F3680 " --> pdb=" O VAL F3715 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'F' and resid 3740 through 3742 Processing sheet with id=AK7, first strand: chain 'F' and resid 3745 through 3747 removed outlier: 7.044A pdb=" N ILE F3746 " --> pdb=" O ASN F3829 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE F3811 " --> pdb=" O GLN F3762 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'F' and resid 3745 through 3747 removed outlier: 7.044A pdb=" N ILE F3746 " --> pdb=" O ASN F3829 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'F' and resid 3836 through 3838 Processing sheet with id=AL1, first strand: chain 'F' and resid 3842 through 3843 removed outlier: 6.879A pdb=" N ILE F3842 " --> pdb=" O ASN F3910 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL1 Processing sheet with id=AL2, first strand: chain 'F' and resid 3871 through 3873 removed outlier: 6.898A pdb=" N TRP F3862 " --> pdb=" O ILE F3872 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'F' and resid 3871 through 3873 removed outlier: 6.898A pdb=" N TRP F3862 " --> pdb=" O ILE F3872 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'F' and resid 3923 through 3924 removed outlier: 7.025A pdb=" N LEU F3923 " --> pdb=" O TYR F3991 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL4 Processing sheet with id=AL5, first strand: chain 'F' and resid 3927 through 3930 removed outlier: 4.082A pdb=" N ASP F3927 " --> pdb=" O ILE F3962 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU F3929 " --> pdb=" O PRO F3960 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'F' and resid 3951 through 3952 Processing sheet with id=AL7, first strand: chain 'F' and resid 4011 through 4015 Processing sheet with id=AL8, first strand: chain 'F' and resid 4037 through 4038 Processing sheet with id=AL9, first strand: chain 'F' and resid 4037 through 4038 Processing sheet with id=AM1, first strand: chain 'G' and resid 3576 through 3577 Processing sheet with id=AM2, first strand: chain 'G' and resid 3586 through 3589 removed outlier: 6.007A pdb=" N GLY G3586 " --> pdb=" O ASN G3622 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'G' and resid 3611 through 3613 Processing sheet with id=AM4, first strand: chain 'G' and resid 3611 through 3613 Processing sheet with id=AM5, first strand: chain 'G' and resid 3662 through 3665 removed outlier: 6.794A pdb=" N PHE G3662 " --> pdb=" O THR G3730 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ASN G3732 " --> pdb=" O PHE G3662 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL G3664 " --> pdb=" O ASN G3732 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY G3680 " --> pdb=" O VAL G3715 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'G' and resid 3740 through 3742 Processing sheet with id=AM7, first strand: chain 'G' and resid 3745 through 3747 removed outlier: 7.044A pdb=" N ILE G3746 " --> pdb=" O ASN G3829 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE G3811 " --> pdb=" O GLN G3762 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'G' and resid 3745 through 3747 removed outlier: 7.044A pdb=" N ILE G3746 " --> pdb=" O ASN G3829 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'G' and resid 3836 through 3838 Processing sheet with id=AN1, first strand: chain 'G' and resid 3842 through 3843 removed outlier: 6.880A pdb=" N ILE G3842 " --> pdb=" O ASN G3910 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN1 Processing sheet with id=AN2, first strand: chain 'G' and resid 3871 through 3873 removed outlier: 6.899A pdb=" N TRP G3862 " --> pdb=" O ILE G3872 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'G' and resid 3871 through 3873 removed outlier: 6.899A pdb=" N TRP G3862 " --> pdb=" O ILE G3872 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'G' and resid 3923 through 3924 removed outlier: 7.025A pdb=" N LEU G3923 " --> pdb=" O TYR G3991 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN4 Processing sheet with id=AN5, first strand: chain 'G' and resid 3927 through 3930 removed outlier: 4.082A pdb=" N ASP G3927 " --> pdb=" O ILE G3962 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU G3929 " --> pdb=" O PRO G3960 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'G' and resid 3951 through 3952 Processing sheet with id=AN7, first strand: chain 'G' and resid 4011 through 4015 Processing sheet with id=AN8, first strand: chain 'G' and resid 4037 through 4038 Processing sheet with id=AN9, first strand: chain 'G' and resid 4037 through 4038 980 hydrogen bonds defined for protein. 2394 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: 5.08 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 6811 1.33 - 1.46: 7762 1.46 - 1.59: 12101 1.59 - 1.72: 17 1.72 - 1.85: 154 Bond restraints: 26845 Sorted by residual: bond pdb=" CB ASN C3839 " pdb=" CG ASN C3839 " ideal model delta sigma weight residual 1.516 1.403 0.113 2.50e-02 1.60e+03 2.05e+01 bond pdb=" CB ASN B3839 " pdb=" CG ASN B3839 " ideal model delta sigma weight residual 1.516 1.403 0.113 2.50e-02 1.60e+03 2.04e+01 bond pdb=" CB ASN E3839 " pdb=" CG ASN E3839 " ideal model delta sigma weight residual 1.516 1.403 0.113 2.50e-02 1.60e+03 2.03e+01 bond pdb=" CB ASN D3839 " pdb=" CG ASN D3839 " ideal model delta sigma weight residual 1.516 1.403 0.113 2.50e-02 1.60e+03 2.03e+01 bond pdb=" CB ASN A3839 " pdb=" CG ASN A3839 " ideal model delta sigma weight residual 1.516 1.403 0.113 2.50e-02 1.60e+03 2.03e+01 ... (remaining 26840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 32610 2.63 - 5.25: 3923 5.25 - 7.88: 556 7.88 - 10.51: 53 10.51 - 13.13: 14 Bond angle restraints: 37156 Sorted by residual: angle pdb=" C GLY F3946 " pdb=" N PRO F3947 " pdb=" CA PRO F3947 " ideal model delta sigma weight residual 119.47 129.32 -9.85 1.16e+00 7.43e-01 7.21e+01 angle pdb=" C GLY B3946 " pdb=" N PRO B3947 " pdb=" CA PRO B3947 " ideal model delta sigma weight residual 119.47 129.30 -9.83 1.16e+00 7.43e-01 7.18e+01 angle pdb=" C GLY E3946 " pdb=" N PRO E3947 " pdb=" CA PRO E3947 " ideal model delta sigma weight residual 119.47 129.29 -9.82 1.16e+00 7.43e-01 7.17e+01 angle pdb=" C GLY A3946 " pdb=" N PRO A3947 " pdb=" CA PRO A3947 " ideal model delta sigma weight residual 119.47 129.28 -9.81 1.16e+00 7.43e-01 7.16e+01 angle pdb=" C GLY G3946 " pdb=" N PRO G3947 " pdb=" CA PRO G3947 " ideal model delta sigma weight residual 119.47 129.28 -9.81 1.16e+00 7.43e-01 7.16e+01 ... (remaining 37151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.11: 15106 15.11 - 30.22: 469 30.22 - 45.33: 91 45.33 - 60.44: 35 60.44 - 75.55: 28 Dihedral angle restraints: 15729 sinusoidal: 5495 harmonic: 10234 Sorted by residual: dihedral pdb=" CB CYS F3583 " pdb=" SG CYS F3583 " pdb=" SG CYS F3720 " pdb=" CB CYS F3720 " ideal model delta sinusoidal sigma weight residual 93.00 153.15 -60.15 1 1.00e+01 1.00e-02 4.82e+01 dihedral pdb=" CB CYS E3583 " pdb=" SG CYS E3583 " pdb=" SG CYS E3720 " pdb=" CB CYS E3720 " ideal model delta sinusoidal sigma weight residual 93.00 153.12 -60.12 1 1.00e+01 1.00e-02 4.82e+01 dihedral pdb=" CB CYS D3583 " pdb=" SG CYS D3583 " pdb=" SG CYS D3720 " pdb=" CB CYS D3720 " ideal model delta sinusoidal sigma weight residual 93.00 153.12 -60.12 1 1.00e+01 1.00e-02 4.82e+01 ... (remaining 15726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2738 0.069 - 0.139: 1341 0.139 - 0.208: 410 0.208 - 0.277: 68 0.277 - 0.347: 7 Chirality restraints: 4564 Sorted by residual: chirality pdb=" CG LEU E4043 " pdb=" CB LEU E4043 " pdb=" CD1 LEU E4043 " pdb=" CD2 LEU E4043 " both_signs ideal model delta sigma weight residual False -2.59 -2.94 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CG LEU G4043 " pdb=" CB LEU G4043 " pdb=" CD1 LEU G4043 " pdb=" CD2 LEU G4043 " both_signs ideal model delta sigma weight residual False -2.59 -2.94 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CG LEU F4043 " pdb=" CB LEU F4043 " pdb=" CD1 LEU F4043 " pdb=" CD2 LEU F4043 " both_signs ideal model delta sigma weight residual False -2.59 -2.94 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 4561 not shown) Planarity restraints: 4781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B4061 " 0.053 2.00e-02 2.50e+03 2.72e-02 1.85e+01 pdb=" CG TRP B4061 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP B4061 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B4061 " -0.028 2.00e-02 2.50e+03 pdb=" NE1 TRP B4061 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP B4061 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B4061 " -0.033 2.00e-02 2.50e+03 pdb=" CZ2 TRP B4061 " 0.034 2.00e-02 2.50e+03 pdb=" CZ3 TRP B4061 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP B4061 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A4061 " -0.053 2.00e-02 2.50e+03 2.71e-02 1.84e+01 pdb=" CG TRP A4061 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP A4061 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP A4061 " 0.028 2.00e-02 2.50e+03 pdb=" NE1 TRP A4061 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP A4061 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A4061 " 0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP A4061 " -0.034 2.00e-02 2.50e+03 pdb=" CZ3 TRP A4061 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP A4061 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C4061 " -0.053 2.00e-02 2.50e+03 2.71e-02 1.83e+01 pdb=" CG TRP C4061 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP C4061 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP C4061 " 0.028 2.00e-02 2.50e+03 pdb=" NE1 TRP C4061 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP C4061 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C4061 " 0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP C4061 " -0.034 2.00e-02 2.50e+03 pdb=" CZ3 TRP C4061 