Starting phenix.real_space_refine on Sun Aug 24 15:48:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sew_40431/08_2025/8sew_40431.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sew_40431/08_2025/8sew_40431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sew_40431/08_2025/8sew_40431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sew_40431/08_2025/8sew_40431.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sew_40431/08_2025/8sew_40431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sew_40431/08_2025/8sew_40431.map" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.151 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 8 5.49 5 S 160 5.16 5 C 13448 2.51 5 N 3296 2.21 5 O 3800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20716 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5151 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 15, 'TRANS': 613} Chain breaks: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4477 SG CYS A4958 57.159 83.295 88.728 1.00 36.39 S ATOM 4502 SG CYS A4961 59.556 83.860 91.636 1.00 36.10 S Restraints were copied for chains: B, C, D Time building chain proxies: 4.29, per 1000 atoms: 0.21 Number of scatterers: 20716 At special positions: 0 Unit cell: (145.544, 145.544, 133.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 160 16.00 P 8 15.00 O 3800 8.00 N 3296 7.00 C 13448 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.03 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " distance=2.03 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " distance=2.03 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.03 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 791.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5102 " pdb="ZN ZN A5102 " - pdb=" ND1 HIS A4983 " pdb="ZN ZN A5102 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4958 " pdb=" ZN B5102 " pdb="ZN ZN B5102 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5102 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4958 " pdb=" ZN C5102 " pdb="ZN ZN C5102 " - pdb=" ND1 HIS C4983 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4958 " pdb=" ZN D5102 " pdb="ZN ZN D5102 " - pdb=" ND1 HIS D4983 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4958 " Number of angles added : 8 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4736 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 78.1% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 3950 through 3970 removed outlier: 3.623A pdb=" N ALA A3954 " --> pdb=" O ASN A3950 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A3960 " --> pdb=" O SER A3956 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A3969 " --> pdb=" O LEU A3965 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3982 Processing helix chain 'A' and resid 3984 through 4006 removed outlier: 3.611A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN A4005 " --> pdb=" O MET A4001 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP A4006 " --> pdb=" O LYS A4002 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4031 removed outlier: 3.621A pdb=" N LEU A4031 " --> pdb=" O LEU A4027 " (cutoff:3.500A) Processing helix chain 'A' and resid 4038 through 4051 Processing helix chain 'A' and resid 4051 through 4060 removed outlier: 3.680A pdb=" N MET A4057 " --> pdb=" O SER A4053 " (cutoff:3.500A) Processing helix chain 'A' and resid 4198 through 4207 Processing helix chain 'A' and resid 4207 through 4225 Processing helix chain 'A' and resid 4229 through 4252 Processing helix chain 'A' and resid 4541 through 4558 Processing helix chain 'A' and resid 4558 through 4577 Processing helix chain 'A' and resid 4638 through 4665 Processing helix chain 'A' and resid 4665 through 4683 Processing helix chain 'A' and resid 4696 through 4703 Processing helix chain 'A' and resid 4719 through 4733 removed outlier: 5.226A pdb=" N ASP A4730 " --> pdb=" O ASP A4726 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE A4731 " --> pdb=" O LYS A4727 " (cutoff:3.500A) Processing helix chain 'A' and resid 4734 through 4741 Processing helix chain 'A' and resid 4744 through 4750 removed outlier: 4.005A pdb=" N GLU A4749 " --> pdb=" O LEU A4745 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE A4750 " --> pdb=" O ALA A4746 " (cutoff:3.500A) Processing helix chain 'A' and resid 4773 through 4785 Processing helix chain 'A' and resid 4786 through 4805 removed outlier: 3.983A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4813 Processing helix chain 'A' and resid 4814 through 4820 removed outlier: 4.144A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) Processing helix chain 'A' and resid 4820 through 4833 removed outlier: 3.784A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASN A4833 " --> pdb=" O SER A4829 " (cutoff:3.500A) Processing helix chain 'A' and resid 4833 through 4859 Processing helix chain 'A' and resid 4860 through 4864 removed outlier: 3.571A pdb=" N TYR A4863 " --> pdb=" O ARG A4860 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A4864 " --> pdb=" O LYS A4861 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4860 through 4864' Processing helix chain 'A' and resid 4878 through 4890 Processing helix chain 'A' and resid 4909 through 4924 Processing helix chain 'A' and resid 4926 through 4957 removed outlier: 4.134A pdb=" N ILE A4932 " --> pdb=" O LEU A4928 " (cutoff:3.500A) Processing helix chain 'A' and resid 4964 through 4969 removed outlier: 3.938A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) Processing helix chain 'A' and resid 4973 through 4981 Processing helix chain 'A' and resid 4984 through 4998 Processing helix chain 'A' and resid 4999 through 5003 Processing helix chain 'A' and resid 5004 through 5016 Processing helix chain 'A' and resid 5027 through 5032 Processing helix chain 'A' and resid 5032 through 5037 Processing helix chain 'B' and resid 3951 through 3970 removed outlier: 3.554A pdb=" N GLN B3960 " --> pdb=" O SER B3956 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B3969 " --> pdb=" O LEU B3965 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3982 Processing helix chain 'B' and resid 3984 through 4006 removed outlier: 3.611A pdb=" N MET B4001 " --> pdb=" O ALA B3997 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN B4005 " --> pdb=" O MET B4001 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP B4006 " --> pdb=" O LYS B4002 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4031 removed outlier: 3.621A pdb=" N LEU B4031 " --> pdb=" O LEU B4027 " (cutoff:3.500A) Processing helix chain 'B' and resid 4038 through 4051 Processing helix chain 'B' and resid 4051 through 4060 removed outlier: 3.680A pdb=" N MET B4057 " --> pdb=" O SER B4053 " (cutoff:3.500A) Processing helix chain 'B' and resid 4198 through 4207 Processing helix chain 'B' and resid 4207 through 4225 Processing helix chain 'B' and resid 4229 through 4252 Processing helix chain 'B' and resid 4541 through 4558 Processing helix chain 'B' and resid 4558 through 4577 Processing helix chain 'B' and resid 4638 through 4665 Processing helix chain 'B' and resid 4665 through 4683 Processing helix chain 'B' and resid 4696 through 4703 Processing helix chain 'B' and resid 4719 through 4733 removed outlier: 5.226A pdb=" N ASP B4730 " --> pdb=" O ASP B4726 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE B4731 " --> pdb=" O LYS B4727 " (cutoff:3.500A) Processing helix chain 'B' and resid 4734 through 4741 Processing helix chain 'B' and resid 4744 through 4750 removed outlier: 4.005A pdb=" N GLU B4749 " --> pdb=" O LEU B4745 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE B4750 " --> pdb=" O ALA B4746 " (cutoff:3.500A) Processing helix chain 'B' and resid 4773 through 4785 Processing helix chain 'B' and resid 4786 through 4805 removed outlier: 3.983A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4806 through 4813 Processing helix chain 'B' and resid 4814 through 4820 removed outlier: 4.144A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) Processing helix chain 'B' and resid 4820 through 4833 removed outlier: 3.784A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASN B4833 " --> pdb=" O SER B4829 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4859 Processing helix chain 'B' and resid 4860 through 4864 removed outlier: 3.571A pdb=" N TYR B4863 " --> pdb=" O ARG B4860 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN B4864 " --> pdb=" O LYS B4861 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4860 through 4864' Processing helix chain 'B' and resid 4878 through 4890 Processing helix chain 'B' and resid 4909 through 4924 Processing helix chain 'B' and resid 4926 through 4957 removed outlier: 4.134A pdb=" N ILE B4932 " --> pdb=" O LEU B4928 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4969 removed outlier: 3.938A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4981 Processing helix chain 'B' and resid 4984 through 4998 Processing helix chain 'B' and resid 4999 through 5003 Processing helix chain 'B' and resid 5004 through 5016 Processing helix chain 'B' and resid 5027 through 5032 Processing helix chain 'B' and resid 5032 through 5037 Processing helix chain 'C' and resid 3951 through 3970 