Starting phenix.real_space_refine on Mon Jun 23 01:28:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9flw_50541/06_2025/9flw_50541.cif Found real_map, /net/cci-nas-00/data/ceres_data/9flw_50541/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9flw_50541/06_2025/9flw_50541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9flw_50541/06_2025/9flw_50541.map" model { file = "/net/cci-nas-00/data/ceres_data/9flw_50541/06_2025/9flw_50541.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9flw_50541/06_2025/9flw_50541.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.115 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, G, F Time building chain proxies: 8.80, per 1000 atoms: 0.34 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 C3583 " - pdb=" SG CYS C3720 " distance=2.03 Simple disulfide: pdb=" SG CYS B3583 " - pdb=" SG CYS B3720 " distance=2.04 Simple disulfide: pdb=" SG CYS E3583 " - pdb=" SG CYS E3720 " distance=2.04 Simple disulfide: pdb=" SG CYS D3583 " - pdb=" SG CYS D3720 " distance=2.04 Simple disulfide: pdb=" SG CYS G3583 " - pdb=" SG CYS G3720 " distance=2.04 Simple disulfide: pdb=" SG CYS F3583 " - pdb=" SG CYS F3720 " distance=2.04 Simple disulfide: pdb=" SG CYS C3665 " - pdb=" SG CYS C3817 " distance=2.03 Simple disulfide: pdb=" SG CYS B3665 " - pdb=" SG CYS B3817 " distance=2.03 Simple disulfide: pdb=" SG CYS E3665 " - pdb=" SG CYS E3817 " distance=2.03 Simple disulfide: pdb=" SG CYS D3665 " - pdb=" SG CYS D3817 " distance=2.03 Simple disulfide: pdb=" SG CYS G3665 " - pdb=" SG CYS G3817 " distance=2.03 Simple disulfide: pdb=" SG CYS F3665 " - pdb=" SG CYS F3817 " distance=2.03 Simple disulfide: pdb=" SG CYS C3747 " - pdb=" SG CYS C3898 " distance=2.04 Simple disulfide: pdb=" SG CYS B3747 " - pdb=" SG CYS B3898 " distance=2.04 Simple disulfide: pdb=" SG CYS E3747 " - pdb=" SG CYS E3898 " distance=2.04 Simple disulfide: pdb=" SG CYS D3747 " - pdb=" SG CYS D3898 " distance=2.04 Simple disulfide: pdb=" SG CYS G3747 " - pdb=" SG CYS G3898 " distance=2.04 Simple disulfide: pdb=" SG CYS F3747 " - pdb=" SG CYS F3898 " distance=2.04 Simple disulfide: pdb=" SG CYS C3760 " - pdb=" SG CYS C3810 " distance=2.03 Simple disulfide: pdb=" SG CYS B3760 " - pdb=" SG CYS B3810 " distance=2.03 Simple disulfide: pdb=" SG CYS E3760 " - pdb=" SG CYS E3810 " distance=2.03 Simple disulfide: pdb=" SG CYS D3760 " - pdb=" SG CYS D3810 " distance=2.03 Simple disulfide: pdb=" SG CYS G3760 " - pdb=" SG CYS G3810 " distance=2.03 Simple disulfide: pdb=" SG CYS F3760 " - pdb=" SG CYS F3810 " distance=2.03 Simple disulfide: pdb=" SG CYS C3843 " - pdb=" SG CYS C3980 " distance=2.03 Simple disulfide: pdb=" SG CYS B3843 " - pdb=" SG CYS B3980 " distance=2.03 Simple disulfide: pdb=" SG CYS E3843 " - pdb=" SG CYS E3980 " distance=2.03 Simple disulfide: pdb=" SG CYS D3843 " - pdb=" SG CYS D3980 " distance=2.03 Simple disulfide: pdb=" SG CYS G3843 " - pdb=" SG CYS G3980 " distance=2.03 Simple disulfide: pdb=" SG CYS F3843 " - pdb=" SG CYS F3980 " distance=2.03 Simple disulfide: pdb=" SG CYS C3924 " - pdb=" SG CYS C4065 " distance=2.04 Simple disulfide: pdb=" SG CYS B3924 " - pdb=" SG CYS B4065 " distance=2.04 Simple disulfide: pdb=" SG CYS E3924 " - pdb=" SG CYS E4065 " distance=2.04 Simple disulfide: pdb=" SG CYS D3924 " - pdb=" SG CYS D4065 " distance=2.04 Simple disulfide: pdb=" SG CYS G3924 " - pdb=" SG CYS G4065 " distance=2.04 Simple disulfide: pdb=" SG CYS F3924 " - pdb=" SG CYS F4065 " 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: 6.64 Conformation dependent library (CDL) restraints added in 4.8 seconds 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: 5.63 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: 11.64 Time building geometry restraints manager: 7.88 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: 0.25 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 58.540 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.910 ------------------------------------------------------------------------------- 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 : 7.93 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (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 TRP 0.055 0.012 TRP D3944 HIS 0.001 0.001 HIS C4001 PHE 0.045 0.005 PHE G3662 TYR 0.033 0.007 TYR F3807 ARG 0.003 0.000 ARG F4025 Details of bonding type rmsd hydrogen bonds : bond 0.14099 ( 791) hydrogen bonds : angle 8.02780 ( 2394) SS BOND : bond 0.00427 ( 42) SS BOND : angle 2.02354 ( 84) covalent geometry : bond 0.01774 (26845) covalent geometry : angle 1.78078 (37156) *********************** 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 : 2.639 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: 0.7372 (tp30) REVERT: A 3927 ASP cc_start: 0.7738 (t0) cc_final: 0.7512 (t0) REVERT: A 3998 THR cc_start: 0.8782 (m) cc_final: 0.8315 (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: 0.8296 (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: 0.8029 (t70) REVERT: C 3924 CYS cc_start: 0.7899 (m) cc_final: 0.7618 (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: 0.7017 (t0) REVERT: D 3998 THR cc_start: 0.8879 (m) cc_final: 0.8393 (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: 0.8364 (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: 0.8413 (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: 0.7419 (t0) REVERT: G 3998 THR cc_start: 0.8704 (m) cc_final: 0.8174 (p) outliers start: 0 outliers final: 0 residues processed: 671 average time/residue: 0.2962 time to fit residues: 336.8697 Evaluate side-chains 273 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 317 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C3695 ASN C3764 GLN E3695 ASN G3695 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.139178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103292 restraints weight = 38950.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.101292 restraints weight = 25855.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.102312 restraints weight = 26471.548| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 26887 Z= 0.214 Angle : 0.658 8.272 37240 Z= 0.349 Chirality : 0.049 0.182 4564 Planarity : 0.005 0.044 4781 Dihedral : 5.174 23.891 3731 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.04 % Allowed : 7.50 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.14), residues: 3542 helix: None (None), residues: 0 sheet: 1.03 (0.13), residues: 1512 loop : 0.90 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F4061 HIS 0.004 0.001 HIS G4001 PHE 0.010 0.001 PHE E3662 TYR 0.022 0.002 TYR A3650 ARG 0.004 0.001 ARG C4075 Details of bonding type rmsd hydrogen bonds : bond 0.04068 ( 791) hydrogen bonds : angle 5.93928 ( 2394) SS BOND : bond 0.00871 ( 42) SS BOND : angle 2.23337 ( 84) covalent geometry : bond 0.00503 (26845) covalent geometry : angle 0.64965 (37156) *********************** 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 425 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 