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP C4061 " -0.028 2.00e-02 2.50e+03 ... (remaining 4778 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 363 2.59 - 3.17: 22361 3.17 - 3.74: 40074 3.74 - 4.32: 56817 4.32 - 4.90: 90003 Nonbonded interactions: 209618 Sorted by model distance: nonbonded pdb=" CD1 LEU F4030 " pdb=" OD1 ASN F4032 " model vdw 2.012 3.460 nonbonded pdb=" CD1 LEU G4030 " pdb=" OD1 ASN G4032 " model vdw 2.012 3.460 nonbonded pdb=" CD1 LEU E4030 " pdb=" OD1 ASN E4032 " model vdw 2.013 3.460 nonbonded pdb=" CD1 LEU C4030 " pdb=" OD1 ASN C4032 " model vdw 2.013 3.460 nonbonded pdb=" CD1 LEU B4030 " pdb=" OD1 ASN B4032 " model vdw 2.013 3.460 ... (remaining 209613 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: 0.07 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.330 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 19.870 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: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 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 0.113 26887 Z= 0.983 Angle : 1.781 13.133 37240 Z= 1.222 Chirality : 0.086 0.347 4564 Planarity : 0.008 0.032 4781 Dihedral : 8.805 75.550 9065 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.21 % 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: 1.57 (0.14), residues: 3542 helix: -4.65 (0.12), residues: 42 sheet: 1.16 (0.13), residues: 1463 loop : 1.28 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F4025 TYR 0.033 0.007 TYR F3807 PHE 0.045 0.005 PHE G3662 TRP 0.055 0.012 TRP D3944 HIS 0.001 0.001 HIS C4001 Details of bonding type rmsd covalent geometry : bond 0.01774 (26845) covalent geometry : angle 1.78078 (37156) SS BOND : bond 0.00427 ( 42) SS BOND : angle 2.02354 ( 84) hydrogen bonds : bond 0.14099 ( 791) hydrogen bonds : angle 8.02780 ( 2394) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 671 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3887 GLU cc_start: 0.7637 (tp30) cc_final: 0.7371 (tp30) REVERT: A 3927 ASP cc_start: 0.7738 (t0) cc_final: 0.7519 (t0) REVERT: A 3998 THR cc_start: 0.8782 (m) cc_final: 0.8314 (p) REVERT: B 3790 SER cc_start: 0.8141 (m) cc_final: 0.7877 (p) REVERT: B 3887 GLU cc_start: 0.7811 (tp30) cc_final: 0.7543 (tp30) REVERT: B 3903 ASP cc_start: 0.8199 (t0) cc_final: 0.7990 (t70) REVERT: B 3998 THR cc_start: 0.8739 (m) cc_final: 0.8297 (p) REVERT: C 3790 SER cc_start: 0.8349 (m) cc_final: 0.7478 (p) REVERT: C 3808 MET cc_start: 0.8197 (ttt) cc_final: 0.7845 (ttt) REVERT: C 3887 GLU cc_start: 0.7948 (tp30) cc_final: 0.7717 (tp30) REVERT: C 3903 ASP cc_start: 0.8255 (t0) cc_final: 0.8030 (t70) REVERT: C 3924 CYS cc_start: 0.7899 (m) cc_final: 0.7617 (m) REVERT: C 3998 THR cc_start: 0.8844 (m) cc_final: 0.8330 (p) REVERT: D 3903 ASP cc_start: 0.8234 (t0) cc_final: 0.7765 (t70) REVERT: D 3924 CYS cc_start: 0.8105 (m) cc_final: 0.7852 (p) REVERT: D 3927 ASP cc_start: 0.7506 (t0) cc_final: 0.7028 (t0) REVERT: D 3998 THR cc_start: 0.8879 (m) cc_final: 0.8397 (p) REVERT: E 3790 SER cc_start: 0.8286 (m) cc_final: 0.7452 (p) REVERT: E 3827 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7367 (mt-10) REVERT: E 3887 GLU cc_start: 0.7648 (tp30) cc_final: 0.7383 (tp30) REVERT: E 3998 THR cc_start: 0.8884 (m) cc_final: 0.8370 (p) REVERT: F 3790 SER cc_start: 0.8441 (m) cc_final: 0.8167 (p) REVERT: F 3887 GLU cc_start: 0.7838 (tp30) cc_final: 0.7592 (tp30) REVERT: F 3998 THR cc_start: 0.8930 (m) cc_final: 0.8414 (p) REVERT: G 3887 GLU cc_start: 0.7672 (tp30) cc_final: 0.7444 (tp30) REVERT: G 3903 ASP cc_start: 0.8169 (t0) cc_final: 0.7958 (t70) REVERT: G 3927 ASP cc_start: 0.7674 (t0) cc_final: 0.7417 (t0) REVERT: G 3998 THR cc_start: 0.8704 (m) cc_final: 0.8173 (p) outliers start: 0 outliers final: 0 residues processed: 671 average time/residue: 0.1217 time to fit residues: 140.0551 Evaluate side-chains 269 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C3764 GLN E3695 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.140948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.105607 restraints weight = 38742.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102739 restraints weight = 25711.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103931 restraints weight = 25442.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.104486 restraints weight = 15197.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.105603 restraints weight = 13035.645| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 26887 Z= 0.178 Angle : 0.643 8.220 37240 Z= 0.341 Chirality : 0.049 0.191 4564 Planarity : 0.005 0.044 4781 Dihedral : 5.041 22.851 3731 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 1.78 % Allowed : 7.67 % Favored : 90.55 % 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 (0.14), residues: 3542 helix: -4.59 (0.12), residues: 42 sheet: 1.10 (0.13), residues: 1505 loop : 1.11 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C4075 TYR 0.022 0.002 TYR A3650 PHE 0.009 0.001 PHE E3662 TRP 0.025 0.002 TRP F4061 HIS 0.004 0.001 HIS G4001 Details of bonding type rmsd covalent geometry : bond 0.00405 (26845) covalent geometry : angle 0.63444 (37156) SS BOND : bond 0.01001 ( 42) SS BOND : angle 2.34410 ( 84) hydrogen bonds : bond 0.03948 ( 791) hydrogen bonds : angle 5.95899 ( 2394) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 367 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: A 3624 SER cc_start: 0.8869 (p) cc_final: 0.8362 (t) REVERT: A 3716 ASP cc_start: 0.8369 (t0) cc_final: 0.8062 (t0) REVERT: A 3927 ASP cc_start: 0.7840 (t0) cc_final: 0.7530 (t70) REVERT: A 3998 THR cc_start: 0.8703 (m) cc_final: 0.7966 (p) REVERT: A 4015 THR cc_start: 0.9325 (m) cc_final: 0.9001 (p) REVERT: A 4017 GLN cc_start: 0.8551 (pm20) cc_final: 0.8172 (pm20) REVERT: B 3716 ASP cc_start: 0.8394 (t0) cc_final: 0.8036 (t0) REVERT: B 3875 SER cc_start: 0.8948 (t) cc_final: 0.8709 (m) REVERT: B 3927 ASP cc_start: 0.7577 (t0) cc_final: 0.7315 (t70) REVERT: B 3998 THR cc_start: 0.8602 (m) cc_final: 0.7871 (p) REVERT: B 4015 THR cc_start: 0.9202 (m) cc_final: 0.8997 (p) REVERT: C 3677 VAL cc_start: 0.8569 (t) cc_final: 0.8330 (m) REVERT: C 3716 ASP cc_start: 0.8361 (t0) cc_final: 0.7947 (t0) REVERT: C 3998 THR cc_start: 0.8656 (m) cc_final: 0.7976 (p) REVERT: C 4007 GLU cc_start: 0.8519 (tt0) cc_final: 0.8306 (tt0) REVERT: D 3716 ASP cc_start: 0.8441 (t0) cc_final: 0.7966 (t0) REVERT: D 3927 ASP cc_start: 0.7691 (t0) cc_final: 0.7452 (t70) REVERT: E 3677 VAL cc_start: 0.8592 (t) cc_final: 0.8301 (m) REVERT: E 3716 ASP cc_start: 0.8350 (t0) cc_final: 0.8009 (t0) REVERT: E 3821 SER cc_start: 0.8410 (p) cc_final: 0.8184 (p) REVERT: E 3875 SER cc_start: 0.9144 (t) cc_final: 0.8893 (m) REVERT: E 3987 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7188 (mm-30) REVERT: E 3998 THR cc_start: 0.8732 (m) cc_final: 0.7961 (p) REVERT: F 3677 VAL cc_start: 0.8556 (t) cc_final: 0.8230 (m) REVERT: F 3875 SER cc_start: 0.9080 (t) cc_final: 0.8839 (m) REVERT: F 3927 ASP cc_start: 0.7761 (t0) cc_final: 0.7440 (t70) REVERT: F 3987 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7246 (mm-30) REVERT: F 3998 THR cc_start: 0.8680 (m) cc_final: 0.7851 (p) REVERT: F 4012 LEU cc_start: 0.8366 (tt) cc_final: 0.8040 (tt) REVERT: F 4015 THR cc_start: 0.9268 (m) cc_final: 0.9062 (p) REVERT: G 3716 ASP cc_start: 0.8326 (t0) cc_final: 0.8031 (t0) REVERT: G 3927 ASP cc_start: 0.7625 (t0) cc_final: 0.7243 (t70) REVERT: G 3932 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8934 (mm-40) REVERT: G 3998 THR cc_start: 0.8500 (m) cc_final: 0.7816 (p) REVERT: G 4012 LEU cc_start: 0.8299 (tt) cc_final: 0.7941 (tt) outliers start: 54 outliers final: 37 residues processed: 416 average time/residue: 0.1178 time to fit residues: 85.3788 Evaluate side-chains 273 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3633 VAL Chi-restraints excluded: chain A residue 3691 SER Chi-restraints excluded: chain A residue 3784 VAL Chi-restraints excluded: chain A residue 3787 THR Chi-restraints excluded: chain A residue 3797 THR Chi-restraints excluded: chain B residue 3633 VAL Chi-restraints excluded: chain B residue 3784 VAL Chi-restraints excluded: chain B residue 3787 THR Chi-restraints excluded: chain B residue 3797 THR Chi-restraints excluded: chain B residue 4022 THR Chi-restraints excluded: chain C residue 3674 THR Chi-restraints excluded: chain C residue 3691 SER Chi-restraints excluded: chain C residue 3722 SER Chi-restraints excluded: chain C residue 3784 VAL Chi-restraints excluded: chain C residue 3787 THR Chi-restraints excluded: chain D residue 3784 VAL Chi-restraints excluded: chain D residue 3787 THR Chi-restraints excluded: chain D residue 3797 THR Chi-restraints excluded: chain E residue 3592 THR Chi-restraints excluded: chain E residue 3633 VAL Chi-restraints excluded: chain E residue 3691 SER Chi-restraints excluded: chain E residue 3784 VAL Chi-restraints excluded: chain E residue 3787 THR Chi-restraints excluded: chain E residue 3797 THR Chi-restraints excluded: chain E residue 4073 ILE Chi-restraints excluded: chain F residue 3633 VAL Chi-restraints excluded: chain F residue 3784 VAL Chi-restraints excluded: chain F residue 3787 THR Chi-restraints excluded: chain F residue 3797 THR Chi-restraints excluded: chain G residue 3592 THR Chi-restraints excluded: chain G residue 3633 VAL Chi-restraints excluded: chain G residue 3691 SER Chi-restraints excluded: chain G residue 3700 THR Chi-restraints excluded: chain G residue 3784 VAL Chi-restraints excluded: chain G residue 3787 THR Chi-restraints excluded: chain G residue 3797 THR Chi-restraints excluded: chain G residue 3821 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 248 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 109 optimal weight: 0.4980 chunk 63 optimal weight: 6.