removed outlier: 3.554A pdb=" N GLN C3960 " --> pdb=" O SER C3956 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C3969 " --> pdb=" O LEU C3965 " (cutoff:3.500A) Processing helix chain 'C' and resid 3973 through 3982 Processing helix chain 'C' and resid 3984 through 4006 removed outlier: 3.611A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN C4005 " --> pdb=" O MET C4001 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP C4006 " --> pdb=" O LYS C4002 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4031 removed outlier: 3.621A pdb=" N LEU C4031 " --> pdb=" O LEU C4027 " (cutoff:3.500A) Processing helix chain 'C' and resid 4038 through 4051 Processing helix chain 'C' and resid 4051 through 4060 removed outlier: 3.680A pdb=" N MET C4057 " --> pdb=" O SER C4053 " (cutoff:3.500A) Processing helix chain 'C' and resid 4198 through 4207 Processing helix chain 'C' and resid 4207 through 4225 Processing helix chain 'C' and resid 4229 through 4252 Processing helix chain 'C' and resid 4541 through 4558 Processing helix chain 'C' and resid 4558 through 4577 Processing helix chain 'C' and resid 4638 through 4665 Processing helix chain 'C' and resid 4665 through 4683 Processing helix chain 'C' and resid 4696 through 4703 Processing helix chain 'C' and resid 4719 through 4733 removed outlier: 5.226A pdb=" N ASP C4730 " --> pdb=" O ASP C4726 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE C4731 " --> pdb=" O LYS C4727 " (cutoff:3.500A) Processing helix chain 'C' and resid 4734 through 4741 Processing helix chain 'C' and resid 4744 through 4750 removed outlier: 4.005A pdb=" N GLU C4749 " --> pdb=" O LEU C4745 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE C4750 " --> pdb=" O ALA C4746 " (cutoff:3.500A) Processing helix chain 'C' and resid 4773 through 4785 Processing helix chain 'C' and resid 4786 through 4805 removed outlier: 3.983A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4806 through 4813 Processing helix chain 'C' and resid 4814 through 4820 removed outlier: 4.144A pdb=" N MET C4818 " --> pdb=" O LEU C4814 " (cutoff:3.500A) Processing helix chain 'C' and resid 4820 through 4833 removed outlier: 3.784A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASN C4833 " --> pdb=" O SER C4829 " (cutoff:3.500A) Processing helix chain 'C' and resid 4833 through 4859 Processing helix chain 'C' and resid 4860 through 4864 removed outlier: 3.571A pdb=" N TYR C4863 " --> pdb=" O ARG C4860 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN C4864 " --> pdb=" O LYS C4861 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4860 through 4864' Processing helix chain 'C' and resid 4878 through 4890 Processing helix chain 'C' and resid 4909 through 4924 Processing helix chain 'C' and resid 4926 through 4957 removed outlier: 4.134A pdb=" N ILE C4932 " --> pdb=" O LEU C4928 " (cutoff:3.500A) Processing helix chain 'C' and resid 4964 through 4969 removed outlier: 3.938A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) Processing helix chain 'C' and resid 4973 through 4981 Processing helix chain 'C' and resid 4984 through 4998 Processing helix chain 'C' and resid 4999 through 5003 Processing helix chain 'C' and resid 5004 through 5016 Processing helix chain 'C' and resid 5027 through 5032 Processing helix chain 'C' and resid 5032 through 5037 Processing helix chain 'D' and resid 3951 through 3970 removed outlier: 3.554A pdb=" N GLN D3960 " --> pdb=" O SER D3956 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE D3969 " --> pdb=" O LEU D3965 " (cutoff:3.500A) Processing helix chain 'D' and resid 3973 through 3982 Processing helix chain 'D' and resid 3984 through 4006 removed outlier: 3.611A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN D4005 " --> pdb=" O MET D4001 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP D4006 " --> pdb=" O LYS D4002 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4031 removed outlier: 3.621A pdb=" N LEU D4031 " --> pdb=" O LEU D4027 " (cutoff:3.500A) Processing helix chain 'D' and resid 4038 through 4051 Processing helix chain 'D' and resid 4051 through 4060 removed outlier: 3.680A pdb=" N MET D4057 " --> pdb=" O SER D4053 " (cutoff:3.500A) Processing helix chain 'D' and resid 4198 through 4207 Processing helix chain 'D' and resid 4207 through 4225 Processing helix chain 'D' and resid 4229 through 4252 Processing helix chain 'D' and resid 4541 through 4558 Processing helix chain 'D' and resid 4558 through 4577 Processing helix chain 'D' and resid 4638 through 4665 Processing helix chain 'D' and resid 4665 through 4683 Processing helix chain 'D' and resid 4696 through 4703 Processing helix chain 'D' and resid 4719 through 4733 removed outlier: 5.226A pdb=" N ASP D4730 " --> pdb=" O ASP D4726 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE D4731 " --> pdb=" O LYS D4727 " (cutoff:3.500A) Processing helix chain 'D' and resid 4734 through 4741 Processing helix chain 'D' and resid 4744 through 4750 removed outlier: 4.005A pdb=" N GLU D4749 " --> pdb=" O LEU D4745 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE D4750 " --> pdb=" O ALA D4746 " (cutoff:3.500A) Processing helix chain 'D' and resid 4773 through 4785 Processing helix chain 'D' and resid 4786 through 4805 removed outlier: 3.983A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4806 through 4813 Processing helix chain 'D' and resid 4814 through 4820 removed outlier: 4.144A pdb=" N MET D4818 " --> pdb=" O LEU D4814 " (cutoff:3.500A) Processing helix chain 'D' and resid 4820 through 4833 removed outlier: 3.784A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASN D4833 " --> pdb=" O SER D4829 " (cutoff:3.500A) Processing helix chain 'D' and resid 4833 through 4859 Processing helix chain 'D' and resid 4860 through 4864 removed outlier: 3.571A pdb=" N TYR D4863 " --> pdb=" O ARG D4860 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN D4864 " --> pdb=" O LYS D4861 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4860 through 4864' Processing helix chain 'D' and resid 4878 through 4890 Processing helix chain 'D' and resid 4909 through 4924 Processing helix chain 'D' and resid 4926 through 4957 removed outlier: 4.134A pdb=" N ILE D4932 " --> pdb=" O LEU D4928 " (cutoff:3.500A) Processing helix chain 'D' and resid 4964 through 4969 removed outlier: 3.938A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) Processing helix chain 'D' and resid 4973 through 4981 Processing helix chain 'D' and resid 4984 through 4998 Processing helix chain 'D' and resid 4999 through 5003 Processing helix chain 'D' and resid 5004 through 5016 Processing helix chain 'D' and resid 5027 through 5032 Processing helix chain 'D' and resid 5032 through 5037 Processing sheet with id=AA1, first strand: chain 'A' and resid 4178 through 4184 Processing sheet with id=AA2, first strand: chain 'A' and resid 4580 through 4583 Processing sheet with id=AA3, first strand: chain 'B' and resid 4178 through 4184 Processing sheet with id=AA4, first strand: chain 'B' and resid 4580 through 4583 Processing sheet with id=AA5, first strand: chain 'C' and resid 4178 through 4184 Processing sheet with id=AA6, first strand: chain 'C' and resid 4580 through 4583 Processing sheet with id=AA7, first strand: chain 'D' and resid 4178 through 4184 Processing sheet with id=AA8, first strand: chain 'D' and resid 4580 through 4583 1388 hydrogen bonds defined for protein. 4068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.98 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6512 1.34 - 1.46: 4856 1.46 - 1.58: 9552 1.58 - 1.69: 12 1.69 - 1.81: 276 Bond restraints: 21208 Sorted by residual: bond pdb=" C4 ADP B5101 " pdb=" C5 ADP B5101 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C4 ADP C5101 " pdb=" C5 ADP C5101 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C4 ADP A5101 " pdb=" C5 ADP A5101 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C4 ADP D5101 " pdb=" C5 ADP D5101 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C5 ADP A5101 " pdb=" C6 ADP A5101 " ideal model delta sigma weight residual 1.490 1.403 0.087 2.00e-02 2.50e+03 1.87e+01 ... (remaining 21203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 28460 2.75 - 5.49: 140 5.49 - 8.24: 28 8.24 - 10.99: 12 10.99 - 13.74: 4 Bond angle restraints: 28644 Sorted by residual: angle pdb=" C LYS A4665 " pdb=" N VAL A4666 " pdb=" CA VAL A4666 " ideal model delta sigma weight residual 120.24 123.16 -2.92 6.30e-01 2.52e+00 2.14e+01 angle pdb=" C LYS B4665 " pdb=" N VAL B4666 " pdb=" CA VAL B4666 " ideal model delta sigma weight residual 120.24 123.16 -2.92 6.30e-01 2.52e+00 2.14e+01 angle pdb=" C LYS D4665 " pdb=" N VAL D4666 " pdb=" CA VAL D4666 " ideal model delta sigma weight residual 120.24 123.16 -2.92 6.30e-01 2.52e+00 2.14e+01 angle pdb=" C LYS C4665 " pdb=" N VAL C4666 " pdb=" CA VAL C4666 " ideal model delta sigma weight residual 120.24 123.16 -2.92 6.30e-01 2.52e+00 2.14e+01 angle pdb=" PA ADP C5101 " pdb=" O3A ADP C5101 " pdb=" PB ADP C5101 " ideal model delta sigma weight residual 120.50 134.24 -13.74 3.00e+00 1.11e-01 2.10e+01 ... (remaining 28639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.20: 12212 30.20 - 60.41: 228 60.41 - 90.61: 12 90.61 - 120.81: 4 120.81 - 151.01: 4 Dihedral angle restraints: 12460 sinusoidal: 5112 harmonic: 7348 Sorted by residual: dihedral pdb=" C2' ADP A5101 " pdb=" C1' ADP A5101 " pdb=" N9 ADP A5101 " pdb=" C4 ADP A5101 " ideal model delta sinusoidal sigma weight residual 91.55 -59.47 151.01 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" C2' ADP D5101 " pdb=" C1' ADP D5101 " pdb=" N9 ADP D5101 " pdb=" C4 ADP D5101 " ideal model delta sinusoidal sigma weight residual 91.55 -59.47 151.01 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" C2' ADP C5101 " pdb=" C1' ADP C5101 " pdb=" N9 ADP C5101 " pdb=" C4 ADP C5101 " ideal model delta sinusoidal sigma weight residual 91.55 -59.47 151.01 1 2.00e+01 2.50e-03 4.50e+01 ... (remaining 12457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1724 0.029 - 0.058: 1004 0.058 - 0.087: 288 0.087 - 0.116: 68 0.116 - 0.144: 12 Chirality restraints: 3096 Sorted by residual: chirality pdb=" C3' ADP C5101 " pdb=" C2' ADP C5101 " pdb=" C4' ADP C5101 " pdb=" O3' ADP C5101 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" C3' ADP D5101 " pdb=" C2' ADP D5101 " pdb=" C4' ADP D5101 " pdb=" O3' ADP D5101 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" C3' ADP A5101 " pdb=" C2' ADP A5101 " pdb=" C4' ADP A5101 " pdb=" O3' ADP A5101 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 3093 not shown) Planarity restraints: 3612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B4913 " 0.124 9.50e-02 1.11e+02 5.56e-02 1.93e+00 pdb=" NE ARG B4913 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG B4913 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B4913 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B4913 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A4913 " -0.124 9.50e-02 1.11e+02 5.56e-02 1.93e+00 pdb=" NE ARG A4913 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A4913 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A4913 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A4913 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D4913 " -0.124 9.50e-02 1.11e+02 5.56e-02 1.93e+00 pdb=" NE ARG D4913 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG D4913 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D4913 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG D4913 " -0.006 2.00e-02 2.50e+03 ... (remaining 3609 not shown) Histogram of nonbonded interaction distances: 0.27 - 1.19: 12 1.19 - 2.12: 24 2.12 - 3.05: 13632 3.05 - 3.97: 54820 3.97 - 4.90: 102550 Warning: very small nonbonded interaction distances. Nonbonded interactions: 171038 Sorted by model distance: nonbonded pdb=" NH2 ARG B4944 " pdb=" OD1 ASP C4938 " model vdw 0.267 3.120 nonbonded pdb=" NH2 ARG C4944 " pdb=" OD1 ASP D4938 " model vdw 0.267 3.120 nonbonded pdb=" OD1 ASP A4938 " pdb=" NH2 ARG D4944 " model vdw 0.267 3.120 nonbonded pdb=" NH2 ARG A4944 " pdb=" OD1 ASP B4938 " model vdw 0.267 3.120 nonbonded pdb=" OE2 GLU A4976 " pdb=" OE2 GLU B4227 " model vdw 0.697 3.040 ... (remaining 171033 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.500 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 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 : 0.014 0.990 21232 Z= 1.374 Angle : 0.595 13.737 28660 Z= 0.295 Chirality : 0.038 0.144 3096 Planarity : 0.004 0.056 3612 Dihedral : 12.563 151.014 7712 Min Nonbonded Distance : 0.267 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.74 % Rotamer: Outliers : 2.14 % Allowed : 4.28 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.17), residues: 2476 helix: 1.99 (0.12), residues: 1644 sheet: 0.31 (0.51), residues: 112 loop : -0.16 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C4913 TYR 0.012 0.001 TYR C4994 PHE 0.020 0.002 PHE C4916 TRP 0.009 0.001 TRP C5019 HIS 0.005 0.001 HIS D4886 Details of bonding type rmsd covalent geometry : bond 0.00432 (21208) covalent geometry : angle 0.59063 (28644) SS BOND : bond 0.00104 ( 4) SS BOND : angle 0.90757 ( 8) hydrogen bonds : bond 0.14631 ( 1388) hydrogen bonds : angle 4.68462 ( 4068) metal coordination : bond 0.01221 ( 16) metal coordination : angle 4.26074 ( 8) Misc. bond : bond 0.99042 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 464 time to evaluate : 0.802 Fit side-chains REVERT: A 3992 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7632 (m-80) REVERT: A 4196 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.5993 (tp30) REVERT: A 4580 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.6354 (t80) REVERT: A 4644 TRP cc_start: 0.7187 (t60) cc_final: 0.6975 (t-100) REVERT: A 4726 ASP cc_start: 0.7010 (m-30) cc_final: 0.6792 (m-30) REVERT: A 4844 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8096 (tp) REVERT: B 3992 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7627 (m-80) REVERT: B 4196 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.5993 (tp30) REVERT: B 4580 TYR cc_start: 0.7422 (OUTLIER) cc_final: 0.6353 (t80) REVERT: B 4644 TRP cc_start: 0.7185 (t60) cc_final: 0.6971 (t-100) REVERT: B 4726 ASP cc_start: 0.7010 (m-30) cc_final: 0.6788 (m-30) REVERT: B 4844 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8096 (tp) REVERT: C 3992 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7627 (m-80) REVERT: C 4196 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.5992 (tp30) REVERT: C 4580 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.6347 (t80) REVERT: C 4644 TRP cc_start: 0.7186 (t60) cc_final: 0.6975 (t-100) REVERT: C 4726 ASP cc_start: 0.7010 (m-30) cc_final: 0.6790 (m-30) REVERT: C 4844 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8092 (tp) REVERT: D 3992 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7634 (m-80) REVERT: D 4196 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.5991 (tp30) REVERT: D 4580 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.6348 (t80) REVERT: D 4644 TRP cc_start: 0.7186 (t60) cc_final: 0.6975 (t-100) REVERT: D 4726 ASP cc_start: 0.7011 (m-30) cc_final: 0.6792 (m-30) REVERT: D 4844 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8094 (tp) outliers start: 48 outliers final: 16 residues processed: 508 average time/residue: 0.5454 time to fit residues: 313.5216 Evaluate side-chains 396 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 364 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3992 PHE Chi-restraints excluded: chain A residue 4183 ILE Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain B residue 3992 PHE Chi-restraints excluded: chain B residue 4183 ILE Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain C residue 3992 PHE Chi-restraints excluded: chain C residue 4183 ILE Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain D residue 3992 PHE Chi-restraints excluded: chain D residue 4183 ILE Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4844 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.3980 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4973 HIS A5031 GLN B4973 HIS B5031 GLN C4973 HIS C5031 GLN D4626 ASN D4973 HIS D5031 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.173401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.139419 restraints weight = 24311.979| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.08 r_work: 0.3316 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21232 Z= 0.156 Angle : 0.614 13.110 28660 Z= 0.306 Chirality : 0.039 0.145 3096 Planarity : 0.004 0.057 3612 Dihedral : 10.145 143.862 2812 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 3.79 % Allowed : 13.01 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.17), residues: 2476 helix: 2.04 (0.12), residues: 1704 sheet: 0.02 (0.49), residues: 112 loop : -0.00 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D4189 TYR 0.010 0.001 TYR D5014 PHE 0.020 0.001 PHE A4916 TRP 0.009 0.001 TRP A3986 HIS 0.004 0.001 HIS D3994 Details of bonding type rmsd covalent geometry : bond 0.00343 (21208) covalent geometry : angle 0.60951 (28644) SS BOND : bond 0.00114 ( 4) SS BOND : angle 0.98903 ( 8) hydrogen bonds : bond 0.05257 ( 1388) hydrogen bonds : angle 4.21803 ( 4068) metal coordination : bond 0.00732 ( 16) metal coordination : angle 4.25158 ( 8) Misc. bond : bond 0.00332 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 400 time to evaluate : 0.801 Fit side-chains REVERT: A 4023 MET cc_start: 0.7913 (ttp) cc_final: 0.7300 (tpp) REVERT: A 4039 MET cc_start: 0.7788 (mtp) cc_final: 0.7484 (ttp) REVERT: A 4042 ARG cc_start: 0.6758 (mtm110) cc_final: 0.6136 (mtm180) REVERT: A 4184 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8064 (ttp) REVERT: A 4196 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.6011 (tp30) REVERT: A 4209 GLN cc_start: 0.7980 (pt0) cc_final: 0.7502 (pm20) REVERT: A 4224 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7615 (pt0) REVERT: A 4554 TYR cc_start: 0.8180 (t80) cc_final: 0.7977 (t80) REVERT: A 4580 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.6552 (t80) REVERT: A 4584 ASP cc_start: 0.6770 (t0) cc_final: 0.6529 (p0) REVERT: A 4644 TRP cc_start: 0.7597 (t60) cc_final: 0.7306 (t-100) REVERT: A 4726 ASP cc_start: 0.7341 (m-30) cc_final: 0.7086 (m-30) REVERT: A 4743 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.6499 (ptm) REVERT: A 4992 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8426 (mt) REVERT: B 3955 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7124 (mtm) REVERT: B 4023 MET cc_start: 0.7906 (ttp) cc_final: 0.7291 (tpp) REVERT: B 4039 MET cc_start: 0.7754 (mtp) cc_final: 0.7466 (ttp) REVERT: B 4042 ARG cc_start: 0.6765 (mtm110) cc_final: 0.6143 (mtm180) REVERT: B 4184 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.8072 (ttp) REVERT: B 4196 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.6004 (tp30) REVERT: B 4209 GLN cc_start: 0.7985 (pt0) cc_final: 0.7512 (pm20) REVERT: B 4224 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7606 (pt0) REVERT: B 4554 TYR cc_start: 0.8191 (t80) cc_final: 0.7988 (t80) REVERT: B 4580 TYR cc_start: 0.7742 (OUTLIER) cc_final: 0.6558 (t80) REVERT: B 4584 ASP cc_start: 0.6776 (t0) cc_final: 0.6535 (p0) REVERT: B 4644 TRP cc_start: 0.7592 (t60) cc_final: 0.7304 (t-100) REVERT: B 4726 ASP cc_start: 0.7343 (m-30) cc_final: 0.7089 (m-30) REVERT: B 4743 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.6498 (ptm) REVERT: B 4992 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8428 (mt) REVERT: C 3955 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7129 (mtm) REVERT: C 4023 MET cc_start: 0.7892 (ttp) cc_final: 0.7283 (tpp) REVERT: C 4039 MET cc_start: 0.7721 (mtp) cc_final: 0.7468 (ttp) REVERT: C 4042 ARG cc_start: 0.6769 (mtm110) cc_final: 0.6145 (mtm180) REVERT: C 4184 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.8066 (ttp) REVERT: C 4196 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6008 (tp30) REVERT: C 4209 GLN cc_start: 0.7996 (pt0) cc_final: 0.7515 (pm20) REVERT: C 4224 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7616 (pt0) REVERT: C 4554 TYR cc_start: 0.8181 (t80) cc_final: 0.7973 (t80) REVERT: C 4580 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.6556 (t80) REVERT: C 4584 ASP cc_start: 0.6770 (t0) cc_final: 0.6531 (p0) REVERT: C 4644 TRP cc_start: 0.7591 (t60) cc_final: 0.7300 (t-100) REVERT: C 4726 ASP cc_start: 0.7342 (m-30) cc_final: 0.7090 (m-30) REVERT: C 4743 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.6497 (ptm) REVERT: C 4992 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8428 (mt) REVERT: D 3955 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.7127 (mtm) REVERT: D 4023 MET cc_start: 0.7909 (ttp) cc_final: 0.7297 (tpp) REVERT: D 4039 MET cc_start: 0.7759 (mtp) cc_final: 0.7473 (ttp) REVERT: D 4042 ARG cc_start: 0.6768 (mtm110) cc_final: 0.6146 (mtm180) REVERT: D 4184 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8054 (ttp) REVERT: D 4196 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6008 (tp30) REVERT: D 4209 GLN cc_start: 0.7983 (pt0) cc_final: 0.7496 (pm20) REVERT: D 4224 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7614 (pt0) REVERT: D 4580 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.6563 (t80) REVERT: D 4584 ASP cc_start: 0.6767 (t0) cc_final: 0.6528 (p0) REVERT: D 4644 TRP cc_start: 0.7599 (t60) cc_final: 0.7305 (t-100) REVERT: D 4726 ASP cc_start: 0.7343 (m-30) cc_final: 0.7088 (m-30) REVERT: D 4743 MET cc_start: 0.6703 (OUTLIER) cc_final: 0.6489 (ptm) REVERT: D 4992 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8423 (mt) outliers start: 85 outliers final: 21 residues processed: 441 average time/residue: 0.5409 time to fit residues: 270.1797 Evaluate side-chains 418 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 370 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4045 VAL Chi-restraints excluded: chain A residue 4183 ILE Chi-restraints excluded: chain A residue 4184 MET Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4224 GLU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 3955 MET Chi-restraints excluded: chain B residue 4045 VAL Chi-restraints excluded: chain B residue 4183 ILE Chi-restraints excluded: chain B residue 4184 MET Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4224 GLU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 3955 MET Chi-restraints excluded: chain C residue 4045 VAL Chi-restraints excluded: chain C residue 4183 ILE Chi-restraints excluded: chain C residue 4184 MET Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4224 GLU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 3955 MET Chi-restraints excluded: chain D residue 4045 VAL Chi-restraints excluded: chain D residue 4183 ILE Chi-restraints excluded: chain D residue 4184 MET Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4224 GLU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4626 ASN Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 119 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 230 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 234 optimal weight: 0.1980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4973 HIS B4973 HIS C4043 GLN C4973 HIS D4973 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.173551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.139613 restraints weight = 24399.196| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.19 r_work: 0.3311 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21232 Z= 0.142 Angle : 0.582 11.739 28660 Z= 0.290 Chirality : 0.038 0.134 3096 Planarity : 0.004 0.056 3612 Dihedral : 9.609 145.419 2792 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 4.41 % Allowed : 13.41 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.17), residues: 2476 helix: 2.14 (0.12), residues: 1704 sheet: -0.33 (0.48), residues: 112 loop : 0.06 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A4736 TYR 0.012 0.001 TYR B5032 PHE 0.019 0.001 PHE B4916 TRP 0.005 0.001 TRP C5019 HIS 0.003 0.001 HIS B4886 Details of bonding type rmsd covalent geometry : bond 0.00311 (21208) covalent geometry : angle 0.57749 (28644) SS BOND : bond 0.00135 ( 4) SS BOND : angle 1.05853 ( 8) hydrogen bonds : bond 0.04697 ( 1388) hydrogen bonds : angle 4.13168 ( 4068) metal coordination : bond 0.00601 ( 16) metal coordination : angle 4.05980 ( 8) Misc. bond : bond 0.00564 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 376 time to evaluate : 0.827 Fit side-chains REVERT: A 3980 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.7892 (mm) REVERT: A 3992 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7180 (m-80) REVERT: A 4015 GLU cc_start: 0.7143 (tt0) cc_final: 0.6902 (mp0) REVERT: A 4023 MET cc_start: 0.7604 (ttp) cc_final: 0.7188 (tpp) REVERT: A 4042 ARG cc_start: 0.6622 (mtm110) cc_final: 0.5964 (mtm180) REVERT: A 4196 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.5969 (tp30) REVERT: A 4209 GLN cc_start: 0.7997 (pt0) cc_final: 0.7512 (pm20) REVERT: A 4212 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: A 4554 TYR cc_start: 0.8194 (t80) cc_final: 0.7965 (t80) REVERT: A 4580 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.6592 (t80) REVERT: A 4584 ASP cc_start: 0.6838 (t0) cc_final: 0.6562 (p0) REVERT: A 4644 TRP cc_start: 0.7753 (t60) cc_final: 0.7468 (t-100) REVERT: A 4726 ASP cc_start: 0.7328 (m-30) cc_final: 0.7126 (m-30) REVERT: A 4736 ARG cc_start: 0.7071 (ttp-110) cc_final: 0.6864 (ttp-110) REVERT: A 4992 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8439 (mt) REVERT: B 3955 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.7094 (mtm) REVERT: B 3980 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.7891 (mm) REVERT: B 3992 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7179 (m-80) REVERT: B 4015 GLU cc_start: 0.7149 (tt0) cc_final: 0.6890 (mp0) REVERT: B 4023 MET cc_start: 0.7590 (ttp) cc_final: 0.7173 (tpp) REVERT: B 4042 ARG cc_start: 0.6621 (mtm110) cc_final: 0.5962 (mtm180) REVERT: B 4196 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.5968 (tp30) REVERT: B 4209 GLN cc_start: 0.8006 (pt0) cc_final: 0.7527 (pm20) REVERT: B 4212 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: B 4554 TYR cc_start: 0.8199 (t80) cc_final: 0.7978 (t80) REVERT: B 4580 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.6586 (t80) REVERT: B 4584 ASP cc_start: 0.6847 (t0) cc_final: 0.6572 (p0) REVERT: B 4644 TRP cc_start: 0.7749 (t60) cc_final: 0.7463 (t-100) REVERT: B 4726 ASP cc_start: 0.7317 (m-30) cc_final: 0.7114 (m-30) REVERT: B 4736 ARG cc_start: 0.7070 (ttp-110) cc_final: 0.6865 (ttp-110) REVERT: B 4992 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8440 (mt) REVERT: C 3955 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7098 (mtm) REVERT: C 3980 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.7888 (mm) REVERT: C 3992 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7179 (m-80) REVERT: C 4015 GLU cc_start: 0.7151 (tt0) cc_final: 0.6893 (mp0) REVERT: C 4023 MET cc_start: 0.7578 (ttp) cc_final: 0.7163 (tpp) REVERT: C 4042 ARG cc_start: 0.6633 (mtm110) cc_final: 0.5973 (mtm180) REVERT: C 4196 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.5966 (tp30) REVERT: C 4209 GLN cc_start: 0.7998 (pt0) cc_final: 0.7513 (pm20) REVERT: C 4212 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: C 4554 TYR cc_start: 0.8192 (t80) cc_final: 0.7961 (t80) REVERT: C 4580 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.6595 (t80) REVERT: C 4584 ASP cc_start: 0.6848 (t0) cc_final: 0.6574 (p0) REVERT: C 4644 TRP cc_start: 0.7755 (t60) cc_final: 0.7467 (t-100) REVERT: C 4726 ASP cc_start: 0.7311 (m-30) cc_final: 0.7107 (m-30) REVERT: C 4736 ARG cc_start: 0.7076 (ttp-110) cc_final: 0.6874 (ttp-110) REVERT: C 4992 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8430 (mt) REVERT: D 3955 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7096 (mtm) REVERT: D 3980 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.7886 (mm) REVERT: D 3992 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7184 (m-80) REVERT: D 4015 GLU cc_start: 0.7142 (tt0) cc_final: 0.6886 (mp0) REVERT: D 4023 MET cc_start: 0.7595 (ttp) cc_final: 0.7182 (tpp) REVERT: D 4042 ARG cc_start: 0.6633 (mtm110) cc_final: 0.5974 (mtm180) REVERT: D 4196 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.5959 (tp30) REVERT: D 4209 GLN cc_start: 0.7992 (pt0) cc_final: 0.7500 (pm20) REVERT: D 4212 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: D 4580 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.6596 (t80) REVERT: D 4584 ASP cc_start: 0.6874 (t0) cc_final: 0.6611 (p0) REVERT: D 4644 TRP cc_start: 0.7757 (t60) cc_final: 0.7468 (t-100) REVERT: D 4726 ASP cc_start: 0.7323 (m-30) cc_final: 0.7121 (m-30) REVERT: D 4736 ARG cc_start: 0.7074 (ttp-110) cc_final: 0.6866 (ttp-110) REVERT: D 4992 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8430 (mt) outliers start: 99 outliers final: 28 residues processed: 420 average time/residue: 0.5647 time to fit residues: 267.8474 Evaluate side-chains 423 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 368 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3980 LEU Chi-restraints excluded: chain A residue 3992 PHE Chi-restraints excluded: chain A residue 4045 VAL Chi-restraints excluded: chain A residue 4183 ILE Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4212 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 3955 MET Chi-restraints excluded: chain B residue 3980 LEU Chi-restraints excluded: chain B residue 3992 PHE Chi-restraints excluded: chain B residue 4045 VAL Chi-restraints excluded: chain B residue 4183 ILE Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4212 GLU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 3955 MET Chi-restraints excluded: chain C residue 3980 LEU Chi-restraints excluded: chain C residue 3992 PHE Chi-restraints excluded: chain C residue 4045 VAL Chi-restraints excluded: chain C residue 4183 ILE Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4212 GLU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 3955 MET Chi-restraints excluded: chain D residue 3980 LEU Chi-restraints excluded: chain D residue 3992 PHE Chi-restraints excluded: chain D residue 4045 VAL Chi-restraints excluded: chain D residue 4183 ILE Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4212 GLU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 93 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 245 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4043 GLN A4973 HIS B4043 GLN B4973 HIS C4973 HIS D4043 GLN D4973 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.173858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139551 restraints weight = 24493.778| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.05 r_work: 0.3334 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21232 Z= 0.146 Angle : 0.564 7.513 28660 Z= 0.283 Chirality : 0.038 0.135 3096 Planarity : 0.004 0.058 3612 Dihedral : 9.476 146.934 2792 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.70 % Favored : 98.14 % Rotamer: Outliers : 3.74 % Allowed : 15.33 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.17), residues: 2476 helix: 2.13 (0.12), residues: 1700 sheet: 0.67 (0.68), residues: 64 loop : -0.05 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D4189 TYR 0.009 0.001 TYR A4994 PHE 0.020 0.001 PHE C4916 TRP 0.005 0.001 TRP A5019 HIS 0.003 0.001 HIS D3994 Details of bonding type rmsd covalent geometry : bond 0.00331 (21208) covalent geometry : angle 0.55906 (28644) SS BOND : bond 0.00200 ( 4) SS BOND : angle 1.26978 ( 8) hydrogen bonds : bond 0.04526 ( 1388) hydrogen bonds : angle 4.16171 ( 4068) metal coordination : bond 0.00714 ( 16) metal coordination : angle 4.11705 ( 8) Misc. bond : bond 0.00245 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 380 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3955 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6899 (mtm) REVERT: A 3992 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7311 (m-80) REVERT: A 4015 GLU cc_start: 0.7142 (tt0) cc_final: 0.6903 (mp0) REVERT: A 4023 MET cc_start: 0.7543 (ttp) cc_final: 0.7232 (tpp) REVERT: A 4042 ARG cc_start: 0.6591 (mtm110) cc_final: 0.6064 (mtm180) REVERT: A 4196 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.5870 (tp30) REVERT: A 4209 GLN cc_start: 0.7975 (pt0) cc_final: 0.7511 (pm20) REVERT: A 4212 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: A 4554 TYR cc_start: 0.8208 (t80) cc_final: 0.7979 (t80) REVERT: A 4580 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.6603 (t80) REVERT: A 4584 ASP cc_start: 0.6843 (t0) cc_final: 0.6630 (p0) REVERT: A 4644 TRP cc_start: 0.7730 (t60) cc_final: 0.7455 (t-100) REVERT: A 4704 LEU cc_start: 0.8955 (tp) cc_final: 0.8349 (mm) REVERT: A 4726 ASP cc_start: 0.7322 (m-30) cc_final: 0.7115 (m-30) REVERT: A 4992 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8439 (mt) REVERT: B 3992 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7312 (m-80) REVERT: B 4015 GLU cc_start: 0.7146 (tt0) cc_final: 0.6909 (mp0) REVERT: B 4023 MET cc_start: 0.7530 (ttp) cc_final: 0.7209 (tpp) REVERT: B 4042 ARG cc_start: 0.6589 (mtm110) cc_final: 0.6058 (mtm180) REVERT: B 4196 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.5872 (tp30) REVERT: B 4209 GLN cc_start: 0.7981 (pt0) cc_final: 0.7516 (pm20) REVERT: B 4212 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: B 4554 TYR cc_start: 0.8198 (t80) cc_final: 0.7978 (t80) REVERT: B 4580 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.6597 (t80) REVERT: B 4584 ASP cc_start: 0.6856 (t0) cc_final: 0.6639 (p0) REVERT: B 4644 TRP cc_start: 0.7731 (t60) cc_final: 0.7454 (t-100) REVERT: B 4704 LEU cc_start: 0.8957 (tp) cc_final: 0.8358 (mm) REVERT: B 4726 ASP cc_start: 0.7309 (m-30) cc_final: 0.7103 (m-30) REVERT: B 4992 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8443 (mt) REVERT: C 3992 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7315 (m-80) REVERT: C 4015 GLU cc_start: 0.7140 (tt0) cc_final: 0.6908 (mp0) REVERT: C 4023 MET cc_start: 0.7508 (ttp) cc_final: 0.7191 (tpp) REVERT: C 4042 ARG cc_start: 0.6597 (mtm110) cc_final: 0.6069 (mtm180) REVERT: C 4196 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.5872 (tp30) REVERT: C 4209 GLN cc_start: 0.7983 (pt0) cc_final: 0.7512 (pm20) REVERT: C 4212 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: C 4554 TYR cc_start: 0.8194 (t80) cc_final: 0.7970 (t80) REVERT: C 4580 TYR cc_start: 0.7705 (OUTLIER) cc_final: 0.6601 (t80) REVERT: C 4584 ASP cc_start: 0.6846 (t0) cc_final: 0.6635 (p0) REVERT: C 4644 TRP cc_start: 0.7733 (t60) cc_final: 0.7455 (t-100) REVERT: C 4704 LEU cc_start: 0.8962 (tp) cc_final: 0.8365 (mm) REVERT: C 4726 ASP cc_start: 0.7300 (m-30) cc_final: 0.7094 (m-30) REVERT: C 4992 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8435 (mt) REVERT: D 3992 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7316 (m-80) REVERT: D 4015 GLU cc_start: 0.7139 (tt0) cc_final: 0.6906 (mp0) REVERT: D 4023 MET cc_start: 0.7529 (ttp) cc_final: 0.7212 (tpp) REVERT: D 4042 ARG cc_start: 0.6597 (mtm110) cc_final: 0.6067 (mtm180) REVERT: D 4196 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.5867 (tp30) REVERT: D 4209 GLN cc_start: 0.7966 (pt0) cc_final: 0.7492 (pm20) REVERT: D 4212 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: D 4580 TYR cc_start: 0.7707 (OUTLIER) cc_final: 0.6598 (t80) REVERT: D 4584 ASP cc_start: 0.6965 (t0) cc_final: 0.6718 (p0) REVERT: D 4644 TRP cc_start: 0.7735 (t60) cc_final: 0.7455 (t-100) REVERT: D 4704 LEU cc_start: 0.8962 (tp) cc_final: 0.8364 (mm) REVERT: D 4726 ASP cc_start: 0.7307 (m-30) cc_final: 0.7101 (m-30) REVERT: D 4992 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8438 (mt) outliers start: 84 outliers final: 32 residues processed: 416 average time/residue: 0.5644 time to fit residues: 265.3260 Evaluate side-chains 417 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 364 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3955 MET Chi-restraints excluded: chain A residue 3992 PHE Chi-restraints excluded: chain A residue 4045 VAL Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4212 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4976 GLU Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 3992 PHE Chi-restraints excluded: chain B residue 4045 VAL Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4212 GLU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4976 GLU Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 3992 PHE Chi-restraints excluded: chain C residue 4045 VAL Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4212 GLU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4976 GLU Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 3992 PHE Chi-restraints excluded: chain D