363 time to evaluate : 2.728 Fit side-chains revert: symmetry clash REVERT: A 3624 SER cc_start: 0.8866 (p) cc_final: 0.8335 (t) REVERT: A 3716 ASP cc_start: 0.8402 (t0) cc_final: 0.8032 (t0) REVERT: A 3924 CYS cc_start: 0.7066 (m) cc_final: 0.6808 (m) REVERT: A 3927 ASP cc_start: 0.7995 (t0) cc_final: 0.7780 (t70) REVERT: A 3998 THR cc_start: 0.8695 (m) cc_final: 0.7966 (p) REVERT: A 4017 GLN cc_start: 0.8597 (pm20) cc_final: 0.8216 (pm20) REVERT: B 3716 ASP cc_start: 0.8441 (t0) cc_final: 0.8063 (t0) REVERT: B 3875 SER cc_start: 0.8978 (t) cc_final: 0.8765 (m) REVERT: B 3927 ASP cc_start: 0.7773 (t0) cc_final: 0.6838 (t70) REVERT: B 3998 THR cc_start: 0.8646 (m) cc_final: 0.7889 (p) REVERT: C 3716 ASP cc_start: 0.8406 (t0) cc_final: 0.7981 (t0) REVERT: C 3998 THR cc_start: 0.8660 (m) cc_final: 0.7984 (p) REVERT: C 4075 ARG cc_start: 0.8656 (mmt90) cc_final: 0.8361 (mmt90) REVERT: D 3716 ASP cc_start: 0.8480 (t0) cc_final: 0.7802 (t0) REVERT: D 3998 THR cc_start: 0.8681 (m) cc_final: 0.7885 (p) REVERT: E 3716 ASP cc_start: 0.8408 (t0) cc_final: 0.8089 (t0) REVERT: E 3821 SER cc_start: 0.8471 (p) cc_final: 0.8240 (p) REVERT: E 3875 SER cc_start: 0.9162 (t) cc_final: 0.8934 (m) REVERT: E 3987 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7129 (mm-30) REVERT: E 3998 THR cc_start: 0.8726 (m) cc_final: 0.7922 (p) REVERT: F 3716 ASP cc_start: 0.8470 (t0) cc_final: 0.8262 (t0) REVERT: F 3875 SER cc_start: 0.9099 (t) cc_final: 0.8857 (m) REVERT: F 3927 ASP cc_start: 0.7814 (t0) cc_final: 0.7456 (t70) REVERT: F 3987 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7214 (mm-30) REVERT: F 3998 THR cc_start: 0.8724 (m) cc_final: 0.7901 (p) REVERT: F 4012 LEU cc_start: 0.8407 (tt) cc_final: 0.8012 (tt) REVERT: G 3716 ASP cc_start: 0.8358 (t0) cc_final: 0.7995 (t0) REVERT: G 3927 ASP cc_start: 0.7874 (t0) cc_final: 0.7508 (t70) REVERT: G 3998 THR cc_start: 0.8532 (m) cc_final: 0.7844 (p) REVERT: G 4012 LEU cc_start: 0.8376 (tt) cc_final: 0.8022 (tt) outliers start: 62 outliers final: 47 residues processed: 420 average time/residue: 0.3675 time to fit residues: 269.1337 Evaluate side-chains 278 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 231 time to evaluate : 2.875 ------------------------------------------------------------------------------- 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 3700 THR 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 4022 THR 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 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 3700 THR 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 3691 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 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 3691 SER 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 275 optimal weight: 1.9990 chunk 319 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 337 optimal weight: 0.4980 chunk 339 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 198 optimal weight: 20.0000 chunk 286 optimal weight: 0.0770 chunk 50 optimal weight: 10.0000 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4001 HIS A4002 ASN ** C3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4001 HIS G4001 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.141272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105297 restraints weight = 38764.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.103074 restraints weight = 25115.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.103929 restraints weight = 28137.249| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26887 Z= 0.119 Angle : 0.581 8.572 37240 Z= 0.304 Chirality : 0.047 0.160 4564 Planarity : 0.005 0.044 4781 Dihedral : 4.736 28.013 3731 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.68 % Allowed : 10.14 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.14), residues: 3542 helix: None (None), residues: 0 sheet: 0.88 (0.13), residues: 1561 loop : 1.01 (0.15), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E4061 HIS 0.006 0.001 HIS F4001 PHE 0.012 0.001 PHE F4005 TYR 0.013 0.001 TYR C3650 ARG 0.004 0.001 ARG E4075 Details of bonding type rmsd hydrogen bonds : bond 0.03277 ( 791) hydrogen bonds : angle 5.45584 ( 2394) SS BOND : bond 0.00560 ( 42) SS BOND : angle 2.24300 ( 84) covalent geometry : bond 0.00273 (26845) covalent geometry : angle 0.57217 (37156) *********************** 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 333 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 282 time to evaluate : 2.652 Fit side-chains revert: symmetry clash REVERT: A 3716 ASP cc_start: 0.8408 (t0) cc_final: 0.8025 (t0) REVERT: A 3927 ASP cc_start: 0.8070 (t0) cc_final: 0.7868 (t70) REVERT: A 3998 THR cc_start: 0.8687 (m) cc_final: 0.7957 (p) REVERT: A 4012 LEU cc_start: 0.8247 (tt) cc_final: 0.7857 (tt) REVERT: A 4015 THR cc_start: 0.9307 (m) cc_final: 0.9042 (p) REVERT: B 3716 ASP cc_start: 0.8454 (t0) cc_final: 0.8024 (t0) REVERT: B 3875 SER cc_start: 0.9032 (t) cc_final: 0.8817 (m) REVERT: B 3927 ASP cc_start: 0.7794 (t0) cc_final: 0.7565 (t70) REVERT: B 3998 THR cc_start: 0.8640 (m) cc_final: 0.7846 (p) REVERT: B 4017 GLN cc_start: 0.8425 (pm20) cc_final: 0.7785 (pm20) REVERT: B 4023 ASP cc_start: 0.7737 (t0) cc_final: 0.6857 (p0) REVERT: C 3677 VAL cc_start: 0.8578 (t) cc_final: 0.8348 (m) REVERT: C 3716 ASP cc_start: 0.8410 (t0) cc_final: 0.8014 (t0) REVERT: C 3998 THR cc_start: 0.8711 (m) cc_final: 0.7937 (p) REVERT: C 4015 THR cc_start: 0.9284 (m) cc_final: 0.9065 (p) REVERT: C 4075 ARG cc_start: 0.8578 (mmt90) cc_final: 0.8281 (mmt90) REVERT: D 3998 THR cc_start: 0.8776 (m) cc_final: 0.7965 (p) REVERT: E 3716 ASP cc_start: 0.8415 (t0) cc_final: 0.8071 (t0) REVERT: E 3821 SER cc_start: 0.8425 (p) cc_final: 0.8210 (p) REVERT: E 3875 SER cc_start: 0.9170 (t) cc_final: 0.8924 (m) REVERT: E 3998 THR cc_start: 0.8735 (m) cc_final: 0.7887 (p) REVERT: E 4073 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8452 (pt) REVERT: E 4075 ARG cc_start: 0.8844 (mmt90) cc_final: 0.8474 (mmt90) REVERT: F 3677 VAL cc_start: 0.8496 (t) cc_final: 0.8259 (m) REVERT: F 3716 ASP cc_start: 0.8522 (t0) cc_final: 0.8283 (t0) REVERT: F 3875 SER cc_start: 0.9083 (t) cc_final: 0.8838 (m) REVERT: F 3998 THR cc_start: 0.8700 (m) cc_final: 0.7881 (p) REVERT: F 4012 LEU cc_start: 0.8296 (tt) cc_final: 0.7897 (tt) REVERT: G 3846 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7855 (mt-10) REVERT: G 3932 GLN cc_start: 0.9299 (mm-40) cc_final: 0.9093 (mm-40) REVERT: G 3998 THR cc_start: 0.8574 (m) cc_final: 0.7807 (p) REVERT: G 4012 LEU cc_start: 0.8328 (tt) cc_final: 0.7950 (tt) outliers start: 51 outliers final: 40 residues processed: 322 average time/residue: 0.3024 time to fit residues: 167.3873 Evaluate side-chains 252 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 211 time to evaluate : 2.646 ------------------------------------------------------------------------------- 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 3985 