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C3695 ASN ** C3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4001 HIS G3695 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.144286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109487 restraints weight = 39130.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107332 restraints weight = 33825.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.109170 restraints weight = 28646.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.109227 restraints weight = 18540.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.110652 restraints weight = 16073.956| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 26887 Z= 0.255 Angle : 0.668 7.859 37240 Z= 0.351 Chirality : 0.049 0.159 4564 Planarity : 0.005 0.044 4781 Dihedral : 5.151 28.783 3731 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.73 % Allowed : 10.11 % Favored : 87.16 % 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: 0.80 (0.14), residues: 3542 helix: None (None), residues: 0 sheet: 0.57 (0.13), residues: 1617 loop : 0.66 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E4075 TYR 0.014 0.002 TYR C3650 PHE 0.014 0.002 PHE E3662 TRP 0.018 0.002 TRP E4061 HIS 0.006 0.001 HIS F4001 Details of bonding type rmsd covalent geometry : bond 0.00609 (26845) covalent geometry : angle 0.65676 (37156) SS BOND : bond 0.00499 ( 42) SS BOND : angle 2.67570 ( 84) hydrogen bonds : bond 0.04018 ( 791) hydrogen bonds : angle 5.50577 ( 2394) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 270 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 3716 ASP cc_start: 0.8381 (t0) cc_final: 0.8138 (t0) REVERT: A 3998 THR cc_start: 0.8709 (m) cc_final: 0.7989 (p) REVERT: A 4012 LEU cc_start: 0.8355 (tt) cc_final: 0.8024 (tt) REVERT: A 4015 THR cc_start: 0.9373 (m) cc_final: 0.9148 (p) REVERT: A 4066 LEU cc_start: 0.8066 (mt) cc_final: 0.7848 (mt) REVERT: B 3716 ASP cc_start: 0.8439 (t0) cc_final: 0.8124 (t0) REVERT: B 3998 THR cc_start: 0.8659 (m) cc_final: 0.7949 (p) REVERT: C 3716 ASP cc_start: 0.8401 (t0) cc_final: 0.8177 (t0) REVERT: C 3998 THR cc_start: 0.8792 (m) cc_final: 0.8065 (p) REVERT: C 4012 LEU cc_start: 0.8326 (tt) cc_final: 0.7969 (tt) REVERT: D 3716 ASP cc_start: 0.8521 (t0) cc_final: 0.8128 (t0) REVERT: D 4012 LEU cc_start: 0.8341 (tt) cc_final: 0.7990 (tt) REVERT: E 3716 ASP cc_start: 0.8404 (t0) cc_final: 0.8184 (t0) REVERT: E 3821 SER cc_start: 0.8480 (p) cc_final: 0.8212 (p) REVERT: E 3998 THR cc_start: 0.8707 (m) cc_final: 0.7922 (p) REVERT: F 3677 VAL cc_start: 0.8545 (t) cc_final: 0.8318 (m) REVERT: F 3998 THR cc_start: 0.8722 (m) cc_final: 0.7898 (p) REVERT: F 4012 LEU cc_start: 0.8506 (tt) cc_final: 0.8161 (tt) REVERT: G 3998 THR cc_start: 0.8578 (m) cc_final: 0.7870 (p) REVERT: G 4012 LEU cc_start: 0.8473 (tt) cc_final: 0.8117 (tt) REVERT: G 4023 ASP cc_start: 0.7565 (t0) cc_final: 0.6980 (p0) outliers start: 83 outliers final: 67 residues processed: 346 average time/residue: 0.1221 time to fit residues: 72.9192 Evaluate side-chains 266 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 199 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3633 VAL Chi-restraints excluded: chain A residue 3700 THR Chi-restraints excluded: chain A residue 3722 SER Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3784 VAL Chi-restraints excluded: chain A residue 3787 THR Chi-restraints excluded: chain A residue 3797 THR Chi-restraints excluded: chain A residue 3881 SER Chi-restraints excluded: chain A residue 3985 THR Chi-restraints excluded: chain A residue 3988 VAL Chi-restraints excluded: chain A residue 4022 THR Chi-restraints excluded: chain B residue 3633 VAL Chi-restraints excluded: chain B residue 3691 SER Chi-restraints excluded: chain B residue 3700 THR Chi-restraints excluded: chain B residue 3722 SER Chi-restraints excluded: chain B residue 3784 VAL Chi-restraints excluded: chain B residue 3787 THR Chi-restraints excluded: chain B residue 3797 THR Chi-restraints excluded: chain B residue 3821 SER Chi-restraints excluded: chain B residue 3853 THR Chi-restraints excluded: chain B residue 3969 SER Chi-restraints excluded: chain B residue 3985 THR Chi-restraints excluded: chain B residue 4022 THR Chi-restraints excluded: chain B residue 4073 ILE Chi-restraints excluded: chain C residue 3624 SER Chi-restraints excluded: chain C residue 3674 THR Chi-restraints excluded: chain C residue 3700 THR Chi-restraints excluded: chain C residue 3722 SER Chi-restraints excluded: chain C residue 3740 ILE Chi-restraints excluded: chain C residue 3784 VAL Chi-restraints excluded: chain C residue 3787 THR Chi-restraints excluded: chain C residue 3985 THR Chi-restraints excluded: chain D residue 3722 SER Chi-restraints excluded: chain D residue 3740 ILE Chi-restraints excluded: chain D residue 3784 VAL Chi-restraints excluded: chain D residue 3787 THR Chi-restraints excluded: chain D residue 3797 THR Chi-restraints excluded: chain D residue 3969 SER Chi-restraints excluded: chain D residue 3985 THR Chi-restraints excluded: chain E residue 3633 VAL Chi-restraints excluded: chain E residue 3700 THR Chi-restraints excluded: chain E residue 3784 VAL Chi-restraints excluded: chain E residue 3787 THR Chi-restraints excluded: chain E residue 3797 THR Chi-restraints excluded: chain E residue 3865 ASP Chi-restraints excluded: chain E residue 3985 THR Chi-restraints excluded: chain E residue 4002 ASN Chi-restraints excluded: chain E residue 4073 ILE Chi-restraints excluded: chain F residue 3633 VAL Chi-restraints excluded: chain F residue 3700 THR Chi-restraints excluded: chain F residue 3784 VAL Chi-restraints excluded: chain F residue 3787 THR Chi-restraints excluded: chain F residue 3797 THR Chi-restraints excluded: chain F residue 3819 SER Chi-restraints excluded: chain F residue 3865 ASP Chi-restraints excluded: chain F residue 3985 THR Chi-restraints excluded: chain G residue 3633 VAL Chi-restraints excluded: chain G residue 3691 SER Chi-restraints excluded: chain G residue 3700 THR Chi-restraints excluded: chain G residue 3722 SER Chi-restraints excluded: chain G residue 3740 ILE Chi-restraints excluded: chain G residue 3784 VAL Chi-restraints excluded: chain G residue 3787 THR Chi-restraints excluded: chain G residue 3797 THR Chi-restraints excluded: chain G residue 3821 SER Chi-restraints excluded: chain G residue 3985 THR Chi-restraints excluded: chain G residue 4022 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 199 optimal weight: 0.0870 chunk 25 optimal weight: 0.8980 chunk 310 optimal weight: 5.9990 chunk 299 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 176 optimal weight: 0.3980 chunk 47 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 chunk 188 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4001 HIS ** C3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4001 HIS D4001 HIS F4001 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.152096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.116827 restraints weight = 38386.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.116805 restraints weight = 23896.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.117075 restraints weight = 27158.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.117783 restraints weight = 16648.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.117943 restraints weight = 14568.347| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 26887 Z= 0.106 Angle : 0.571 13.654 37240 Z= 0.294 Chirality : 0.047 0.165 4564 Planarity : 0.004 0.045 4781 Dihedral : 4.740 31.721 3731 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.65 % Allowed : 12.08 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.01 (0.14), residues: 3542 helix: None (None), residues: 0 sheet: 0.84 (0.13), residues: 1540 loop : 0.68 (0.14), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E3861 TYR 0.011 0.001 TYR B3807 PHE 0.010 0.001 PHE B3965 TRP 0.016 0.001 TRP A4061 HIS 0.005 0.001 HIS B4001 Details of bonding type rmsd covalent geometry : bond 0.00242 (26845) covalent geometry : angle 0.55963 (37156) SS BOND : bond 0.00528 ( 42) SS BOND : angle 2.45766 ( 84) hydrogen bonds : bond 0.02951 ( 791) hydrogen bonds : angle 5.09557 ( 2394) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 255 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 3716 ASP cc_start: 0.8374 (t0) cc_final: 0.8122 (t0) REVERT: A 3998 THR cc_start: 0.8754 (m) cc_final: 0.8096 (p) REVERT: A 4012 LEU cc_start: 0.8264 (tt) cc_final: 0.7921 (tt) REVERT: A 4017 GLN cc_start: 0.8657 (pm20) cc_final: 0.8362 (pm20) REVERT: A 4073 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8517 (pt) REVERT: B 3716 ASP cc_start: 0.8392 (t0) cc_final: 0.8078 (t0) REVERT: B 3925 GLN cc_start: 0.8774 (tt0) cc_final: 0.8512 (tt0) REVERT: B 3998 THR cc_start: 0.8751 (m) cc_final: 0.8186 (p) REVERT: C 3998 THR cc_start: 0.8831 (m) cc_final: 0.8236 (p) REVERT: C 4012 LEU cc_start: 0.8306 (tt) cc_final: 0.7982 (tt) REVERT: D 4012 LEU cc_start: 0.8320 (tt) cc_final: 0.8004 (tt) REVERT: E 3716 ASP cc_start: 0.8286 (t0) cc_final: 0.8084 (t0) REVERT: E 3998 THR cc_start: 0.8791 (m) cc_final: 0.8036 (p) REVERT: E 4012 LEU cc_start: 0.8231 (tt) cc_final: 0.7920 (tt) REVERT: E 4015 THR cc_start: 0.9361 (m) cc_final: 0.9150 (p) REVERT: F 3588 SER cc_start: 0.9529 (p) cc_final: 0.9187 (t) REVERT: F 3677 VAL cc_start: 0.8604 (t) cc_final: 0.8383 (m) REVERT: F 3998 THR cc_start: 0.8721 (m) cc_final: 0.8042 (p) REVERT: F 4012 LEU cc_start: 0.8473 (tt) cc_final: 0.8124 (tt) REVERT: G 3998 THR cc_start: 0.8657 (m) cc_final: 0.8017 (p) REVERT: G 4012 LEU cc_start: 0.8243 (tt) cc_final: 0.8030 (tt) REVERT: G 4023 ASP cc_start: 0.7549 (t0) cc_final: 0.7050 (p0) outliers start: 50 outliers final: 28 