residue 4045 VAL Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4212 GLU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4976 GLU Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 98 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 125 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 chunk 192 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 186 optimal weight: 30.0000 chunk 161 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4886 HIS A4973 HIS B4973 HIS C4973 HIS D4973 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.170893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.136931 restraints weight = 24470.010| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.22 r_work: 0.3281 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 21232 Z= 0.240 Angle : 0.654 9.112 28660 Z= 0.328 Chirality : 0.042 0.141 3096 Planarity : 0.005 0.092 3612 Dihedral : 9.502 149.936 2784 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 4.68 % Allowed : 14.48 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.17), residues: 2476 helix: 1.80 (0.12), residues: 1704 sheet: 0.37 (0.68), residues: 64 loop : -0.10 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B4189 TYR 0.013 0.002 TYR C4994 PHE 0.029 0.002 PHE B4916 TRP 0.007 0.001 TRP D5019 HIS 0.005 0.001 HIS B4886 Details of bonding type rmsd covalent geometry : bond 0.00575 (21208) covalent geometry : angle 0.64780 (28644) SS BOND : bond 0.00372 ( 4) SS BOND : angle 1.64282 ( 8) hydrogen bonds : bond 0.05285 ( 1388) hydrogen bonds : angle 4.46612 ( 4068) metal coordination : bond 0.01676 ( 16) metal coordination : angle 5.08511 ( 8) Misc. bond : bond 0.00655 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 366 time to evaluate : 0.667 Fit side-chains REVERT: A 3955 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6978 (mtm) REVERT: A 3980 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.7776 (mm) REVERT: A 4015 GLU cc_start: 0.7168 (tt0) cc_final: 0.6940 (mp0) REVERT: A 4023 MET cc_start: 0.7920 (ttp) cc_final: 0.7421 (ttt) REVERT: A 4042 ARG cc_start: 0.6566 (mtm110) cc_final: 0.5834 (mtm180) REVERT: A 4196 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6101 (tp30) REVERT: A 4209 GLN cc_start: 0.8081 (pt0) cc_final: 0.7569 (pm20) REVERT: A 4212 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: A 4580 TYR cc_start: 0.7705 (OUTLIER) cc_final: 0.6657 (t80) REVERT: A 4584 ASP cc_start: 0.6890 (t0) cc_final: 0.6612 (p0) REVERT: A 4644 TRP cc_start: 0.7707 (t60) cc_final: 0.7399 (t-100) REVERT: A 4726 ASP cc_start: 0.7321 (m-30) cc_final: 0.7094 (m-30) REVERT: A 4911 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7694 (mm) REVERT: B 3980 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.7774 (mm) REVERT: B 4015 GLU cc_start: 0.7164 (tt0) cc_final: 0.6956 (mp0) REVERT: B 4023 MET cc_start: 0.7897 (ttp) cc_final: 0.7391 (ttt) REVERT: B 4042 ARG cc_start: 0.6569 (mtm110) cc_final: 0.5834 (mtm180) REVERT: B 4196 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6114 (tp30) REVERT: B 4209 GLN cc_start: 0.8082 (pt0) cc_final: 0.7570 (pm20) REVERT: B 4212 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: B 4580 TYR cc_start: 0.7712 (OUTLIER) cc_final: 0.6662 (t80) REVERT: B 4584 ASP cc_start: 0.6903 (t0) cc_final: 0.6624 (p0) REVERT: B 4644 TRP cc_start: 0.7696 (t60) cc_final: 0.7392 (t-100) REVERT: B 4726 ASP cc_start: 0.7328 (m-30) cc_final: 0.7101 (m-30) REVERT: B 4911 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7692 (mm) REVERT: C 4015 GLU cc_start: 0.7159 (tt0) cc_final: 0.6956 (mp0) REVERT: C 4023 MET cc_start: 0.7884 (ttp) cc_final: 0.7379 (ttt) REVERT: C 4042 ARG cc_start: 0.6629 (mtm110) cc_final: 0.5906 (mtm180) REVERT: C 4196 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6118 (tp30) REVERT: C 4209 GLN cc_start: 0.8085 (pt0) cc_final: 0.7566 (pm20) REVERT: C 4212 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: C 4580 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.6662 (t80) REVERT: C 4584 ASP cc_start: 0.6904 (t0) cc_final: 0.6623 (p0) REVERT: C 4644 TRP cc_start: 0.7706 (t60) cc_final: 0.7397 (t-100) REVERT: C 4726 ASP cc_start: 0.7311 (m-30) cc_final: 0.7085 (m-30) REVERT: C 4911 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7684 (mm) REVERT: D 3980 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.7775 (mm) REVERT: D 4015 GLU cc_start: 0.7157 (tt0) cc_final: 0.6953 (mp0) REVERT: D 4023 MET cc_start: 0.7897 (ttp) cc_final: 0.7395 (ttt) REVERT: D 4042 ARG cc_start: 0.6581 (mtm110) cc_final: 0.5849 (mtm180) REVERT: D 4196 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6105 (tp30) REVERT: D 4209 GLN cc_start: 0.8074 (pt0) cc_final: 0.7550 (pm20) REVERT: D 4212 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: D 4580 TYR cc_start: 0.7712 (OUTLIER) cc_final: 0.6665 (t80) REVERT: D 4584 ASP cc_start: 0.6892 (t0) cc_final: 0.6622 (p0) REVERT: D 4644 TRP cc_start: 0.7705 (t60) cc_final: 0.7396 (t-100) REVERT: D 4726 ASP cc_start: 0.7322 (m-30) cc_final: 0.7095 (m-30) REVERT: D 4911 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7691 (mm) outliers start: 105 outliers final: 44 residues processed: 430 average time/residue: 0.5408 time to fit residues: 263.9206 Evaluate side-chains 426 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 362 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3955 MET Chi-restraints excluded: chain A residue 3980 LEU Chi-restraints excluded: chain A residue 4045 VAL Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4212 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4705 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4773 VAL Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4976 GLU Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 3980 LEU Chi-restraints excluded: chain B residue 4045 VAL Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4212 GLU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4705 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4773 VAL Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4976 GLU Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 4045 VAL Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4212 GLU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4705 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4773 VAL Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4976 GLU Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 3980 LEU Chi-restraints excluded: chain D residue 4045 VAL Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4212 GLU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4705 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4773 VAL Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4976 GLU Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 2 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 185 optimal weight: 0.1980 chunk 148 optimal weight: 2.9990 chunk 186 optimal weight: 30.0000 chunk 144 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 181 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 219 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4034 ASN A4973 HIS B4034 ASN B4973 HIS C4034 ASN C4973 HIS D4034 ASN D4973 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.175146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.140984 restraints weight = 24400.297| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.01 r_work: 0.3363 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21232 Z= 0.122 Angle : 0.594 12.540 28660 Z= 0.293 Chirality : 0.037 0.158 3096 Planarity : 0.004 0.081 3612 Dihedral : 9.245 148.604 2784 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.41 % Allowed : 17.42 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.17), residues: 2476 helix: 2.08 (0.12), residues: 1720 sheet: 0.32 (0.68), residues: 64 loop : -0.13 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A4736 TYR 0.012 0.001 TYR C4580 PHE 0.019 0.001 PHE A4922 TRP 0.005 0.001 TRP D5019 HIS 0.003 0.001 HIS B3994 Details of bonding type rmsd covalent geometry : bond 0.00265 (21208) covalent geometry : angle 0.59046 (28644) SS BOND : bond 0.00145 ( 4) SS BOND : angle 1.15731 ( 8) hydrogen bonds : bond 0.04133 ( 1388) hydrogen bonds : angle 4.25066 ( 4068) metal coordination : bond 0.00243 ( 16) metal coordination : angle 3.75210 ( 8) Misc. bond : bond 0.00628 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 395 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3955 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6983 (mtm) REVERT: A 3986 TRP cc_start: 0.8365 (m100) cc_final: 0.7527 (m100) REVERT: A 4015 GLU cc_start: 0.7044 (tt0) cc_final: 0.6815 (mp0) REVERT: A 4023 MET cc_start: 0.7137 (ttp) cc_final: 0.6897 (ttt) REVERT: A 4042 ARG cc_start: 0.6487 (mtm110) cc_final: 0.5771 (mtm180) REVERT: A 4196 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.5863 (tp30) REVERT: A 4199 GLU cc_start: 0.7487 (pm20) cc_final: 0.7072 (tp30) REVERT: A 4209 GLN cc_start: 0.7939 (pt0) cc_final: 0.7471 (pm20) REVERT: A 4212 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: A 4554 TYR cc_start: 0.8098 (t80) cc_final: 0.7890 (t80) REVERT: A 4580 TYR cc_start: 0.6978 (t80) cc_final: 0.6455 (t80) REVERT: A 