THR Chi-restraints excluded: chain A residue 4022 THR Chi-restraints excluded: chain A residue 4073 ILE Chi-restraints excluded: chain B residue 3633 VAL Chi-restraints excluded: chain B residue 3722 SER Chi-restraints excluded: chain B residue 3784 VAL Chi-restraints excluded: chain B residue 3924 CYS Chi-restraints excluded: chain B residue 3926 LEU 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 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 C residue 3985 THR Chi-restraints excluded: chain C residue 4002 ASN Chi-restraints excluded: chain D residue 3722 SER Chi-restraints excluded: chain D residue 3784 VAL Chi-restraints excluded: chain D residue 3985 THR Chi-restraints excluded: chain E residue 3633 VAL Chi-restraints excluded: chain E residue 3691 SER Chi-restraints excluded: chain E residue 3700 THR Chi-restraints excluded: chain E residue 3865 ASP Chi-restraints excluded: chain E residue 3985 THR 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 3787 THR 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 3722 SER Chi-restraints excluded: chain G residue 3784 VAL Chi-restraints excluded: chain G residue 3787 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 134 optimal weight: 6.9990 chunk 156 optimal weight: 20.0000 chunk 116 optimal weight: 0.7980 chunk 207 optimal weight: 9.9990 chunk 335 optimal weight: 1.9990 chunk 327 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 264 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 159 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 E4001 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.150152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114633 restraints weight = 38544.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.113958 restraints weight = 25940.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.114535 restraints weight = 28369.142| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26887 Z= 0.166 Angle : 0.582 7.395 37240 Z= 0.304 Chirality : 0.047 0.161 4564 Planarity : 0.005 0.045 4781 Dihedral : 4.886 30.825 3731 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.29 % Allowed : 10.73 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.14), residues: 3542 helix: None (None), residues: 0 sheet: 0.93 (0.13), residues: 1561 loop : 0.83 (0.15), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A4061 HIS 0.004 0.001 HIS B4001 PHE 0.012 0.001 PHE G3965 TYR 0.010 0.001 TYR C3650 ARG 0.004 0.001 ARG A3818 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 791) hydrogen bonds : angle 5.14514 ( 2394) SS BOND : bond 0.00633 ( 42) SS BOND : angle 2.28059 ( 84) covalent geometry : bond 0.00392 (26845) covalent geometry : angle 0.57199 (37156) *********************** 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 339 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 239 time to evaluate : 3.040 Fit side-chains revert: symmetry clash REVERT: A 3716 ASP cc_start: 0.8363 (t0) cc_final: 0.8130 (t0) REVERT: A 3998 THR cc_start: 0.8786 (m) cc_final: 0.8089 (p) REVERT: A 4012 LEU cc_start: 0.8265 (tt) cc_final: 0.7944 (tt) REVERT: A 4015 THR cc_start: 0.9361 (m) cc_final: 0.9158 (p) REVERT: A 4017 GLN cc_start: 0.8676 (pm20) cc_final: 0.8372 (pm20) REVERT: A 4073 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8533 (pt) REVERT: B 3716 ASP cc_start: 0.8385 (t0) cc_final: 0.8074 (t0) REVERT: B 3998 THR cc_start: 0.8618 (m) cc_final: 0.7844 (p) REVERT: B 4023 ASP cc_start: 0.7709 (t0) cc_final: 0.7119 (p0) REVERT: C 3716 ASP cc_start: 0.8412 (t0) cc_final: 0.8198 (t0) REVERT: C 3925 GLN cc_start: 0.8715 (tt0) cc_final: 0.8470 (tt0) REVERT: C 3998 THR cc_start: 0.8834 (m) cc_final: 0.8191 (p) REVERT: C 4012 LEU cc_start: 0.8362 (tt) cc_final: 0.8027 (tt) REVERT: C 4023 ASP cc_start: 0.7641 (t0) cc_final: 0.7132 (p0) REVERT: D 3716 ASP cc_start: 0.8528 (t0) cc_final: 0.8070 (t0) REVERT: D 3998 THR cc_start: 0.8830 (m) cc_final: 0.8137 (p) REVERT: D 4012 LEU cc_start: 0.8363 (tt) cc_final: 0.8030 (tt) REVERT: E 3716 ASP cc_start: 0.8315 (t0) cc_final: 0.8108 (t0) REVERT: E 3998 THR cc_start: 0.8807 (m) cc_final: 0.8071 (p) REVERT: E 4075 ARG cc_start: 0.8858 (mmt90) cc_final: 0.8655 (mmt90) REVERT: F 3588 SER cc_start: 0.9527 (p) cc_final: 0.9175 (t) REVERT: F 3677 VAL cc_start: 0.8572 (t) cc_final: 0.8344 (m) REVERT: F 3998 THR cc_start: 0.8753 (m) cc_final: 0.7937 (p) REVERT: F 4012 LEU cc_start: 0.8223 (tt) cc_final: 0.7886 (tt) REVERT: F 4023 ASP cc_start: 0.7541 (t70) cc_final: 0.6897 (t70) REVERT: G 3998 THR cc_start: 0.8661 (m) cc_final: 0.8011 (p) REVERT: G 4012 LEU cc_start: 0.8280 (tt) cc_final: 0.8028 (tt) REVERT: G 4023 ASP cc_start: 0.7504 (t0) cc_final: 0.6997 (p0) outliers start: 100 outliers final: 78 residues processed: 329 average time/residue: 0.2996 time to fit residues: 169.6279 Evaluate side-chains 271 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 192 time to evaluate : 2.577 ------------------------------------------------------------------------------- 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 3691 SER Chi-restraints excluded: chain A residue 3700 THR Chi-restraints excluded: chain A residue 3722 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 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 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 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 C residue 4002 ASN Chi-restraints excluded: chain C residue 4073 ILE Chi-restraints excluded: chain D residue 3691 SER 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 3985 THR Chi-restraints excluded: chain D residue 4073 ILE Chi-restraints excluded: chain E residue 3624 SER Chi-restraints excluded: chain E residue 3633 VAL Chi-restraints excluded: chain E residue 3700 THR Chi-restraints excluded: chain E residue 3722 SER Chi-restraints excluded: chain E residue 3741 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 3924 CYS Chi-restraints excluded: chain E residue 3985 THR Chi-restraints excluded: chain E residue 4073 ILE Chi-restraints excluded: chain F residue 3624 SER Chi-restraints excluded: chain F residue 3633 VAL Chi-restraints excluded: chain F residue 3691 SER 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 3969 SER Chi-restraints excluded: chain F residue 3985 THR Chi-restraints excluded: chain F residue 4073 ILE 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 3741 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 3808 MET Chi-restraints excluded: chain G residue 3821 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 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 42 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 203 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 293 optimal weight: 20.0000 chunk 148 optimal weight: 10.0000 chunk 263 optimal weight: 8.9990 chunk 287 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4001 HIS C4001 HIS C4002 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.139897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104216 restraints weight = 39103.