residues processed: 298 average time/residue: 0.1302 time to fit residues: 66.4387 Evaluate side-chains 228 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3633 VAL Chi-restraints excluded: chain A residue 3722 SER Chi-restraints excluded: chain A residue 3865 ASP Chi-restraints excluded: chain A residue 4073 ILE Chi-restraints excluded: chain B residue 3633 VAL Chi-restraints excluded: chain B residue 3691 SER Chi-restraints excluded: chain B residue 3722 SER Chi-restraints excluded: chain B residue 4022 THR Chi-restraints excluded: chain B residue 4073 ILE Chi-restraints excluded: chain C residue 3674 THR Chi-restraints excluded: chain C residue 3722 SER Chi-restraints excluded: chain D residue 3722 SER Chi-restraints excluded: chain D residue 3881 SER Chi-restraints excluded: chain E residue 3633 VAL Chi-restraints excluded: chain E residue 3722 SER Chi-restraints excluded: chain E residue 3865 ASP Chi-restraints excluded: chain E residue 3923 LEU Chi-restraints excluded: chain E residue 4002 ASN Chi-restraints excluded: chain E residue 4073 ILE Chi-restraints excluded: chain F residue 3633 VAL Chi-restraints excluded: chain F residue 3865 ASP Chi-restraints excluded: chain F residue 4073 ILE Chi-restraints excluded: chain G residue 3633 VAL Chi-restraints excluded: chain G residue 3674 THR Chi-restraints excluded: chain G residue 3722 SER Chi-restraints excluded: chain G residue 3821 SER Chi-restraints excluded: chain G residue 3924 CYS Chi-restraints excluded: chain G residue 4022 THR Chi-restraints excluded: chain G residue 4073 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 31 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 327 optimal weight: 1.9990 chunk 324 optimal weight: 4.9990 chunk 245 optimal weight: 6.9990 chunk 279 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 203 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D4001 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.144979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109873 restraints weight = 38665.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.106745 restraints weight = 34716.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.107853 restraints weight = 29738.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.108367 restraints weight = 20519.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.109660 restraints weight = 16235.456| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 26887 Z= 0.329 Angle : 0.703 9.183 37240 Z= 0.370 Chirality : 0.051 0.173 4564 Planarity : 0.005 0.051 4781 Dihedral : 5.589 35.017 3731 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.81 % Favored : 96.13 % Rotamer: Outliers : 3.49 % Allowed : 11.62 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.38 (0.14), residues: 3542 helix: None (None), residues: 0 sheet: 0.32 (0.12), residues: 1603 loop : 0.34 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E3818 TYR 0.015 0.002 TYR D3863 PHE 0.029 0.002 PHE B3577 TRP 0.022 0.002 TRP E4061 HIS 0.004 0.001 HIS B4001 Details of bonding type rmsd covalent geometry : bond 0.00787 (26845) covalent geometry : angle 0.69010 (37156) SS BOND : bond 0.00503 ( 42) SS BOND : angle 2.95239 ( 84) hydrogen bonds : bond 0.04112 ( 791) hydrogen bonds : angle 5.29877 ( 2394) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 218 time to evaluate : 0.870 Fit side-chains REVERT: A 3716 ASP cc_start: 0.8432 (t0) cc_final: 0.8231 (t0) REVERT: A 3998 THR cc_start: 0.8788 (m) cc_final: 0.8083 (p) REVERT: A 4012 LEU cc_start: 0.8317 (tt) cc_final: 0.8008 (tt) REVERT: B 3716 ASP cc_start: 0.8472 (t0) cc_final: 0.8167 (t0) REVERT: B 3998 THR cc_start: 0.8710 (m) cc_final: 0.8119 (p) REVERT: B 4012 LEU cc_start: 0.8421 (tt) cc_final: 0.8155 (tt) REVERT: C 3998 THR cc_start: 0.8857 (m) cc_final: 0.8236 (p) REVERT: C 4012 LEU cc_start: 0.8294 (tt) cc_final: 0.7930 (tt) REVERT: D 3716 ASP cc_start: 0.8596 (t0) cc_final: 0.8299 (t0) REVERT: D 3998 THR cc_start: 0.8789 (m) cc_final: 0.8146 (p) REVERT: D 4012 LEU cc_start: 0.8431 (tt) cc_final: 0.8088 (tt) REVERT: D 4023 ASP cc_start: 0.7429 (t70) cc_final: 0.6777 (p0) REVERT: E 3716 ASP cc_start: 0.8466 (t0) cc_final: 0.8204 (t0) REVERT: E 3821 SER cc_start: 0.8738 (p) cc_final: 0.8481 (p) REVERT: E 3998 THR cc_start: 0.8653 (m) cc_final: 0.7897 (p) REVERT: E 4012 LEU cc_start: 0.8292 (tt) cc_final: 0.7974 (tt) REVERT: E 4015 THR cc_start: 0.9390 (m) cc_final: 0.9153 (p) REVERT: F 3588 SER cc_start: 0.9544 (p) cc_final: 0.9101 (t) REVERT: F 3925 GLN cc_start: 0.8748 (tt0) cc_final: 0.8475 (tt0) REVERT: F 3998 THR cc_start: 0.8765 (m) cc_final: 0.7935 (p) REVERT: G 3998 THR cc_start: 0.8691 (m) cc_final: 0.8059 (p) REVERT: G 4012 LEU cc_start: 0.8433 (tt) cc_final: 0.8194 (tt) REVERT: G 4023 ASP cc_start: 0.7731 (t0) cc_final: 0.7169 (p0) outliers start: 106 outliers final: 89 residues processed: 309 average time/residue: 0.1299 time to fit residues: 68.9262 Evaluate side-chains 285 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 196 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3624 SER Chi-restraints excluded: chain A residue 3633 VAL Chi-restraints excluded: chain A residue 3700 THR Chi-restraints excluded: chain A residue 3722 SER Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3784 VAL Chi-restraints excluded: chain A residue 3787 THR Chi-restraints excluded: chain A residue 3797 THR Chi-restraints excluded: chain A residue 3808 MET Chi-restraints excluded: chain A residue 3865 ASP Chi-restraints excluded: chain A residue 3924 CYS Chi-restraints excluded: chain A residue 3985 THR Chi-restraints excluded: chain A residue 4022 THR Chi-restraints excluded: chain A residue 4073 ILE Chi-restraints excluded: chain B residue 3592 THR Chi-restraints excluded: chain B residue 3624 SER Chi-restraints excluded: chain B residue 3633 VAL Chi-restraints excluded: chain B residue 3691 SER Chi-restraints excluded: chain B residue 3700 THR Chi-restraints excluded: chain B residue 3722 SER Chi-restraints excluded: chain B residue 3744 SER Chi-restraints excluded: chain B residue 3784 VAL Chi-restraints excluded: chain B residue 3787 THR Chi-restraints excluded: chain B residue 3797 THR Chi-restraints excluded: chain B residue 3821 SER Chi-restraints excluded: chain B residue 3886 SER Chi-restraints excluded: chain B residue 3985 THR Chi-restraints excluded: chain B residue 4022 THR Chi-restraints excluded: chain B residue 4073 ILE Chi-restraints excluded: chain C residue 3592 THR Chi-restraints excluded: chain C residue 3624 SER Chi-restraints excluded: chain C residue 3674 THR Chi-restraints excluded: chain C residue 3700 THR Chi-restraints excluded: chain C residue 3722 SER Chi-restraints excluded: chain C residue 3740 ILE Chi-restraints excluded: chain C residue 3784 VAL Chi-restraints excluded: chain C residue 3787 THR Chi-restraints excluded: chain C residue 3881 SER Chi-restraints excluded: chain C residue 3985 THR Chi-restraints excluded: chain C residue 4073 ILE Chi-restraints excluded: chain D residue 3592 THR Chi-restraints excluded: chain D residue 3674 THR Chi-restraints excluded: chain D residue 3722 SER Chi-restraints excluded: chain D residue 3740 ILE Chi-restraints excluded: chain D residue 3784 VAL Chi-restraints excluded: chain D residue 3787 THR Chi-restraints excluded: chain D residue 3797 THR Chi-restraints excluded: chain D residue 3881 SER Chi-restraints excluded: chain D residue 3985 THR Chi-restraints excluded: chain E residue 3592 THR Chi-restraints excluded: chain E residue 3624 SER Chi-restraints excluded: chain E residue 3633 VAL Chi-restraints excluded: chain E residue 3674 THR Chi-restraints excluded: chain E residue 3700 THR Chi-restraints excluded: chain E residue 3722 SER Chi-restraints excluded: chain E residue 3787 THR Chi-restraints excluded: chain E residue 3797 THR Chi-restraints excluded: chain E residue 3827 GLU Chi-restraints excluded: chain E residue 3865 ASP Chi-restraints excluded: chain E residue 3985 THR Chi-restraints excluded: chain E residue 4002 ASN Chi-restraints excluded: chain F residue 3624 SER Chi-restraints excluded: chain F residue 3633 VAL Chi-restraints excluded: chain F residue 3700 THR Chi-restraints excluded: chain F residue 3784 VAL Chi-restraints excluded: chain F residue 3787 THR Chi-restraints excluded: chain F residue 3797 THR Chi-restraints excluded: chain F residue 3865 ASP Chi-restraints excluded: chain F residue 3881 SER Chi-restraints excluded: chain F residue 3923 LEU Chi-restraints excluded: chain F residue 3969 SER Chi-restraints excluded: chain F residue 3985 THR Chi-restraints excluded: chain F residue 4073 ILE Chi-restraints excluded: chain G residue 3624 SER Chi-restraints excluded: chain G residue 3633 VAL Chi-restraints excluded: chain G residue 3674 THR Chi-restraints excluded: chain G residue 3691 SER Chi-restraints excluded: chain G residue 3700 THR Chi-restraints excluded: chain G residue 3722 SER Chi-restraints excluded: chain G residue 3730 THR Chi-restraints excluded: chain G residue 3740 ILE Chi-restraints excluded: chain G residue 3784 VAL Chi-restraints excluded: chain G residue 3787 THR Chi-restraints excluded: chain G residue 3797 THR Chi-restraints excluded: chain G residue 3821 SER Chi-restraints excluded: chain G residue 3881 SER Chi-restraints excluded: chain G residue 3985 THR Chi-restraints excluded: chain G residue 4022 THR Chi-restraints excluded: chain G residue 4073 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 229 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D4001 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.148872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.113275 restraints weight = 38598.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112178 restraints weight = 25912.