4584 ASP cc_start: 0.6726 (t0) cc_final: 0.6443 (p0) REVERT: A 4644 TRP cc_start: 0.7732 (t60) cc_final: 0.7422 (t-100) REVERT: A 4726 ASP cc_start: 0.7332 (m-30) cc_final: 0.7060 (m-30) REVERT: A 4992 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8434 (mt) REVERT: B 3986 TRP cc_start: 0.8373 (m100) cc_final: 0.7524 (m100) REVERT: B 4015 GLU cc_start: 0.7055 (tt0) cc_final: 0.6846 (mp0) REVERT: B 4023 MET cc_start: 0.7111 (ttp) cc_final: 0.6878 (ttt) REVERT: B 4042 ARG cc_start: 0.6494 (mtm110) cc_final: 0.5774 (mtm180) REVERT: B 4196 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.5866 (tp30) REVERT: B 4199 GLU cc_start: 0.7497 (pm20) cc_final: 0.7077 (tp30) REVERT: B 4209 GLN cc_start: 0.7942 (pt0) cc_final: 0.7470 (pm20) REVERT: B 4212 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: B 4580 TYR cc_start: 0.6986 (t80) cc_final: 0.6454 (t80) REVERT: B 4584 ASP cc_start: 0.6737 (t0) cc_final: 0.6449 (p0) REVERT: B 4644 TRP cc_start: 0.7730 (t60) cc_final: 0.7420 (t-100) REVERT: B 4726 ASP cc_start: 0.7335 (m-30) cc_final: 0.7060 (m-30) REVERT: B 4992 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8439 (mt) REVERT: C 3986 TRP cc_start: 0.8435 (m100) cc_final: 0.7671 (m100) REVERT: C 4015 GLU cc_start: 0.7056 (tt0) cc_final: 0.6848 (mp0) REVERT: C 4023 MET cc_start: 0.7097 (ttp) cc_final: 0.6859 (ttt) REVERT: C 4042 ARG cc_start: 0.6511 (mtm110) cc_final: 0.5794 (mtm180) REVERT: C 4196 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.5858 (tp30) REVERT: C 4199 GLU cc_start: 0.7491 (pm20) cc_final: 0.7074 (tp30) REVERT: C 4209 GLN cc_start: 0.7947 (pt0) cc_final: 0.7469 (pm20) REVERT: C 4212 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: C 4554 TYR cc_start: 0.8092 (t80) cc_final: 0.7888 (t80) REVERT: C 4580 TYR cc_start: 0.6973 (t80) cc_final: 0.6453 (t80) REVERT: C 4584 ASP cc_start: 0.6731 (t0) cc_final: 0.6443 (p0) REVERT: C 4644 TRP cc_start: 0.7736 (t60) cc_final: 0.7424 (t-100) REVERT: C 4726 ASP cc_start: 0.7322 (m-30) cc_final: 0.7053 (m-30) REVERT: C 4992 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8436 (mt) REVERT: D 3986 TRP cc_start: 0.8370 (m100) cc_final: 0.7527 (m100) REVERT: D 4015 GLU cc_start: 0.7056 (tt0) cc_final: 0.6850 (mp0) REVERT: D 4023 MET cc_start: 0.7122 (ttp) cc_final: 0.6886 (ttt) REVERT: D 4042 ARG cc_start: 0.6504 (mtm110) cc_final: 0.5783 (mtm180) REVERT: D 4196 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.5847 (tp30) REVERT: D 4199 GLU cc_start: 0.7485 (pm20) cc_final: 0.7071 (tp30) REVERT: D 4209 GLN cc_start: 0.7931 (pt0) cc_final: 0.7453 (pm20) REVERT: D 4212 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: D 4580 TYR cc_start: 0.6931 (t80) cc_final: 0.6418 (t80) REVERT: D 4584 ASP cc_start: 0.6736 (t0) cc_final: 0.6455 (p0) REVERT: D 4644 TRP cc_start: 0.7734 (t60) cc_final: 0.7422 (t-100) REVERT: D 4726 ASP cc_start: 0.7323 (m-30) cc_final: 0.7050 (m-30) REVERT: D 4992 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8437 (mt) outliers start: 54 outliers final: 16 residues processed: 425 average time/residue: 0.5506 time to fit residues: 264.1128 Evaluate side-chains 407 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 378 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3955 MET Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4212 GLU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4212 GLU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4212 GLU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4212 GLU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 236 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 218 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 164 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4034 ASN A4973 HIS B4034 ASN B4973 HIS C4034 ASN C4973 HIS D4034 ASN D4973 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.172517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.138584 restraints weight = 24523.901| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.11 r_work: 0.3317 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 21232 Z= 0.189 Angle : 0.681 17.130 28660 Z= 0.329 Chirality : 0.040 0.158 3096 Planarity : 0.005 0.094 3612 Dihedral : 9.107 149.839 2768 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.74 % Rotamer: Outliers : 2.76 % Allowed : 17.96 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.17), residues: 2476 helix: 1.88 (0.12), residues: 1704 sheet: 0.21 (0.68), residues: 64 loop : -0.17 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D4189 TYR 0.011 0.002 TYR B4560 PHE 0.025 0.002 PHE A4922 TRP 0.005 0.001 TRP D4541 HIS 0.004 0.001 HIS C4886 Details of bonding type rmsd covalent geometry : bond 0.00447 (21208) covalent geometry : angle 0.67620 (28644) SS BOND : bond 0.00247 ( 4) SS BOND : angle 1.44213 ( 8) hydrogen bonds : bond 0.04678 ( 1388) hydrogen bonds : angle 4.41291 ( 4068) metal coordination : bond 0.01068 ( 16) metal coordination : angle 4.65504 ( 8) Misc. bond : bond 0.01374 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 369 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3955 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.7010 (mtm) REVERT: A 3986 TRP cc_start: 0.8372 (m100) cc_final: 0.7731 (m100) REVERT: A 4023 MET cc_start: 0.7249 (ttp) cc_final: 0.6972 (ttt) REVERT: A 4042 ARG cc_start: 0.6518 (mtm110) cc_final: 0.5788 (mtm180) REVERT: A 4196 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6029 (tp30) REVERT: A 4209 GLN cc_start: 0.8022 (pt0) cc_final: 0.7538 (pm20) REVERT: A 4212 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: A 4554 TYR cc_start: 0.8190 (t80) cc_final: 0.7988 (t80) REVERT: A 4580 TYR cc_start: 0.6900 (t80) cc_final: 0.6366 (t80) REVERT: A 4584 ASP cc_start: 0.6701 (t0) cc_final: 0.6365 (p0) REVERT: A 4644 TRP cc_start: 0.7722 (t60) cc_final: 0.7418 (t-100) REVERT: A 4726 ASP cc_start: 0.7338 (m-30) cc_final: 0.7090 (m-30) REVERT: A 4736 ARG cc_start: 0.6864 (ttp-110) cc_final: 0.6375 (ttp-110) REVERT: A 4911 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7608 (mm) REVERT: B 3986 TRP cc_start: 0.8372 (m100) cc_final: 0.7727 (m100) REVERT: B 4023 MET cc_start: 0.7226 (ttp) cc_final: 0.6951 (ttt) REVERT: B 4042 ARG cc_start: 0.6515 (mtm110) cc_final: 0.5783 (mtm180) REVERT: B 4196 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.5959 (tp30) REVERT: B 4209 GLN cc_start: 0.8030 (pt0) cc_final: 0.7542 (pm20) REVERT: B 4212 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: B 4580 TYR cc_start: 0.6903 (t80) cc_final: 0.6371 (t80) REVERT: B 4584 ASP cc_start: 0.6726 (t0) cc_final: 0.6380 (p0) REVERT: B 4644 TRP cc_start: 0.7720 (t60) cc_final: 0.7416 (t-100) REVERT: B 4726 ASP cc_start: 0.7331 (m-30) cc_final: 0.7081 (m-30) REVERT: B 4736 ARG cc_start: 0.6860 (ttp-110) cc_final: 0.6372 (ttp-110) REVERT: B 4911 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7620 (mm) REVERT: C 3986 TRP cc_start: 0.8373 (m100) cc_final: 0.7725 (m100) REVERT: C 4023 MET cc_start: 0.7216 (ttp) cc_final: 0.6939 (ttt) REVERT: C 4042 ARG cc_start: 0.6525 (mtm110) cc_final: 0.5796 (mtm180) REVERT: C 4196 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6027 (tp30) REVERT: C 4209 GLN cc_start: 0.8026 (pt0) cc_final: 0.7533 (pm20) REVERT: C 4212 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: C 4554 TYR cc_start: 0.8186 (t80) cc_final: 0.7984 (t80) REVERT: C 4580 TYR cc_start: 0.6902 (t80) cc_final: 0.6374 (t80) REVERT: C 4584 ASP cc_start: 0.6716 (t0) cc_final: 0.6374 (p0) REVERT: C 4644 TRP cc_start: 0.7725 (t60) cc_final: 0.7419 (t-100) REVERT: C 4726 ASP cc_start: 0.7324 (m-30) cc_final: 0.7082 (m-30) REVERT: C 4736 ARG cc_start: 0.6860 (ttp-110) cc_final: 0.6370 (ttp-110) REVERT: C 4911 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7605 (mm) REVERT: D 3986 TRP cc_start: 0.8367 (m100) cc_final: 0.7725 (m100) REVERT: D 4023 MET cc_start: 0.7223 (ttp) cc_final: 0.6949 (ttt) REVERT: D 4042 ARG cc_start: 0.6528 (mtm110) cc_final: 0.5799 (mtm180) REVERT: D 4196 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6018 (tp30) REVERT: D 4209 GLN cc_start: 0.8010 (pt0) cc_final: 0.7516 (pm20) REVERT: D 4212 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: D 4580 TYR cc_start: 0.6893 (t80) cc_final: 0.6370 (t80) REVERT: D 4584 ASP cc_start: 0.6739 (t0) cc_final: 0.6468 (p0) REVERT: D 4644 TRP cc_start: 0.7723 (t60) cc_final: 0.7417 (t-100) REVERT: D 4726 ASP cc_start: 0.7324 (m-30) cc_final: 0.7078 (m-30) REVERT: D 4736 ARG cc_start: 0.6861 (ttp-110) cc_final: 0.6375 (ttp-110) REVERT: D 4911 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7613 (mm) outliers start: 62 outliers final: 28 residues processed: 407 average time/residue: 0.5394 time to fit residues: 248.2063 Evaluate side-chains 395 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 354 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3955 MET Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4212 GLU Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4976 GLU Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4212 GLU Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4976 GLU Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4212 GLU Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4976 