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.101229 restraints weight = 33436.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.102780 restraints weight = 30794.379| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.108 26887 Z= 0.377 Angle : 0.738 10.166 37240 Z= 0.391 Chirality : 0.052 0.202 4564 Planarity : 0.005 0.054 4781 Dihedral : 5.792 31.061 3731 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.65 % Allowed : 11.82 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 3542 helix: None (None), residues: 0 sheet: 0.27 (0.12), residues: 1631 loop : 0.28 (0.15), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C4061 HIS 0.003 0.001 HIS B4001 PHE 0.023 0.002 PHE B3577 TYR 0.016 0.002 TYR D3863 ARG 0.003 0.001 ARG A4075 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 791) hydrogen bonds : angle 5.40210 ( 2394) SS BOND : bond 0.00567 ( 42) SS BOND : angle 3.21805 ( 84) covalent geometry : bond 0.00901 (26845) covalent geometry : angle 0.72311 (37156) *********************** 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 328 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 217 time to evaluate : 3.647 Fit side-chains REVERT: A 3691 SER cc_start: 0.9119 (OUTLIER) cc_final: 0.8918 (m) REVERT: A 3998 THR cc_start: 0.8793 (m) cc_final: 0.8091 (p) REVERT: A 4012 LEU cc_start: 0.8462 (tt) cc_final: 0.8138 (tt) REVERT: B 3588 SER cc_start: 0.9551 (p) cc_final: 0.9016 (t) REVERT: B 3716 ASP cc_start: 0.8500 (t0) cc_final: 0.8200 (t0) REVERT: B 3998 THR cc_start: 0.8756 (m) cc_final: 0.8180 (p) REVERT: B 4023 ASP cc_start: 0.7790 (t0) cc_final: 0.7104 (p0) REVERT: C 3925 GLN cc_start: 0.8780 (tt0) cc_final: 0.8489 (tt0) REVERT: C 3998 THR cc_start: 0.8888 (m) cc_final: 0.8289 (p) REVERT: C 4012 LEU cc_start: 0.8349 (tt) cc_final: 0.8008 (tt) REVERT: C 4023 ASP cc_start: 0.8042 (t0) cc_final: 0.7204 (p0) REVERT: D 3716 ASP cc_start: 0.8630 (t0) cc_final: 0.8333 (t0) REVERT: D 3998 THR cc_start: 0.8864 (m) cc_final: 0.8192 (p) REVERT: D 4012 LEU cc_start: 0.8437 (tt) cc_final: 0.8088 (tt) REVERT: E 3716 ASP cc_start: 0.8512 (t0) cc_final: 0.8248 (t0) REVERT: E 3925 GLN cc_start: 0.8956 (tp40) cc_final: 0.8718 (tp40) REVERT: E 3998 THR cc_start: 0.8668 (m) cc_final: 0.7942 (p) REVERT: E 4012 LEU cc_start: 0.8380 (tt) cc_final: 0.8063 (tt) REVERT: E 4015 THR cc_start: 0.9388 (m) cc_final: 0.9135 (p) REVERT: E 4075 ARG cc_start: 0.8875 (mmt90) cc_final: 0.8635 (mmt90) REVERT: F 3588 SER cc_start: 0.9546 (p) cc_final: 0.9103 (t) REVERT: F 3716 ASP cc_start: 0.8520 (t0) cc_final: 0.8272 (t0) REVERT: F 3998 THR cc_start: 0.8828 (m) cc_final: 0.8033 (p) REVERT: F 4023 ASP cc_start: 0.7492 (t70) cc_final: 0.6718 (p0) REVERT: G 3998 THR cc_start: 0.8760 (m) cc_final: 0.8173 (p) REVERT: G 4012 LEU cc_start: 0.8446 (tt) cc_final: 0.8212 (tt) REVERT: G 4023 ASP cc_start: 0.7756 (t0) cc_final: 0.7206 (p0) outliers start: 111 outliers final: 89 residues processed: 313 average time/residue: 0.3449 time to fit residues: 183.6896 Evaluate side-chains 282 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 192 time to evaluate : 3.088 ------------------------------------------------------------------------------- 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 3691 SER 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 3865 ASP Chi-restraints excluded: chain A residue 3881 SER 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 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 3853 THR Chi-restraints excluded: chain B residue 3886 SER Chi-restraints excluded: chain B residue 3926 LEU 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 C residue 4002 ASN Chi-restraints excluded: chain D residue 3592 THR Chi-restraints excluded: chain D residue 3624 SER 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 3624 SER Chi-restraints excluded: chain E residue 3633 VAL Chi-restraints excluded: chain E residue 3700 THR Chi-restraints excluded: chain E residue 3722 SER Chi-restraints excluded: chain E residue 3741 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 4073 ILE Chi-restraints excluded: chain F residue 3624 SER Chi-restraints excluded: chain F residue 3633 VAL Chi-restraints excluded: chain F residue 3691 SER Chi-restraints excluded: chain F residue 3700 THR Chi-restraints excluded: chain F residue 3760 CYS 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 3881 SER Chi-restraints excluded: chain F residue 3985 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 3741 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 3808 MET 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 24 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 251 optimal weight: 6.9990 chunk 257 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 324 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 239 optimal weight: 0.7980 chunk 320 optimal weight: 0.0050 chunk 297 optimal weight: 8.9990 chunk 295 optimal weight: 2.9990 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F4001 HIS ** G3661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.147847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.112345 restraints weight = 38370.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.111115 restraints weight = 27491.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.111451 restraints weight = 32214.259| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26887 Z= 0.153 Angle : 0.595 10.839 37240 Z= 0.310 Chirality : 0.047 0.195 4564 Planarity : 0.005 0.045 4781 Dihedral : 5.188 34.286 3731 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.36 % Allowed : 12.38 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.14), residues: 3542 helix: None (None), residues: 0 sheet: 0.48 (0.13), residues: 1589 loop : 0.36 (0.15), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A4061 HIS 0.002 0.001 HIS G4001 PHE 0.022 0.001 PHE D3577 TYR 0.012 0.001 TYR E3807 ARG 0.007 0.001 ARG E3861 Details of bonding type rmsd hydrogen bonds : bond 0.03176 ( 791) hydrogen bonds : angle 5.03959 ( 2394) SS BOND : bond 0.00482 ( 42) SS BOND : angle 2.28631 ( 84) covalent geometry : bond 0.00361 (26845) covalent geometry : angle 0.58604 (37156) *********************** 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 338 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 236 time to evaluate : 2.791 Fit side-chains REVERT: A 3588 SER cc_start: 0.9471 (p) cc_final: 0.9085 (t) REVERT: A 3932 GLN cc_start: 0.9103 (mm-40) cc_final: 0.8894 (mm-40) REVERT: A 3998 THR cc_start: 0.8891 (m) cc_final: 0.8323 (p) REVERT: A 4012 LEU cc_start: 0.8347 (tt) cc_final: 0.8097 (tt) REVERT: B 3579 ASP cc_start: 0.8031 (p0) cc_final: 0.7530 (p0) REVERT: B 3587 ASN cc_start: 0.9421 (m-40) cc_final: 0.9211 (m-40) REVERT: B 3588 SER cc_start: 0.9425 (p) cc_final: 0.8823 (t) REVERT: B 3716 ASP cc_start: 0.8457 (t0) cc_final: 0.8168 (t0) REVERT: B 3932 