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112602 restraints weight = 30703.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.113478 restraints weight = 18103.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.113594 restraints weight = 15422.798| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26887 Z= 0.137 Angle : 0.579 7.465 37240 Z= 0.301 Chirality : 0.047 0.178 4564 Planarity : 0.005 0.043 4781 Dihedral : 5.060 32.111 3731 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.47 % Allowed : 13.36 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.56 (0.14), residues: 3542 helix: None (None), residues: 0 sheet: 0.41 (0.13), residues: 1617 loop : 0.49 (0.15), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E4075 TYR 0.012 0.001 TYR E3807 PHE 0.031 0.001 PHE F3577 TRP 0.027 0.002 TRP F4061 HIS 0.003 0.001 HIS A4001 Details of bonding type rmsd covalent geometry : bond 0.00323 (26845) covalent geometry : angle 0.57241 (37156) SS BOND : bond 0.00447 ( 42) SS BOND : angle 1.91734 ( 84) hydrogen bonds : bond 0.03035 ( 791) hydrogen bonds : angle 4.97267 ( 2394) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 221 time to evaluate : 1.051 Fit side-chains REVERT: A 3588 SER cc_start: 0.9459 (p) cc_final: 0.9051 (t) REVERT: A 3716 ASP cc_start: 0.8425 (t0) cc_final: 0.8213 (t0) REVERT: A 3998 THR cc_start: 0.8889 (m) cc_final: 0.8323 (p) REVERT: B 3587 ASN cc_start: 0.9468 (m-40) cc_final: 0.9018 (m-40) REVERT: B 3716 ASP cc_start: 0.8419 (t0) cc_final: 0.8081 (t0) REVERT: B 3998 THR cc_start: 0.8827 (m) cc_final: 0.8325 (p) REVERT: C 3998 THR cc_start: 0.8915 (m) cc_final: 0.8345 (p) REVERT: C 4012 LEU cc_start: 0.8260 (tt) cc_final: 0.7954 (tt) REVERT: C 4066 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8313 (tt) REVERT: D 3588 SER cc_start: 0.9434 (p) cc_final: 0.9129 (t) REVERT: D 3716 ASP cc_start: 0.8611 (t0) cc_final: 0.8293 (t0) REVERT: D 3925 GLN cc_start: 0.8730 (tt0) cc_final: 0.8504 (tt0) REVERT: D 3998 THR cc_start: 0.8805 (m) cc_final: 0.8157 (p) REVERT: D 4012 LEU cc_start: 0.8424 (tt) cc_final: 0.8103 (tt) REVERT: D 4023 ASP cc_start: 0.7436 (t70) cc_final: 0.6969 (p0) REVERT: E 3588 SER cc_start: 0.9439 (p) cc_final: 0.9115 (t) REVERT: E 3716 ASP cc_start: 0.8436 (t0) cc_final: 0.8179 (t0) REVERT: E 3925 GLN cc_start: 0.8844 (tp40) cc_final: 0.8348 (tp40) REVERT: E 3998 THR cc_start: 0.8724 (m) cc_final: 0.8002 (p) REVERT: E 4012 LEU cc_start: 0.8245 (tt) cc_final: 0.7942 (tt) REVERT: E 4023 ASP cc_start: 0.7316 (t70) cc_final: 0.6733 (p0) REVERT: F 3588 SER cc_start: 0.9447 (p) cc_final: 0.9124 (t) REVERT: F 3998 THR cc_start: 0.8826 (m) cc_final: 0.8021 (p) REVERT: F 4075 ARG cc_start: 0.8793 (mmt90) cc_final: 0.8094 (mtt-85) REVERT: G 3998 THR cc_start: 0.8768 (m) cc_final: 0.8199 (p) REVERT: G 4023 ASP cc_start: 0.7720 (t0) cc_final: 0.7261 (p0) outliers start: 75 outliers final: 64 residues processed: 282 average time/residue: 0.1295 time to fit residues: 63.1589 Evaluate side-chains 264 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 199 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3633 VAL Chi-restraints excluded: chain A residue 3700 THR Chi-restraints excluded: chain A residue 3722 SER Chi-restraints excluded: chain A residue 3730 THR Chi-restraints excluded: chain A residue 3797 THR Chi-restraints excluded: chain A residue 3808 MET Chi-restraints excluded: chain A residue 3865 ASP Chi-restraints excluded: chain A residue 3985 THR Chi-restraints excluded: chain A residue 4022 THR Chi-restraints excluded: chain A residue 4073 ILE Chi-restraints excluded: chain B residue 3592 THR Chi-restraints excluded: chain B residue 3633 VAL Chi-restraints excluded: chain B residue 3691 SER Chi-restraints excluded: chain B residue 3700 THR Chi-restraints excluded: chain B residue 3722 SER Chi-restraints excluded: chain B residue 3787 THR Chi-restraints excluded: chain B residue 3853 THR Chi-restraints excluded: chain B residue 3985 THR Chi-restraints excluded: chain B residue 4022 THR Chi-restraints excluded: chain B residue 4073 ILE Chi-restraints excluded: chain C residue 3674 THR Chi-restraints excluded: chain C residue 3700 THR Chi-restraints excluded: chain C residue 3722 SER Chi-restraints excluded: chain C residue 3730 THR Chi-restraints excluded: chain C residue 3787 THR Chi-restraints excluded: chain C residue 3985 THR Chi-restraints excluded: chain C residue 4066 LEU Chi-restraints excluded: chain C residue 4073 ILE Chi-restraints excluded: chain D residue 3592 THR Chi-restraints excluded: chain D residue 3722 SER Chi-restraints excluded: chain D residue 3740 ILE Chi-restraints excluded: chain D residue 3787 THR Chi-restraints excluded: chain D residue 3886 SER Chi-restraints excluded: chain D residue 3985 THR Chi-restraints excluded: chain E residue 3592 THR Chi-restraints excluded: chain E residue 3633 VAL Chi-restraints excluded: chain E residue 3674 THR Chi-restraints excluded: chain E residue 3722 SER Chi-restraints excluded: chain E residue 3787 THR Chi-restraints excluded: chain E residue 3827 GLU Chi-restraints excluded: chain E residue 3865 ASP Chi-restraints excluded: chain E residue 3886 SER Chi-restraints excluded: chain E residue 3985 THR Chi-restraints excluded: chain E residue 4002 ASN Chi-restraints excluded: chain E residue 4073 ILE Chi-restraints excluded: chain F residue 3633 VAL Chi-restraints excluded: chain F residue 3730 THR Chi-restraints excluded: chain F residue 3753 THR Chi-restraints excluded: chain F residue 3787 THR Chi-restraints excluded: chain F residue 3853 THR Chi-restraints excluded: chain F residue 3865 ASP Chi-restraints excluded: chain F residue 3923 LEU Chi-restraints excluded: chain F residue 3985 THR Chi-restraints excluded: chain F residue 4073 ILE Chi-restraints excluded: chain G residue 3592 THR Chi-restraints excluded: chain G residue 3633 VAL Chi-restraints excluded: chain G residue 3674 THR Chi-restraints excluded: chain G residue 3722 SER Chi-restraints excluded: chain G residue 3787 THR Chi-restraints excluded: chain G residue 3808 MET Chi-restraints excluded: chain G residue 3821 SER Chi-restraints excluded: chain G residue 3886 SER Chi-restraints excluded: chain G residue 3985 THR Chi-restraints excluded: chain G residue 4022 THR Chi-restraints excluded: chain G residue 4073 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 112 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 75 optimal weight: 0.0050 chunk 255 optimal weight: 0.5980 chunk 85 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D4001 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.148857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.113742 restraints weight = 38574.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111907 restraints weight = 29125.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113080 restraints weight = 29549.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.113563 restraints weight = 17050.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.113965 restraints weight = 15037.812| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26887 Z= 0.148 Angle : 0.570 7.415 37240 Z= 0.295 Chirality : 0.047 0.170 4564 Planarity : 0.004 0.041 4781 Dihedral : 5.009 35.699 3731 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.86 % Allowed : 13.79 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.56 (0.14), residues: 3542 helix: None (None), residues: 0 sheet: 0.39 (0.13), residues: 1617 loop : 0.51 (0.15), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E4075 TYR 0.011 0.001 TYR G3807 PHE 0.017 0.001 PHE A3577 TRP 0.026 0.001 TRP C4061 HIS 0.002 0.001 HIS A4001 Details of bonding type rmsd covalent geometry : bond 0.00355 (26845) covalent geometry : angle 0.56447 (37156) SS BOND : bond 0.00404 ( 42) SS BOND : angle 1.80929 ( 84) hydrogen bonds : bond 0.03005 ( 791) hydrogen bonds : angle 4.82569 ( 2394) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 212 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3588 SER cc_start: 0.9464 (p) cc_final: 0.9021 (t) REVERT: A 3998 THR cc_start: 0.8870 (m) cc_final: 0.8316 (p) REVERT: B 3587 ASN cc_start: 0.9440 (m-40) cc_final: 0.9043 (m-40) REVERT: B 3925 GLN cc_start: 0.8874 (tt0) cc_final: 0.8556 (tt0) REVERT: B 3990 ILE cc_start: 0.9471 (mp) cc_final: 0.9267 (mp) REVERT: B 3998 THR cc_start: 0.8806 (m) cc_final: 0.8326 (p) REVERT: C 3924 CYS cc_start: 0.6074 (m) cc_final: 0.5846 (m) REVERT: C 3998 THR cc_start: 0.8929 (m) cc_final: 0.8347 (p) REVERT: C 4012 LEU cc_start: 0.8265 (tt) cc_final: 0.7966 (tt) REVERT: C 4023 ASP cc_start: 0.8013 (t0) cc_final: 0.7330 (p0) REVERT: D 3588 SER cc_start: 0.9425 (p) cc_final: 0.9117 (t) REVERT: D 3925 GLN cc_start: 0.8688 (tt0) cc_final: 0.8434 (tt0) REVERT: D 3998 THR cc_start: 0.8886 (m) cc_final: 0.8231 (p) REVERT: D 4012 LEU cc_start: 0.8383 (tt) cc_final: 0.7921 (tt) REVERT: D 4023 ASP cc_start: 0.7442 (t70) cc_final: 0.7086 (p0) REVERT: E 3716 ASP cc_start: 0.8441 (t0) cc_final: 0.8195 (t0) REVERT: E 3925 GLN cc_start: 0.8864 (tp40) cc_final: 0.8496 (tp40) REVERT: E 3998 THR cc_start: 0.8733 (m) cc_final: 0.8077 (p) REVERT: E 4012 LEU cc_start: 0.8285 (tt) cc_final: 0.7998 (tt) REVERT: E 4023 ASP cc_start: 0.7339 (t70) cc_final: 0.6855 (p0) REVERT: F 3588 SER cc_start: 0.9421 (p) cc_final: 0.9123 (t) REVERT: F 3716 ASP cc_start: 0.8475 (t0) cc_final: 0.8181 (t0) REVERT: F 3998 THR cc_start: 0.8764 (m) cc_final: 0.7975 (p) REVERT: F 4023 ASP cc_start: 0.7661 (t0) cc_final: 0.6880 (p0) REVERT: F 4075 ARG cc_start: 0.8753 (mmt90) cc_final: 0.8103 (mtt-85) REVERT: G 3998 THR cc_start: 0.8763 (m) cc_final: 0.8214 (p) REVERT: G 4023 ASP cc_start: 0.7730 (t0) cc_final: 0.7272 (p0) outliers start: 87 outliers final: 80 residues