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8774 (mm-40) REVERT: B 3998 THR cc_start: 0.8797 (m) cc_final: 0.8224 (p) REVERT: B 4023 ASP cc_start: 0.7815 (t0) cc_final: 0.7371 (p0) REVERT: C 3588 SER cc_start: 0.9482 (p) cc_final: 0.9042 (t) REVERT: C 3962 ILE cc_start: 0.9000 (tp) cc_final: 0.8800 (tp) REVERT: C 3998 THR cc_start: 0.8869 (m) cc_final: 0.8246 (p) REVERT: C 4023 ASP cc_start: 0.8014 (t0) cc_final: 0.7187 (p0) REVERT: D 3588 SER cc_start: 0.9454 (p) cc_final: 0.9120 (t) REVERT: D 3716 ASP cc_start: 0.8642 (t0) cc_final: 0.8237 (t0) REVERT: D 3998 THR cc_start: 0.8912 (m) cc_final: 0.8259 (p) REVERT: D 4012 LEU cc_start: 0.8479 (tt) cc_final: 0.8131 (tt) REVERT: E 3716 ASP cc_start: 0.8502 (t0) cc_final: 0.8239 (t0) REVERT: E 3998 THR cc_start: 0.8744 (m) cc_final: 0.8048 (p) REVERT: E 4012 LEU cc_start: 0.8337 (tt) cc_final: 0.8049 (tt) REVERT: E 4015 THR cc_start: 0.9387 (m) cc_final: 0.9153 (p) REVERT: E 4075 ARG cc_start: 0.8841 (mmt90) cc_final: 0.8602 (mtt-85) REVERT: F 3588 SER cc_start: 0.9450 (p) cc_final: 0.9122 (t) REVERT: F 3716 ASP cc_start: 0.8551 (t0) cc_final: 0.8346 (t0) REVERT: F 3998 THR cc_start: 0.8831 (m) cc_final: 0.8052 (p) REVERT: F 4023 ASP cc_start: 0.7537 (t70) cc_final: 0.6907 (p0) REVERT: F 4075 ARG cc_start: 0.8814 (mmt90) cc_final: 0.8110 (mtt-85) REVERT: G 3998 THR cc_start: 0.8777 (m) cc_final: 0.8202 (p) REVERT: G 4023 ASP cc_start: 0.7723 (t0) cc_final: 0.7202 (p0) outliers start: 102 outliers final: 90 residues processed: 319 average time/residue: 0.3166 time to fit residues: 173.2412 Evaluate side-chains 291 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 201 time to evaluate : 2.603 ------------------------------------------------------------------------------- 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 3808 MET Chi-restraints excluded: chain A residue 3865 ASP Chi-restraints excluded: chain A residue 3881 SER 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 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 3926 LEU 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 3985 THR Chi-restraints excluded: chain C residue 4002 ASN Chi-restraints excluded: chain D residue 3592 THR Chi-restraints excluded: chain D residue 3624 SER 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 3797 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 3700 THR Chi-restraints excluded: chain E residue 3722 SER Chi-restraints excluded: chain E residue 3730 THR Chi-restraints excluded: chain E residue 3741 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 3985 THR Chi-restraints excluded: chain E residue 4073 ILE Chi-restraints excluded: chain F residue 3624 SER Chi-restraints excluded: chain F residue 3633 VAL Chi-restraints excluded: chain F residue 3691 SER 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 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 3985 THR 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 3730 THR Chi-restraints excluded: chain G residue 3740 ILE Chi-restraints excluded: chain G residue 3741 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 3808 MET Chi-restraints excluded: chain G residue 3821 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 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 115 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 chunk 162 optimal weight: 0.2980 chunk 338 optimal weight: 2.9990 chunk 341 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 95 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 276 optimal weight: 1.9990 chunk 202 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G3661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4001 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.145714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.111578 restraints weight = 38657.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.107879 restraints weight = 31796.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.109044 restraints weight = 30156.713| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26887 Z= 0.187 Angle : 0.611 7.764 37240 Z= 0.317 Chirality : 0.048 0.235 4564 Planarity : 0.005 0.043 4781 Dihedral : 5.239 34.817 3731 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.52 % Allowed : 12.71 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3542 helix: None (None), residues: 0 sheet: 0.37 (0.13), residues: 1603 loop : 0.35 (0.15), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E4061 HIS 0.003 0.001 HIS C4001 PHE 0.019 0.001 PHE A3577 TYR 0.011 0.001 TYR D3807 ARG 0.005 0.001 ARG E3861 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 791) hydrogen bonds : angle 4.95077 ( 2394) SS BOND : bond 0.00410 ( 42) SS BOND : angle 2.21646 ( 84) covalent geometry : bond 0.00447 (26845) covalent geometry : angle 0.60255 (37156) *********************** 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 327 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 220 time to evaluate : 2.884 Fit side-chains REVERT: A 3588 SER cc_start: 0.9495 (p) cc_final: 0.9058 (t) REVERT: A 3998 THR cc_start: 0.8902 (m) cc_final: 0.8292 (p) REVERT: A 4012 LEU cc_start: 0.8399 (tt) cc_final: 0.8142 (tt) REVERT: B 3579 ASP cc_start: 0.8054 (p0) cc_final: 0.7458 (p0) REVERT: B 3587 ASN cc_start: 0.9437 (m-40) cc_final: 0.9211 (m-40) REVERT: B 3588 SER cc_start: 0.9348 (p) cc_final: 0.8819 (t) REVERT: B 3716 ASP cc_start: 0.8448 (t0) cc_final: 0.8160 (t0) REVERT: B 3932 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8810 (mm-40) REVERT: B 3998 THR cc_start: 0.8750 (m) cc_final: 0.8170 (p) REVERT: B 4023 ASP cc_start: 0.7973 (t0) cc_final: 0.7357 (p0) REVERT: C 3962 ILE cc_start: 0.9031 (tp) cc_final: 0.8794 (tp) REVERT: C 3998 THR cc_start: 0.8970 (m) cc_final: 0.8449 (p) REVERT: C 4012 LEU cc_start: 0.8254 (tt) cc_final: 0.7949 (tt) REVERT: C 4023 ASP cc_start: 0.8071 (t0) cc_final: 0.7233 (p0) REVERT: D 3588 SER cc_start: 0.9468 (p) cc_final: 0.9110 (t) REVERT: D 3716 ASP cc_start: 0.8656 (t0) cc_final: 0.8239 (t0) REVERT: D 3998 THR cc_start: 0.8949 (m) cc_final: 0.8278 (p) REVERT: D 4012 LEU cc_start: 0.8339 (tt) cc_final: 0.7851 (tt) REVERT: E 3716 ASP cc_start: 0.8525 (t0) cc_final: 0.8221 (t0) REVERT: E 3998 THR cc_start: 0.8707 (m) cc_final: 0.8082 (p) REVERT: E 4012 LEU cc_start: 0.8418 (tt) cc_final: 0.8135 (tt) REVERT: E 4015 THR cc_start: 0.9380 (m) cc_final: 0.9135 (p) REVERT: E 4023 ASP cc_start: 0.7366 (t70) cc_final: 0.6652 (p0) REVERT: E 4075 ARG cc_start: 0.8810 (mmt90) cc_final: 0.8560 (mtt-85) REVERT: F 3579 ASP cc_start: 0.8127 (p0) cc_final: 0.7499 (p0) REVERT: F 3588 SER cc_start: 0.9464 (p) cc_final: 0.9055 (t) REVERT: F 3716 ASP cc_start: 0.8490 (t0) cc_final: 0.8226 (t0) REVERT: F 3998 THR cc_start: 0.8815 (m) cc_final: 0.8067 (p) REVERT: F 4023 ASP cc_start: 0.7664 (t70) cc_final: 0.6966 (p0) REVERT: F 4061 TRP cc_start: 0.9125 (t-100) cc_final: 0.8855 (t-100) REVERT: F 4075 ARG cc_start: 0.8840 (mmt90) cc_final: 0.8131 (mtt-85) REVERT: G 3998 THR cc_start: 0.8777 (m) cc_final: 0.8171 (p) REVERT: G 4023 ASP cc_start: 0.7810 (t0) cc_final: 0.7218 (p0) outliers start: 107 outliers final: 102 residues processed: 309 average time/residue: 0.3130 time to fit residues: 164.8729 Evaluate side-chains 302 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 200 time to evaluate : 2.525 ------------------------------------------------------------------------------- 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 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 3881 SER 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 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 3926 LEU Chi-restraints excluded: chain B residue 3985 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 3730 THR 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 3886 SER Chi-restraints excluded: chain C residue 3985 THR Chi-restraints excluded: chain C residue 4065 CYS Chi-restraints excluded: chain D residue 3592 THR Chi-restraints excluded: chain D residue 3624 SER 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 3784 VAL Chi-restraints excluded: chain D residue 3787 THR Chi-restraints excluded: chain D residue 3797 THR 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 3741 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 3985 THR Chi-restraints excluded: chain E residue 4073 ILE Chi-restraints excluded: chain F residue 3624 SER Chi-restraints excluded: chain F residue 3633 VAL Chi-restraints excluded: chain F residue 3691 SER 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 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 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 3730 THR Chi-restraints excluded: chain G residue 3740 ILE Chi-restraints excluded: chain G residue 3741 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 3808 MET Chi-restraints excluded: chain G residue 3821 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 245 optimal weight: 0.8980 chunk 210 optimal weight: 0.9980 chunk 240 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 196 optimal weight: 0.3980 chunk 127 optimal weight: 1.9990 chunk 235 optimal weight: 0.6980 chunk 289 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E3589 ASN G3661 ASN G4001 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.149642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.114778 restraints weight = 38569.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.112346 restraints weight = 31659.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113738 restraints weight = 28930.929| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 26887 Z= 0.104 Angle : 0.561 13.186 37240 Z= 0.288 Chirality : 0.046 0.168 4564 Planarity : 0.004 0.050 4781 Dihedral : 4.765 31.512 3731 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.11 % Allowed : 14.61 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.14), residues: 3542 helix: None (None), residues: 0 sheet: 0.59 (0.13), residues: 1617 loop : 0.60 (0.15), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C4061 HIS 0.002 0.000 HIS G4001 PHE 0.022 0.001 PHE G3577 TYR 0.012 0.001 TYR B3807 ARG 0.006 0.001 ARG E3861 Details of bonding type rmsd hydrogen bonds : bond 0.02730 ( 791) hydrogen bonds : angle 4.73208 ( 2394) SS BOND : bond 0.00472 ( 42) SS BOND : angle 1.73761 ( 84) covalent geometry : bond 0.00246 (26845) covalent geometry : angle 0.55584 (37156) *********************** 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 306 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 242 time to evaluate : 2.871 Fit side-chains REVERT: A 3588 SER cc_start: 0.9448 (p) cc_final: 0.9101 (t) REVERT: A 3932 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8771 (mm-40) REVERT: A 3998 THR cc_start: 0.8911 (m) cc_final: 0.8408 (p) REVERT: A 4012 LEU cc_start: 0.8321 (tt) cc_final: 0.8081 (tt) REVERT: A 4023 ASP cc_start: 0.7692 (t0) cc_final: 0.7047 (p0) REVERT: A 4075 ARG cc_start: 0.8703 (mmt90) cc_final: 0.8283 (mmt90) REVERT: B 3579 ASP cc_start: 0.8001 (p0) cc_final: 0.7532 (p0) REVERT: B 3588 SER cc_start: 0.9256 (p) cc_final: 0.8950 (t) REVERT: B 3716 ASP cc_start: 0.8400 (t0) cc_final: 0.8113 (t0) REVERT: B 3932 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8876 (mm-40) REVERT: B 3998 THR cc_start: 0.8795 (m) cc_final: 0.8259 (p) REVERT: B 4023 ASP cc_start: 0.7899 (t0) cc_final: 0.7400 (p0) REVERT: C 3962 ILE cc_start: 0.8936 (tp) cc_final: 0.8650 (tp) REVERT: C 3998 THR cc_start: 0.8951 (m) cc_final: 0.8462 (p) REVERT: C 4012 LEU cc_start: 0.8239 (tt) cc_final: 0.7944 (tt) REVERT: C 4023 ASP cc_start: 0.8013 (t0) cc_final: 0.7252 (p0) REVERT: D 3588 SER cc_start: 0.9413 (p) cc_final: 0.9148 (t) REVERT: D 3998 THR cc_start: 0.8956 (m) cc_final: 0.8311 (p) REVERT: D 4073 ILE cc_start: 0.8970 (tt) cc_final: 0.8739 (pt) REVERT: E 3716 ASP cc_start: 0.8445 (t0) cc_final: 0.8229 (t0) REVERT: E 3998 THR cc_start: 0.8832 (m) cc_final: 0.8205 (p) REVERT: E 4012 LEU cc_start: 0.8374 (tt) cc_final: 0.8138 (tt) REVERT: E 4015 THR cc_start: 0.9396 (m) cc_final: 0.9173 (p) REVERT: E 4023 ASP cc_start: 0.7301 (t70) cc_final: 0.6806 (p0) REVERT: E 4075 ARG cc_start: 0.8757 (mmt90) cc_final: 0.8553 (mtt-85) REVERT: F 3579 ASP cc_start: 0.8157 (p0) cc_final: 0.7572 (p0) REVERT: F 3588 SER cc_start: 0.9416 (p) cc_final: 0.9167 (t) REVERT: F 3716 ASP cc_start: 0.8410 (t0) cc_final: 0.8185 (t0) REVERT: F 3998 THR cc_start: 0.8850 (m) cc_final: 0.8123 (p) REVERT: F 4023 ASP cc_start: 0.7601 (t70) cc_final: 0.6981 (p0) REVERT: F 4061 TRP cc_start: 0.9127 (t-100) cc_final: 0.8885 (t-100) REVERT: F 4075 ARG cc_start: 0.8777 (mmt90) cc_final: 0.8159 (mtt-85) REVERT: G 3588 SER cc_start: 0.9385 (p) cc_final: 0.9125 (t) REVERT: G 3998 THR cc_start: 0.8818 (m) cc_final: 0.8278 (p) REVERT: G 4023 ASP cc_start: 0.7705 (t0) cc_final: 0.7272 (p0) outliers start: 64 outliers final: 54 residues processed: 298 average time/residue: 0.3191 time to fit residues: 161.8218 Evaluate side-chains 260 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 206 time to evaluate : 2.723 ------------------------------------------------------------------------------- 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 3722 SER Chi-restraints excluded: chain A residue 3730 THR Chi-restraints excluded: chain A residue 3787 THR Chi-restraints excluded: chain A residue 3865 ASP Chi-restraints excluded: chain A residue 3881 SER 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 3722 SER Chi-restraints excluded: chain B residue 3787 THR Chi-restraints excluded: chain B residue 3821 SER Chi-restraints excluded: chain C residue 3592 THR Chi-restraints excluded: chain C residue 3674 THR Chi-restraints excluded: chain C residue 3722 SER Chi-restraints excluded: chain C residue 3730 THR Chi-restraints excluded: chain C residue 3886 SER Chi-restraints excluded: chain C residue 3923 LEU Chi-restraints excluded: chain D residue 3592 THR Chi-restraints excluded: chain D residue 3722 SER