processed: 283 average time/residue: 0.1286 time to fit residues: 62.0384 Evaluate side-chains 273 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 193 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3633 VAL Chi-restraints excluded: chain A residue 3674 THR Chi-restraints excluded: chain A residue 3700 THR Chi-restraints excluded: chain A residue 3722 SER Chi-restraints excluded: chain A residue 3730 THR Chi-restraints excluded: chain A residue 3787 THR Chi-restraints excluded: chain A residue 3797 THR Chi-restraints excluded: chain A residue 3808 MET Chi-restraints excluded: chain A residue 3865 ASP Chi-restraints excluded: chain A residue 3985 THR Chi-restraints excluded: chain A residue 4073 ILE Chi-restraints excluded: chain B residue 3592 THR Chi-restraints excluded: chain B residue 3624 SER Chi-restraints excluded: chain B residue 3633 VAL Chi-restraints excluded: chain B residue 3691 SER Chi-restraints excluded: chain B residue 3700 THR Chi-restraints excluded: chain B residue 3722 SER Chi-restraints excluded: chain B residue 3730 THR Chi-restraints excluded: chain B residue 3787 THR Chi-restraints excluded: chain B residue 3821 SER Chi-restraints excluded: chain B residue 3853 THR Chi-restraints excluded: chain B residue 3985 THR Chi-restraints excluded: chain B residue 4022 THR Chi-restraints excluded: chain B residue 4073 ILE Chi-restraints excluded: chain C residue 3674 THR Chi-restraints excluded: chain C residue 3700 THR Chi-restraints excluded: chain C residue 3722 SER Chi-restraints excluded: chain C residue 3730 THR Chi-restraints excluded: chain C residue 3787 THR Chi-restraints excluded: chain C residue 3985 THR Chi-restraints excluded: chain C residue 4073 ILE Chi-restraints excluded: chain D residue 3592 THR Chi-restraints excluded: chain D residue 3674 THR Chi-restraints excluded: chain D residue 3722 SER Chi-restraints excluded: chain D residue 3740 ILE Chi-restraints excluded: chain D residue 3787 THR Chi-restraints excluded: chain D residue 3881 SER Chi-restraints excluded: chain D residue 3886 SER Chi-restraints excluded: chain D residue 3923 LEU Chi-restraints excluded: chain D residue 3985 THR Chi-restraints excluded: chain E residue 3592 THR Chi-restraints excluded: chain E residue 3624 SER Chi-restraints excluded: chain E residue 3633 VAL Chi-restraints excluded: chain E residue 3674 THR Chi-restraints excluded: chain E residue 3700 THR Chi-restraints excluded: chain E residue 3722 SER Chi-restraints excluded: chain E residue 3730 THR Chi-restraints excluded: chain E residue 3787 THR Chi-restraints excluded: chain E residue 3797 THR Chi-restraints excluded: chain E residue 3827 GLU Chi-restraints excluded: chain E residue 3865 ASP Chi-restraints excluded: chain E residue 3886 SER Chi-restraints excluded: chain E residue 3923 LEU Chi-restraints excluded: chain E residue 3985 THR Chi-restraints excluded: chain E residue 4002 ASN Chi-restraints excluded: chain F residue 3624 SER Chi-restraints excluded: chain F residue 3633 VAL Chi-restraints excluded: chain F residue 3700 THR Chi-restraints excluded: chain F residue 3722 SER Chi-restraints excluded: chain F residue 3730 THR Chi-restraints excluded: chain F residue 3753 THR Chi-restraints excluded: chain F residue 3787 THR Chi-restraints excluded: chain F residue 3821 SER Chi-restraints excluded: chain F residue 3853 THR Chi-restraints excluded: chain F residue 3865 ASP Chi-restraints excluded: chain F residue 3923 LEU Chi-restraints excluded: chain F residue 3985 THR Chi-restraints excluded: chain F residue 4073 ILE Chi-restraints excluded: chain G residue 3592 THR Chi-restraints excluded: chain G residue 3624 SER Chi-restraints excluded: chain G residue 3633 VAL Chi-restraints excluded: chain G residue 3674 THR Chi-restraints excluded: chain G residue 3722 SER Chi-restraints excluded: chain G residue 3740 ILE Chi-restraints excluded: chain G residue 3787 THR Chi-restraints excluded: chain G residue 3808 MET Chi-restraints excluded: chain G residue 3821 SER Chi-restraints excluded: chain G residue 3886 SER Chi-restraints excluded: chain G residue 3985 THR Chi-restraints excluded: chain G residue 4073 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 28 optimal weight: 0.9980 chunk 247 optimal weight: 20.0000 chunk 200 optimal weight: 10.0000 chunk 146 optimal weight: 8.9990 chunk 242 optimal weight: 0.0030 chunk 179 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 262 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3695 ASN D4001 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.146188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111561 restraints weight = 38907.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107893 restraints weight = 34628.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.109484 restraints weight = 29501.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.109797 restraints weight = 19854.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110474 restraints weight = 15979.907| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 26887 Z= 0.194 Angle : 0.599 6.867 37240 Z= 0.311 Chirality : 0.048 0.179 4564 Planarity : 0.004 0.042 4781 Dihedral : 5.201 35.544 3731 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.23 % Allowed : 13.76 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.39 (0.14), residues: 3542 helix: None (None), residues: 0 sheet: 0.33 (0.12), residues: 1610 loop : 0.34 (0.15), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E4075 TYR 0.012 0.001 TYR E3807 PHE 0.022 0.002 PHE G3577 TRP 0.020 0.002 TRP F4061 HIS 0.002 0.001 HIS A4001 Details of bonding type rmsd covalent geometry : bond 0.00465 (26845) covalent geometry : angle 0.59228 (37156) SS BOND : bond 0.00396 ( 42) SS BOND : angle 1.95863 ( 84) hydrogen bonds : bond 0.03192 ( 791) hydrogen bonds : angle 4.85302 ( 2394) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 213 time to evaluate : 0.837 Fit side-chains REVERT: A 3588 SER cc_start: 0.9427 (p) cc_final: 0.9038 (t) REVERT: A 3998 THR cc_start: 0.8897 (m) cc_final: 0.8288 (p) REVERT: A 4075 ARG cc_start: 0.8647 (mmt90) cc_final: 0.8399 (mmt90) REVERT: B 3587 ASN cc_start: 0.9446 (m-40) cc_final: 0.9131 (m-40) REVERT: B 3588 SER cc_start: 0.9190 (p) cc_final: 0.8941 (t) REVERT: B 3716 ASP cc_start: 0.8440 (t0) cc_final: 0.8195 (t0) REVERT: B 3998 THR cc_start: 0.8837 (m) cc_final: 0.8367 (p) REVERT: C 3998 THR cc_start: 0.8985 (m) cc_final: 0.8480 (p) REVERT: C 4012 LEU cc_start: 0.8239 (tt) cc_final: 0.7957 (tt) REVERT: C 4023 ASP cc_start: 0.8097 (t0) cc_final: 0.7403 (p0) REVERT: D 3588 SER cc_start: 0.9434 (p) cc_final: 0.9090 (t) REVERT: D 3716 ASP cc_start: 0.8607 (t0) cc_final: 0.8311 (t0) REVERT: D 3925 GLN cc_start: 0.8736 (tt0) cc_final: 0.8487 (tt0) REVERT: D 3998 THR cc_start: 0.8923 (m) cc_final: 0.8269 (p) REVERT: D 4012 LEU cc_start: 0.8390 (tt) cc_final: 0.8164 (tt) REVERT: D 4023 ASP cc_start: 0.7528 (t70) cc_final: 0.7083 (p0) REVERT: E 3716 ASP cc_start: 0.8485 (t0) cc_final: 0.8213 (t0) REVERT: E 3925 GLN cc_start: 0.8881 (tp40) cc_final: 0.8465 (tp40) REVERT: E 3998 THR cc_start: 0.8711 (m) cc_final: 0.8072 (p) REVERT: E 4012 LEU cc_start: 0.8377 (tt) cc_final: 0.8068 (tt) REVERT: E 4023 ASP cc_start: 0.7355 (t70) cc_final: 0.6869 (p0) REVERT: E 4075 ARG cc_start: 0.8714 (mmt90) cc_final: 0.8497 (mmt180) REVERT: F 3588 SER cc_start: 0.9426 (p) cc_final: 0.9101 (t) REVERT: F 3716 ASP cc_start: 0.8512 (t0) cc_final: 0.8169 (t0) REVERT: F 3998 THR cc_start: 0.8797 (m) cc_final: 0.8094 (p) REVERT: F 4023 ASP cc_start: 0.7759 (t0) cc_final: 0.6988 (p0) REVERT: F 4075 ARG cc_start: 0.8770 (mmt90) cc_final: 0.8120 (mtt-85) REVERT: G 3664 VAL cc_start: 0.9495 (p) cc_final: 0.9115 (m) REVERT: G 3998 THR cc_start: 0.8803 (m) cc_final: 0.8240 (p) REVERT: G 4023 ASP cc_start: 0.7886 (t0) cc_final: 0.7345 (p0) outliers start: 98 outliers final: 93 residues processed: 293 average time/residue: 0.1362 time to fit residues: 67.8254 Evaluate side-chains 290 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 197 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3624 SER Chi-restraints excluded: chain A residue 3633 VAL Chi-restraints excluded: chain A residue 3674 THR Chi-restraints excluded: chain A residue 3700 THR Chi-restraints excluded: chain A residue 3722 SER Chi-restraints excluded: chain A residue 3730 THR Chi-restraints excluded: chain A residue 3787 THR Chi-restraints excluded: chain A residue 3797 THR Chi-restraints excluded: chain A residue 3808 MET Chi-restraints excluded: chain A residue 3865 ASP Chi-restraints excluded: chain A residue 3924 CYS Chi-restraints excluded: chain A residue 3985 THR Chi-restraints excluded: chain A residue 4022 THR Chi-restraints excluded: chain A residue 4073 ILE Chi-restraints excluded: chain B residue 3592 THR Chi-restraints excluded: chain B residue 3624 SER Chi-restraints excluded: chain B residue 3633 VAL Chi-restraints excluded: chain B residue 3691 SER Chi-restraints excluded: chain B residue 3700 THR Chi-restraints excluded: chain B residue 3722 SER Chi-restraints excluded: chain B residue 3730 THR Chi-restraints excluded: chain B residue 3784 VAL Chi-restraints excluded: chain B residue 3787 THR Chi-restraints excluded: chain B residue 3797 THR Chi-restraints excluded: chain B residue 3821 SER Chi-restraints excluded: chain B residue 3853 THR Chi-restraints excluded: chain B residue 3985 THR Chi-restraints excluded: chain B residue 4022 THR Chi-restraints excluded: chain C residue 3592 THR Chi-restraints excluded: chain C residue 3624 SER Chi-restraints excluded: chain C residue 3674 THR Chi-restraints excluded: chain C residue 3700 THR Chi-restraints excluded: chain C residue 3722 SER Chi-restraints excluded: chain C residue 3730 