Chi-restraints excluded: chain D residue 3730 THR Chi-restraints excluded: chain D residue 3787 THR Chi-restraints excluded: chain D residue 3886 SER Chi-restraints excluded: chain D residue 3923 LEU Chi-restraints excluded: chain D residue 3926 LEU Chi-restraints excluded: chain D residue 3969 SER 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 3741 THR Chi-restraints excluded: chain E residue 3787 THR Chi-restraints excluded: chain E residue 3865 ASP Chi-restraints excluded: chain E residue 3886 SER Chi-restraints excluded: chain E residue 4073 ILE Chi-restraints excluded: chain F residue 3633 VAL Chi-restraints excluded: chain F residue 3691 SER Chi-restraints excluded: chain F residue 3730 THR Chi-restraints excluded: chain F residue 3753 THR Chi-restraints excluded: chain F residue 3865 ASP 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 3722 SER Chi-restraints excluded: chain G residue 3730 THR Chi-restraints excluded: chain G residue 3741 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 185 optimal weight: 0.9990 chunk 284 optimal weight: 0.0030 chunk 307 optimal weight: 20.0000 chunk 92 optimal weight: 0.8980 chunk 269 optimal weight: 0.9980 chunk 264 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 278 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3734 ASN E3589 ASN G3661 ASN G4001 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.150602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115895 restraints weight = 38863.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.114116 restraints weight = 29660.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.115079 restraints weight = 31538.993| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4882 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 : 0.560 13.992 37240 Z= 0.287 Chirality : 0.046 0.168 4564 Planarity : 0.004 0.058 4781 Dihedral : 4.624 32.623 3731 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.01 % Allowed : 15.17 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.14), residues: 3542 helix: None (None), residues: 0 sheet: 0.69 (0.13), residues: 1617 loop : 0.68 (0.15), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A4061 HIS 0.002 0.001 HIS G4001 PHE 0.021 0.001 PHE E3577 TYR 0.011 0.001 TYR B3807 ARG 0.005 0.000 ARG E3861 Details of bonding type rmsd hydrogen bonds : bond 0.02706 ( 791) hydrogen bonds : angle 4.61773 ( 2394) SS BOND : bond 0.00421 ( 42) SS BOND : angle 1.73062 ( 84) covalent geometry : bond 0.00244 (26845) covalent geometry : angle 0.55483 (37156) *********************** 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 293 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 232 time to evaluate : 2.603 Fit side-chains revert: symmetry clash REVERT: A 3588 SER cc_start: 0.9418 (p) cc_final: 0.9133 (t) REVERT: A 3932 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8748 (mm-40) REVERT: A 3998 THR cc_start: 0.8899 (m) cc_final: 0.8400 (p) REVERT: A 4012 LEU cc_start: 0.8415 (tt) cc_final: 0.8139 (tt) REVERT: A 4075 ARG cc_start: 0.8680 (mmt90) cc_final: 0.8306 (mmt90) REVERT: B 3579 ASP cc_start: 0.8080 (p0) cc_final: 0.7610 (p0) REVERT: B 3588 SER cc_start: 0.9199 (p) cc_final: 0.8988 (t) REVERT: B 3716 ASP cc_start: 0.8372 (t0) cc_final: 0.8118 (t0) REVERT: B 3932 GLN cc_start: 0.9108 (mm-40) cc_final: 0.8897 (mm-40) REVERT: B 3998 THR cc_start: 0.8798 (m) cc_final: 0.8289 (p) REVERT: B 4023 ASP cc_start: 0.7905 (t0) cc_final: 0.7390 (p0) REVERT: C 3932 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8818 (mm-40) REVERT: C 3998 THR cc_start: 0.8958 (m) cc_final: 0.8479 (p) REVERT: C 4012 LEU cc_start: 0.8248 (tt) cc_final: 0.7942 (tt) REVERT: C 4023 ASP cc_start: 0.7993 (t0) cc_final: 0.7324 (p0) REVERT: D 3588 SER cc_start: 0.9414 (p) cc_final: 0.9168 (t) REVERT: D 3998 THR cc_start: 0.8961 (m) cc_final: 0.8328 (p) REVERT: D 4073 ILE cc_start: 0.8978 (tt) cc_final: 0.8766 (pt) REVERT: E 3998 THR cc_start: 0.8824 (m) cc_final: 0.8293 (p) REVERT: E 4012 LEU cc_start: 0.8413 (tt) cc_final: 0.8179 (tt) REVERT: E 4015 THR cc_start: 0.9394 (m) cc_final: 0.9175 (p) REVERT: E 4023 ASP cc_start: 0.7249 (t70) cc_final: 0.6894 (p0) REVERT: E 4075 ARG cc_start: 0.8735 (mmt90) cc_final: 0.8157 (mtt-85) REVERT: F 3579 ASP cc_start: 0.8156 (p0) cc_final: 0.7601 (p0) REVERT: F 3716 ASP cc_start: 0.8416 (t0) cc_final: 0.8206 (t0) REVERT: F 3998 THR cc_start: 0.8820 (m) cc_final: 0.8103 (p) REVERT: F 4023 ASP cc_start: 0.7586 (t70) cc_final: 0.7004 (p0) REVERT: F 4061 TRP cc_start: 0.9129 (t-100) cc_final: 0.8905 (t-100) REVERT: F 4075 ARG cc_start: 0.8754 (mmt90) cc_final: 0.8168 (mtt-85) REVERT: G 3588 SER cc_start: 0.9394 (p) cc_final: 0.9156 (t) REVERT: G 3998 THR cc_start: 0.8794 (m) cc_final: 0.8256 (p) REVERT: G 4023 ASP cc_start: 0.7680 (t0) cc_final: 0.7285 (p0) outliers start: 61 outliers final: 59 residues processed: 287 average time/residue: 0.3011 time to fit residues: 146.9148 Evaluate side-chains 272 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 213 time to evaluate : 2.815 ------------------------------------------------------------------------------- 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 3787 THR Chi-restraints excluded: chain A residue 3797 THR Chi-restraints excluded: chain A residue 3881 SER 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 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 4073 ILE Chi-restraints excluded: chain C residue 3592 THR Chi-restraints excluded: chain C residue 3674 THR Chi-restraints excluded: chain C residue 3722 SER Chi-restraints excluded: chain C residue 3730 THR Chi-restraints excluded: chain C residue 3923 LEU Chi-restraints excluded: chain D residue 3592 THR Chi-restraints excluded: chain D residue 3722 SER Chi-restraints excluded: chain D residue 3730 THR Chi-restraints excluded: chain D residue 3787 THR Chi-restraints excluded: chain D residue 3886 SER Chi-restraints excluded: chain D residue 3923 LEU Chi-restraints excluded: chain D residue 3926 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 3722 SER Chi-restraints excluded: chain E residue 3730 THR Chi-restraints excluded: chain E residue 3741 THR Chi-restraints excluded: chain E residue 3787 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 4073 ILE Chi-restraints excluded: chain F residue 3633 VAL Chi-restraints excluded: chain F residue 3691 SER Chi-restraints excluded: chain F residue 3730 THR Chi-restraints excluded: chain F residue 3753 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 3886 SER 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 3722 SER Chi-restraints excluded: chain G residue 3730 THR Chi-restraints excluded: chain G residue 3741 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 43 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 258 optimal weight: 1.9990 chunk 181 optimal weight: 0.0770 chunk 266 optimal weight: 5.9990 chunk 201 optimal weight: 7.9990 chunk 346 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 345 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 chunk 206 optimal weight: 7.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E3589 ASN E3910 ASN F4001 HIS G4001 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.148695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.115117 restraints weight = 38729.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.111837 restraints weight = 31582.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113005 restraints weight = 30904.563| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4929 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= 0.139 Angle : 0.575 13.726 37240 Z= 0.294 Chirality : 0.047 0.167 4564 Planarity : 0.005 0.061 4781 Dihedral : 4.780 32.371 3731 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.04 % Allowed : 15.50 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.14), residues: 3542 helix: None (None), residues: 0 sheet: 0.63 (0.12), residues: 1645 loop : 0.70 (0.15), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E4061 HIS 0.002 0.001 HIS G4001 PHE 0.023 0.001 PHE E3577 TYR 0.010 0.001 TYR F3807 ARG 0.005 0.000 ARG B4075 Details of bonding type rmsd hydrogen bonds : bond 0.02896 ( 791) hydrogen bonds : angle 4.59586 ( 2394) SS BOND : bond 0.00361 ( 42) SS BOND : angle 1.65342 ( 84) covalent geometry : bond 0.00334 (26845) covalent geometry : angle 0.57011 (37156) ********************** 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 288 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 226 time to evaluate : 2.704 Fit side-chains REVERT: A 3588 SER cc_start: 0.9462 (p) cc_final: 0.9101 (t) REVERT: A 3932 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8784 (mm-40) REVERT: A 3998 THR cc_start: 0.8926 (m) cc_final: 0.8407 (p) REVERT: A 4075 ARG cc_start: 0.8696 (mmt90) cc_final: 0.8281 (mmt90) REVERT: B 3579 ASP cc_start: 0.8058 (p0) cc_final: 0.7546 (p0) REVERT: B 3588 SER cc_start: 0.9204 (p) cc_final: 0.9000 (t) REVERT: B 3716 ASP cc_start: 0.8420 (t0) cc_final: 0.8180 (t0) REVERT: B 3932 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8833 (mm-40) REVERT: B 3998 THR cc_start: 0.8767 (m) cc_final: 0.8226 (p) REVERT: B 4023 ASP cc_start: 0.7871 (t0) cc_final: 0.7293 (p0) REVERT: C 3932 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8842 (mm-40) REVERT: C 3998 THR cc_start: 0.8998 (m) cc_final: 0.8464 (p) REVERT: C 4012 LEU cc_start: 0.8307 (tt) cc_final: 0.8006 (tt) REVERT: C 4023 ASP cc_start: 0.8030 (t0) cc_final: 0.7441 (p0) REVERT: D 3588 SER cc_start: 0.9426 (p) cc_final: 0.9132 (t) REVERT: D 3998 THR cc_start: 0.8960 (m) cc_final: 0.8305 (p) REVERT: E 3587 ASN cc_start: 0.9281 (m-40) cc_final: 0.8960 (m-40) REVERT: E 3998 THR cc_start: 0.8855 (m) cc_final: 0.8272 (p) REVERT: E 4012 LEU cc_start: 0.8508 (tt) cc_final: 0.8249 (tt) REVERT: E 4015 THR cc_start: 0.9378 (m) cc_final: 0.9138 (p) REVERT: E 4023 ASP cc_start: 0.7287 (t70) cc_final: 0.6868 (p0) REVERT: E 4075 ARG cc_start: 0.8771 (mmt90) cc_final: 0.8132 (mtt-85) REVERT: F 3716 ASP cc_start: 0.8526 (t0) cc_final: 0.8250 (t0) REVERT: F 3998 THR cc_start: 0.8761 (m) cc_final: 0.8018 (p) REVERT: F 4023 ASP cc_start: 0.7664 (t70) cc_final: 0.6995 (p0) REVERT: F 4061 TRP cc_start: 0.9127 (t-100) cc_final: 0.8811 (t-100) REVERT: F 4075 ARG cc_start: 0.8815 (mmt90) cc_final: 0.8216 (mtt-85) REVERT: G 3588 SER cc_start: 0.9386 (p) cc_final: 0.9146 (t) REVERT: G 3998 THR cc_start: 0.8787 (m) cc_final: 0.8222 (p) REVERT: G 4023 ASP cc_start: 0.7800 (t0) cc_final: 0.7268 (p0) outliers start: 62 outliers final: 60 residues processed: 282 average time/residue: 0.3197 time to fit residues: 152.8031 Evaluate side-chains 266 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 206 time to evaluate : 2.771 ------------------------------------------------------------------------------- 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 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 3881 SER 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 3787 THR Chi-restraints excluded: chain B residue 3821 SER Chi-restraints excluded: chain B residue 3923 LEU Chi-restraints excluded: chain C residue 3674 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 3923 LEU Chi-restraints excluded: chain D residue 3592 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 3886 SER Chi-restraints excluded: chain D residue 3923 LEU Chi-restraints excluded: chain D residue 3926 LEU Chi-restraints excluded: chain E residue 3589 ASN 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 3730 THR Chi-restraints excluded: chain E residue 3741 THR Chi-restraints excluded: chain E residue 3787 THR Chi-restraints excluded: chain E residue 3865 ASP Chi-restraints excluded: chain E residue 3886 SER Chi-restraints excluded: chain E residue 4073 ILE Chi-restraints excluded: chain F residue 3633 VAL Chi-restraints excluded: chain F residue 3691 SER Chi-restraints excluded: chain F residue 3730 THR Chi-restraints excluded: chain F residue 3753 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 3886 SER 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 3722 SER Chi-restraints excluded: chain G residue 3730 THR Chi-restraints excluded: chain G residue 3741 THR 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 4022 THR Chi-restraints excluded: chain G residue 4073 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 91 optimal weight: 2.9990 chunk 311 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 223 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 329 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 306 optimal weight: 20.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G4001 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.146878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.112848 restraints weight = 38940.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.109161 restraints weight = 32507.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.110469 restraints weight = 28842.505| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 26887 Z= 0.209 Angle : 0.617 14.020 37240 Z= 0.319 Chirality : 0.048 0.191 4564 Planarity : 0.005 0.060 4781 Dihedral : 5.123 34.176 3731 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.30 % Allowed : 15.37 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.14), residues: 3542 helix: None (None), residues: 0 sheet: 0.46 (0.13), residues: 1617 loop : 0.53 (0.15), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D4061 HIS 0.003 0.001 HIS G3953 PHE 0.023 0.002 PHE G3577 TYR 0.016 0.001 TYR C3942 ARG 0.004 0.000 ARG E3861 Details of bonding type rmsd hydrogen bonds : bond 0.03235 ( 791) hydrogen bonds : angle 4.74100 ( 2394) SS BOND : bond 0.00358 ( 42) SS BOND : angle 2.05386 ( 84) covalent geometry : bond 0.00502 (26845) covalent geometry : angle 0.60977 (37156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7257.34 seconds wall clock time: 129 minutes 7.91 seconds (7747.91 seconds total)