THR Chi-restraints excluded: chain C residue 3784 VAL Chi-restraints excluded: chain C residue 3787 THR Chi-restraints excluded: chain C residue 3831 ILE Chi-restraints excluded: chain C residue 3881 SER Chi-restraints excluded: chain C residue 3985 THR Chi-restraints excluded: chain D residue 3592 THR Chi-restraints excluded: chain D residue 3674 THR Chi-restraints excluded: chain D residue 3722 SER Chi-restraints excluded: chain D residue 3730 THR Chi-restraints excluded: chain D residue 3740 ILE Chi-restraints excluded: chain D residue 3787 THR Chi-restraints excluded: chain D residue 3881 SER Chi-restraints excluded: chain D residue 3886 SER Chi-restraints excluded: chain D residue 3923 LEU Chi-restraints excluded: chain D residue 3985 THR Chi-restraints excluded: chain E residue 3592 THR Chi-restraints excluded: chain E residue 3624 SER Chi-restraints excluded: chain E residue 3633 VAL Chi-restraints excluded: chain E residue 3674 THR Chi-restraints excluded: chain E residue 3700 THR Chi-restraints excluded: chain E residue 3722 SER Chi-restraints excluded: chain E residue 3730 THR Chi-restraints excluded: chain E residue 3787 THR Chi-restraints excluded: chain E residue 3797 THR Chi-restraints excluded: chain E residue 3827 GLU Chi-restraints excluded: chain E residue 3865 ASP Chi-restraints excluded: chain E residue 3886 SER Chi-restraints excluded: chain E residue 3923 LEU Chi-restraints excluded: chain E residue 3985 THR Chi-restraints excluded: chain E residue 4002 ASN Chi-restraints excluded: chain F residue 3624 SER Chi-restraints excluded: chain F residue 3633 VAL Chi-restraints excluded: chain F residue 3700 THR Chi-restraints excluded: chain F residue 3722 SER Chi-restraints excluded: chain F residue 3730 THR Chi-restraints excluded: chain F residue 3753 THR Chi-restraints excluded: chain F residue 3784 VAL Chi-restraints excluded: chain F residue 3787 THR Chi-restraints excluded: chain F residue 3797 THR Chi-restraints excluded: chain F residue 3808 MET Chi-restraints excluded: chain F residue 3821 SER Chi-restraints excluded: chain F residue 3853 THR Chi-restraints excluded: chain F residue 3865 ASP Chi-restraints excluded: chain F residue 3923 LEU Chi-restraints excluded: chain F residue 3985 THR Chi-restraints excluded: chain F residue 4065 CYS Chi-restraints excluded: chain F residue 4073 ILE Chi-restraints excluded: chain G residue 3592 THR Chi-restraints excluded: chain G residue 3624 SER Chi-restraints excluded: chain G residue 3633 VAL Chi-restraints excluded: chain G residue 3674 THR Chi-restraints excluded: chain G residue 3700 THR Chi-restraints excluded: chain G residue 3722 SER Chi-restraints excluded: chain G residue 3740 ILE Chi-restraints excluded: chain G residue 3787 THR Chi-restraints excluded: chain G residue 3808 MET Chi-restraints excluded: chain G residue 3821 SER Chi-restraints excluded: chain G residue 3886 SER Chi-restraints excluded: chain G residue 3985 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 297 optimal weight: 20.0000 chunk 345 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 chunk 344 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 252 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D4001 HIS E3589 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.145508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.110991 restraints weight = 38956.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.107370 restraints weight = 34449.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.108936 restraints weight = 29789.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.109428 restraints weight = 19021.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110112 restraints weight = 15710.255| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 26887 Z= 0.207 Angle : 0.615 7.083 37240 Z= 0.320 Chirality : 0.048 0.190 4564 Planarity : 0.005 0.044 4781 Dihedral : 5.286 35.483 3731 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.26 % Allowed : 13.89 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.33 (0.14), residues: 3542 helix: None (None), residues: 0 sheet: 0.34 (0.12), residues: 1603 loop : 0.25 (0.15), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E4075 TYR 0.011 0.001 TYR E3807 PHE 0.022 0.002 PHE G3577 TRP 0.032 0.002 TRP A4061 HIS 0.002 0.001 HIS A4001 Details of bonding type rmsd covalent geometry : bond 0.00497 (26845) covalent geometry : angle 0.60707 (37156) SS BOND : bond 0.00410 ( 42) SS BOND : angle 2.17725 ( 84) hydrogen bonds : bond 0.03269 ( 791) hydrogen bonds : angle 4.89915 ( 2394) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 204 time to evaluate : 0.887 Fit side-chains REVERT: A 3588 SER cc_start: 0.9456 (p) cc_final: 0.9027 (t) REVERT: A 3998 THR cc_start: 0.8961 (m) cc_final: 0.8424 (p) REVERT: A 4075 ARG cc_start: 0.8644 (mmt90) cc_final: 0.8422 (mmt90) REVERT: B 3587 ASN cc_start: 0.9403 (m-40) cc_final: 0.9081 (m-40) REVERT: B 3588 SER cc_start: 0.9203 (p) cc_final: 0.8949 (t) REVERT: B 3716 ASP cc_start: 0.8450 (t0) cc_final: 0.8195 (t0) REVERT: B 3998 THR cc_start: 0.8833 (m) cc_final: 0.8378 (p) REVERT: C 3998 THR cc_start: 0.8991 (m) cc_final: 0.8485 (p) REVERT: C 4012 LEU cc_start: 0.8328 (tt) cc_final: 0.8036 (tt) REVERT: C 4023 ASP cc_start: 0.8127 (t0) cc_final: 0.7435 (p0) REVERT: D 3588 SER cc_start: 0.9421 (p) cc_final: 0.9071 (t) REVERT: D 3716 ASP cc_start: 0.8624 (t0) cc_final: 0.8326 (t0) REVERT: D 3925 GLN cc_start: 0.8758 (tt0) cc_final: 0.8498 (tt0) REVERT: D 3998 THR cc_start: 0.8922 (m) cc_final: 0.8247 (p) REVERT: D 4012 LEU cc_start: 0.8305 (tt) cc_final: 0.8093 (tt) REVERT: D 4023 ASP cc_start: 0.7627 (t70) cc_final: 0.7123 (p0) REVERT: E 3716 ASP cc_start: 0.8484 (t0) cc_final: 0.8231 (t0) REVERT: E 3925 GLN cc_start: 0.8927 (tp40) cc_final: 0.8560 (tp40) REVERT: E 3998 THR cc_start: 0.8698 (m) cc_final: 0.8062 (p) REVERT: E 4012 LEU cc_start: 0.8481 (tt) cc_final: 0.8197 (tt) REVERT: E 4023 ASP cc_start: 0.7418 (t70) cc_final: 0.6839 (p0) REVERT: F 3588 SER cc_start: 0.9422 (p) cc_final: 0.9092 (t) REVERT: F 3716 ASP cc_start: 0.8561 (t0) cc_final: 0.8232 (t0) REVERT: F 3998 THR cc_start: 0.8801 (m) cc_final: 0.8044 (p) REVERT: F 4023 ASP cc_start: 0.7786 (t0) cc_final: 0.7108 (p0) REVERT: F 4075 ARG cc_start: 0.8755 (mmt90) cc_final: 0.8129 (mtt-85) REVERT: G 3664 VAL cc_start: 0.9519 (p) cc_final: 0.9149 (m) REVERT: G 3998 THR cc_start: 0.8815 (m) cc_final: 0.8273 (p) REVERT: G 4023 ASP cc_start: 0.7936 (t0) cc_final: 0.7401 (p0) outliers start: 99 outliers final: 96 residues processed: 286 average time/residue: 0.1284 time to fit residues: 62.6425 Evaluate side-chains 291 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 195 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3624 SER Chi-restraints excluded: chain A residue 3633 VAL Chi-restraints excluded: chain A residue 3674 THR Chi-restraints excluded: chain A residue 3700 THR Chi-restraints excluded: chain A residue 3722 SER Chi-restraints excluded: chain A residue 3730 THR Chi-restraints excluded: chain A residue 3787 THR Chi-restraints excluded: chain A residue 3797 THR Chi-restraints excluded: chain A residue 3808 MET Chi-restraints excluded: chain A residue 3865 ASP Chi-restraints excluded: chain A residue 3985 THR Chi-restraints excluded: chain A residue 4073 ILE Chi-restraints excluded: chain B residue 3592 THR Chi-restraints excluded: chain B residue 3624 SER Chi-restraints excluded: chain B residue 3633 VAL Chi-restraints excluded: chain B residue 3691 SER Chi-restraints excluded: chain B residue 3700 THR Chi-restraints excluded: chain B residue 3722 SER Chi-restraints excluded: chain B residue 3730 THR Chi-restraints excluded: chain B residue 3784 VAL Chi-restraints excluded: chain B residue 3787 THR Chi-restraints excluded: chain B residue 3797 THR Chi-restraints excluded: chain B residue 3821 SER Chi-restraints excluded: chain B residue 3853 THR Chi-restraints excluded: chain B residue 3985 THR Chi-restraints excluded: chain B residue 4022 THR Chi-restraints excluded: chain C residue 3624 SER Chi-restraints excluded: chain C residue 3674 THR Chi-restraints excluded: chain C residue 3700 THR Chi-restraints excluded: chain C residue 3722 SER Chi-restraints excluded: chain C residue 3730 THR Chi-restraints excluded: chain C residue 3784 VAL Chi-restraints excluded: chain C residue 3787 THR Chi-restraints excluded: chain C residue 3831 ILE Chi-restraints excluded: chain C residue 3881 SER Chi-restraints excluded: chain C residue 3985 THR Chi-restraints excluded: chain C residue 4073 ILE Chi-restraints excluded: chain D residue 3592 THR Chi-restraints excluded: chain D residue 3674 THR Chi-restraints excluded: chain D residue 3722 SER Chi-restraints excluded: chain D residue 3730 THR Chi-restraints excluded: chain D residue 3740 ILE Chi-restraints excluded: chain D residue 3787 THR Chi-restraints excluded: chain D residue 3797 THR Chi-restraints excluded: chain D residue 3881 SER Chi-restraints excluded: chain D residue 3886 SER Chi-restraints excluded: chain D residue 3923 LEU Chi-restraints excluded: chain D residue 3985 THR Chi-restraints excluded: chain E residue 3589 ASN Chi-restraints excluded: chain E residue 3592 THR Chi-restraints excluded: chain E residue 3624 SER Chi-restraints excluded: chain E residue 3633 VAL Chi-restraints excluded: chain E residue 3674 THR Chi-restraints excluded: chain E residue 3700 THR Chi-restraints excluded: chain E residue 3722 SER Chi-restraints excluded: chain E residue 3730 THR Chi-restraints excluded: chain E residue 3787 THR Chi-restraints excluded: chain E residue 3797 THR Chi-restraints excluded: chain E residue 3865 ASP Chi-restraints excluded: chain E residue 3886 SER Chi-restraints excluded: chain E residue 3923 LEU Chi-restraints excluded: chain E residue 3985 THR Chi-restraints excluded: chain E residue 4002 ASN Chi-restraints excluded: chain F residue 3624 SER Chi-restraints excluded: chain F residue 3633 VAL Chi-restraints excluded: chain F residue 3700 THR Chi-restraints excluded: chain F residue 3722 SER Chi-restraints excluded: chain F residue 3730 THR Chi-restraints excluded: chain F residue 3753 THR Chi-restraints excluded: chain F residue 3784 VAL Chi-restraints excluded: chain F residue 3787 THR Chi-restraints excluded: chain F residue 3797 THR Chi-restraints excluded: chain F residue 3808 MET Chi-restraints excluded: chain F residue 3821 SER Chi-restraints excluded: chain F residue 3853 THR Chi-restraints excluded: chain F residue 3865 ASP Chi-restraints excluded: chain F residue 3881 SER Chi-restraints excluded: chain F residue 3923 LEU Chi-restraints excluded: chain F residue 3985 THR Chi-restraints excluded: chain F residue 4073 ILE Chi-restraints excluded: chain G residue 3592 THR Chi-restraints excluded: chain G residue 3624 SER Chi-restraints excluded: chain G residue 3633 VAL Chi-restraints excluded: chain G residue 3674 THR Chi-restraints excluded: chain G residue 3691 SER Chi-restraints excluded: chain G residue 3700 THR Chi-restraints excluded: chain G residue 3722 SER Chi-restraints excluded: chain G residue 3740 ILE Chi-restraints excluded: chain G residue 3787 THR Chi-restraints excluded: chain G residue 3797 THR Chi-restraints excluded: chain G residue 3808 MET Chi-restraints excluded: chain G residue 3821 SER Chi-restraints excluded: chain G residue 3886 SER Chi-restraints excluded: chain G residue 3924 CYS Chi-restraints excluded: chain G residue 3985 THR Chi-restraints excluded: chain G residue 4022 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 117 optimal weight: 1.9990 chunk 258 optimal weight: 0.8980 chunk 230 optimal weight: 0.4980 chunk 223 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 280 optimal weight: 0.9990 chunk 2 optimal weight: 20.0000 chunk 237 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 177 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D4001 HIS E3589 ASN ** E3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.149268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.114642 restraints weight = 38832.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.112691 restraints weight = 31690.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.113914 restraints weight = 29780.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114313 restraints weight = 19029.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.115385 restraints weight = 16514.726| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26887 Z= 0.103 Angle : 0.557 7.514 37240 Z= 0.287 Chirality : 0.047 0.202 4564 Planarity : 0.004 0.045 4781 Dihedral : 4.766 32.543 3731 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.74 % Allowed : 15.47 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.68 (0.14), residues: 3542 helix: None (None), residues: 0 sheet: 0.46 (0.12), residues: 1666 loop : 0.61 (0.15), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B4075 TYR 0.012 0.001 TYR B3807 PHE 0.018 0.001 PHE C3577 TRP 0.024 0.001 TRP B4061 HIS 0.001 0.000 HIS A4001 Details of bonding type rmsd covalent geometry : bond 0.00244 (26845) covalent geometry : angle 0.55213 (37156) SS BOND : bond 0.00467 ( 42) SS BOND : angle 1.56830 ( 84) hydrogen bonds : bond 0.02700 ( 791) hydrogen bonds : angle 4.69318 ( 2394) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 226 time to evaluate : 0.811 Fit side-chains REVERT: A 3588 SER cc_start: 0.9419 (p) cc_final: 0.9078 (t) REVERT: A 3998 THR cc_start: 0.8884 (m) cc_final: 0.8393 (p) REVERT: B 3716 ASP cc_start: 0.8401 (t0) cc_final: 0.8126 (t0) REVERT: B 3925 GLN cc_start: 0.8755 (tt0) cc_final: 0.8439 (tt0) REVERT: B 3998 THR cc_start: 0.8821 (m) cc_final: 0.8396 (p) REVERT: B 4012 LEU cc_start: 0.8375 (tp) cc_final: 0.8029 (tp) REVERT: C 3998 THR cc_start: 0.9004 (m) cc_final: 0.8539 (p) REVERT: C 4012 LEU cc_start: 0.8236 (tt) cc_final: 0.7972 (tt) REVERT: D 3588 SER cc_start: 0.9328 (p) cc_final: 0.9108 (t) REVERT: D 3716 ASP cc_start: 0.8560 (t0) cc_final: 0.8342 (t0) REVERT: D 3925 GLN cc_start: 0.8660 (tt0) cc_final: 0.8409 (tt0) REVERT: D 3998 THR cc_start: 0.8933 (m) cc_final: 0.8300 (p) REVERT: D 4023 ASP cc_start: 0.7478 (t70) cc_final: 0.7168 (p0) REVERT: E 3716 ASP cc_start: 0.8417 (t0) cc_final: 0.8206 (t0) REVERT: E 3925 GLN cc_start: 0.8865 (tp40) cc_final: 0.8536 (tp40) REVERT: E 3998 THR cc_start: 0.8800 (m) cc_final: 0.8153 (p) REVERT: E 4012 LEU cc_start: 0.8428 (tt) cc_final: 0.8170 (tt) REVERT: E 4023 ASP cc_start: 0.7330 (t70) cc_final: 0.6898 (p0) REVERT: F 3716 ASP cc_start: 0.8474 (t0) cc_final: 0.8190 (t0) REVERT: F 3998 THR cc_start: 0.8777 (m) cc_final: 0.8067 (p) REVERT: F 4023 ASP cc_start: 0.7677 (t0) cc_final: 0.7219 (p0) REVERT: F 4075 ARG cc_start: 0.8648 (mmt90) cc_final: 0.8119 (mtt-85) REVERT: G 3588 SER cc_start: 0.9416 (p) cc_final: 0.9148 (t) REVERT: G 3998 THR cc_start: 0.8836 (m) cc_final: 0.8311 (p) REVERT: G 4023 ASP cc_start: 0.7778 (t0) cc_final: 0.7444 (p0) outliers start: 53 outliers final: 50 residues processed: 269 average time/residue: 0.1372 time to fit residues: 62.4595 Evaluate side-chains 251 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 201 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3633 VAL Chi-restraints excluded: chain A residue 3722 SER Chi-restraints excluded: chain A residue 3730 THR Chi-restraints excluded: chain A residue 3865 ASP Chi-restraints excluded: chain A residue 4073 ILE Chi-restraints excluded: chain B residue 3592 THR Chi-restraints excluded: chain B residue 3633 VAL Chi-restraints excluded: chain B residue 3691 SER Chi-restraints excluded: chain B residue 3722 SER Chi-restraints excluded: chain B residue 3730 THR Chi-restraints excluded: chain B residue 3797 THR Chi-restraints excluded: chain B residue 3853 THR Chi-restraints excluded: chain B residue 3985 THR Chi-restraints excluded: chain B residue 4022 THR Chi-restraints excluded: chain C residue 3674 THR Chi-restraints excluded: chain C residue 3722 SER Chi-restraints excluded: chain C residue 3881 SER Chi-restraints excluded: chain C residue 4073 ILE Chi-restraints excluded: chain D residue 3592 THR Chi-restraints excluded: chain D residue 3674 THR Chi-restraints excluded: chain D residue 3722 SER Chi-restraints excluded: chain D residue 3886 SER Chi-restraints excluded: chain D residue 3923 LEU Chi-restraints excluded: chain E residue 3589 ASN Chi-restraints excluded: chain E residue 3592 THR Chi-restraints excluded: chain E residue 3624 SER Chi-restraints excluded: chain E residue 3633 VAL Chi-restraints excluded: chain E residue 3674 THR Chi-restraints excluded: chain E residue 3700 THR Chi-restraints excluded: chain E residue 3722 SER Chi-restraints excluded: chain E residue 3730 THR Chi-restraints excluded: chain E residue 3865 ASP Chi-restraints excluded: chain E residue 3923 LEU Chi-restraints excluded: chain E residue 4002 ASN Chi-restraints excluded: chain F residue 3633 VAL Chi-restraints excluded: chain F residue 3700 THR Chi-restraints excluded: chain F residue 3730 THR Chi-restraints excluded: chain F residue 3753 THR Chi-restraints excluded: chain F residue 3853 THR Chi-restraints excluded: chain F residue 3865 ASP Chi-restraints excluded: chain F residue 3881 SER Chi-restraints excluded: chain F residue 3923 LEU Chi-restraints excluded: chain F residue 4073 ILE Chi-restraints excluded: chain G residue 3633 VAL Chi-restraints excluded: chain G residue 3674 THR Chi-restraints excluded: chain G residue 3722 SER Chi-restraints excluded: chain G residue 3808 MET Chi-restraints excluded: chain G residue 3821 SER Chi-restraints excluded: chain G residue 3886 SER Chi-restraints excluded: chain G residue 3924 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 143 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 166 optimal weight: 2.9990 chunk 222 optimal weight: 0.4980 chunk 266 optimal weight: 5.9990 chunk 250 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 216 optimal weight: 3.9990 chunk 304 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D3734 ASN D4001 HIS E3589 ASN ** E3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.148568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.113843 restraints weight = 38462.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.111562 restraints weight = 32948.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.112917 restraints weight = 29925.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.113285 restraints weight = 18511.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.113570 restraints weight = 16518.267| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26887 Z= 0.124 Angle : 0.565 10.183 37240 Z= 0.290 Chirality : 0.047 0.245 4564 Planarity : 0.005 0.062 4781 Dihedral : 4.765 32.089 3731 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.94 % Allowed : 15.57 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.74 (0.14), residues: 3542 helix: None (None), residues: 0 sheet: 0.53 (0.12), residues: 1659 loop : 0.63 (0.15), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C4025 TYR 0.011 0.001 TYR G3807 PHE 0.051 0.001 PHE E3577 TRP 0.022 0.001 TRP A4061 HIS 0.001 0.001 HIS B4001 Details of bonding type rmsd covalent geometry : bond 0.00299 (26845) covalent geometry : angle 0.56000 (37156) SS BOND : bond 0.00338 ( 42) SS BOND : angle 1.68721 ( 84) hydrogen bonds : bond 0.02816 ( 791) hydrogen bonds : angle 4.65691 ( 2394) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3073.40 seconds wall clock time: 54 minutes 10.56 seconds (3250.56 seconds total)