GLU Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4212 GLU Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4976 GLU Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 143 optimal weight: 0.2980 chunk 175 optimal weight: 0.6980 chunk 170 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4034 ASN A4973 HIS B4034 ASN B4973 HIS C4034 ASN C4973 HIS D4034 ASN D4973 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.174976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.140706 restraints weight = 24632.283| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.97 r_work: 0.3335 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21232 Z= 0.127 Angle : 0.612 13.182 28660 Z= 0.298 Chirality : 0.037 0.133 3096 Planarity : 0.004 0.083 3612 Dihedral : 9.008 149.424 2768 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.92 % Allowed : 19.34 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.17), residues: 2476 helix: 2.11 (0.12), residues: 1696 sheet: 0.18 (0.69), residues: 64 loop : -0.18 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C4189 TYR 0.009 0.001 TYR A4994 PHE 0.022 0.001 PHE B4922 TRP 0.006 0.001 TRP D5019 HIS 0.003 0.001 HIS A3994 Details of bonding type rmsd covalent geometry : bond 0.00285 (21208) covalent geometry : angle 0.60882 (28644) SS BOND : bond 0.00008 ( 4) SS BOND : angle 1.27540 ( 8) hydrogen bonds : bond 0.04047 ( 1388) hydrogen bonds : angle 4.25074 ( 4068) metal coordination : bond 0.00181 ( 16) metal coordination : angle 3.82582 ( 8) Misc. bond : bond 0.00975 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 377 time to evaluate : 0.821 Fit side-chains REVERT: A 3986 TRP cc_start: 0.8327 (m100) cc_final: 0.7699 (m100) REVERT: A 4042 ARG cc_start: 0.6517 (mtm110) cc_final: 0.5803 (mtm180) REVERT: A 4196 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6093 (tp30) REVERT: A 4199 GLU cc_start: 0.7768 (pm20) cc_final: 0.7193 (tp30) REVERT: A 4209 GLN cc_start: 0.7961 (pt0) cc_final: 0.7507 (pm20) REVERT: A 4212 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: A 4580 TYR cc_start: 0.6743 (t80) cc_final: 0.6215 (t80) REVERT: A 4584 ASP cc_start: 0.6571 (t0) cc_final: 0.6301 (p0) REVERT: A 4644 TRP cc_start: 0.7672 (t60) cc_final: 0.7350 (t-100) REVERT: A 4704 LEU cc_start: 0.8949 (tp) cc_final: 0.8317 (mm) REVERT: A 4726 ASP cc_start: 0.7369 (m-30) cc_final: 0.7101 (m-30) REVERT: A 4992 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8434 (mt) REVERT: B 3986 TRP cc_start: 0.8324 (m100) cc_final: 0.7692 (m100) REVERT: B 4042 ARG cc_start: 0.6516 (mtm110) cc_final: 0.5801 (mtm180) REVERT: B 4196 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6102 (tp30) REVERT: B 4199 GLU cc_start: 0.7770 (pm20) cc_final: 0.7198 (tp30) REVERT: B 4209 GLN cc_start: 0.7963 (pt0) cc_final: 0.7509 (pm20) REVERT: B 4212 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: B 4580 TYR cc_start: 0.6743 (t80) cc_final: 0.6208 (t80) REVERT: B 4584 ASP cc_start: 0.6583 (t0) cc_final: 0.6309 (p0) REVERT: B 4644 TRP cc_start: 0.7669 (t60) cc_final: 0.7347 (t-100) REVERT: B 4704 LEU cc_start: 0.8954 (tp) cc_final: 0.8325 (mm) REVERT: B 4726 ASP cc_start: 0.7375 (m-30) cc_final: 0.7100 (m-30) REVERT: B 4992 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8440 (mt) REVERT: C 3986 TRP cc_start: 0.8316 (m100) cc_final: 0.7676 (m100) REVERT: C 4042 ARG cc_start: 0.6513 (mtm110) cc_final: 0.5788 (mtm180) REVERT: C 4196 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6107 (tp30) REVERT: C 4199 GLU cc_start: 0.7770 (pm20) cc_final: 0.7196 (tp30) REVERT: C 4209 GLN cc_start: 0.7968 (pt0) cc_final: 0.7505 (pm20) REVERT: C 4212 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7409 (mp0) REVERT: C 4580 TYR cc_start: 0.6739 (t80) cc_final: 0.6205 (t80) REVERT: C 4584 ASP cc_start: 0.6583 (t0) cc_final: 0.6306 (p0) REVERT: C 4644 TRP cc_start: 0.7671 (t60) cc_final: 0.7350 (t-100) REVERT: C 4704 LEU cc_start: 0.8954 (tp) cc_final: 0.8331 (mm) REVERT: C 4726 ASP cc_start: 0.7347 (m-30) cc_final: 0.7079 (m-30) REVERT: C 4992 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8437 (mt) REVERT: D 3986 TRP cc_start: 0.8319 (m100) cc_final: 0.7693 (m100) REVERT: D 4042 ARG cc_start: 0.6522 (mtm110) cc_final: 0.5807 (mtm180) REVERT: D 4196 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6087 (tp30) REVERT: D 4199 GLU cc_start: 0.7757 (pm20) cc_final: 0.7188 (tp30) REVERT: D 4209 GLN cc_start: 0.7951 (pt0) cc_final: 0.7489 (pm20) REVERT: D 4212 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: D 4580 TYR cc_start: 0.6739 (t80) cc_final: 0.6207 (t80) REVERT: D 4584 ASP cc_start: 0.6586 (t0) cc_final: 0.6317 (p0) REVERT: D 4644 TRP cc_start: 0.7671 (t60) cc_final: 0.7346 (t-100) REVERT: D 4704 LEU cc_start: 0.8955 (tp) cc_final: 0.8331 (mm) REVERT: D 4726 ASP cc_start: 0.7353 (m-30) cc_final: 0.7087 (m-30) REVERT: D 4992 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8435 (mt) outliers start: 43 outliers final: 24 residues processed: 411 average time/residue: 0.5562 time to fit residues: 258.6475 Evaluate side-chains 405 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 369 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4212 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4212 GLU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4212 GLU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4212 GLU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 34 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 223 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4034 ASN A4973 HIS B4034 ASN B4973 HIS C4034 ASN C4973 HIS D4034 ASN D4973 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.175739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.142363 restraints weight = 24589.392| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.02 r_work: 0.3349 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21232 Z= 0.137 Angle : 0.628 12.232 28660 Z= 0.305 Chirality : 0.038 0.216 3096 Planarity : 0.005 0.083 3612 Dihedral : 9.011 149.985 2768 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.92 % Allowed : 19.39 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.17), residues: 2476 helix: 2.09 (0.12), residues: 1700 sheet: 0.14 (0.69), residues: 64 loop : -0.23 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A4736 TYR 0.011 0.001 TYR D4629 PHE 0.024 0.001 PHE A3996 TRP 0.006 0.001 TRP B5019 HIS 0.003 0.001 HIS B4886 Details of bonding type rmsd covalent geometry : bond 0.00313 (21208) covalent geometry : angle 0.62445 (28644) SS BOND : bond 0.00031 ( 4) SS BOND : angle 1.35837 ( 8) hydrogen bonds : bond 0.04134 ( 1388) hydrogen bonds : angle 4.29169 ( 4068) metal coordination : bond 0.00420 ( 16) metal coordination : angle 3.87676 ( 8) Misc. bond : bond 0.00856 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 374 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3955 MET cc_start: 0.7357 (mmm) cc_final: 0.7114 (mmm) REVERT: A 3986 TRP cc_start: 0.8388 (m100) cc_final: 0.7820 (m100) REVERT: A 4042 ARG cc_start: 0.6520 (mtm110) cc_final: 0.5797 (mtm180) REVERT: A 4196 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6165 (tp30) REVERT: A 4199 GLU cc_start: 0.7867 (pm20) cc_final: 0.7365 (tp30) REVERT: A 4209 GLN cc_start: 0.7966 (pt0) cc_final: 0.7511 (pm20) REVERT: A 4212 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: A 4580 TYR cc_start: 0.6737 (t80) cc_final: 0.6232 (t80) REVERT: A 4584 ASP cc_start: 0.6637 (t0) cc_final: 0.6320 (p0) REVERT: A 4644 TRP cc_start: 0.7642 (t60) cc_final: 0.7320 (t-100) REVERT: A 4726 ASP cc_start: 0.7357 (m-30) cc_final: 0.7092 (m-30) REVERT: A 4879 MET cc_start: 0.7401 (tpt) cc_final: 0.7116 (tpt) REVERT: A 4992 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8471 (mt) REVERT: B 3986 TRP cc_start: 0.8386 (m100) cc_final: 0.7811 (m100) REVERT: B 4042 ARG cc_start: 0.6517 (mtm110) cc_final: 0.5792 (mtm180) REVERT: B 4196 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6106 (tp30) REVERT: B 4199 GLU cc_start: 0.7854 (pm20) cc_final: 0.7365 (tp30) REVERT: B 4209 GLN cc_start: 0.7984 (pt0) cc_final: 0.7530 (pm20) REVERT: B 4212 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: B 4580 TYR cc_start: 0.6735 (t80) cc_final: 0.6228 (t80) REVERT: B 4584 ASP cc_start: 0.6632 (t0) cc_final: 0.6321 (p0) REVERT: B 4644 TRP cc_start: 0.7630 (t60) cc_final: 0.7309 (t-100) REVERT: B 4726 ASP cc_start: 0.7362 (m-30) cc_final: 0.7097 (m-30) REVERT: B 4879 MET cc_start: 0.7380 (tpt) cc_final: 0.7099 (tpt) REVERT: B 4992 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8475 (mt) REVERT: C 3986 TRP cc_start: 0.8381 (m100) cc_final: 0.7794 (m100) REVERT: C 4042 ARG cc_start: 0.6516 (mtm110) cc_final: 0.5788 (mtm180) REVERT: C 4196 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6107 (tp30) REVERT: C 4199 GLU cc_start: 0.7864 (pm20) cc_final: 0.7362 (tp30) REVERT: C 4209 GLN cc_start: 0.7970 (pt0) cc_final: 0.7506 (pm20) REVERT: C 4212 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: C 4580 TYR cc_start: 0.6734 (t80) cc_final: 0.6224 (t80) REVERT: C 4584 ASP cc_start: 0.6638 (t0) cc_final: 0.6321 (p0) REVERT: C 4644 TRP cc_start: 0.7630 (t60) cc_final: 0.7308 (t-100) REVERT: C 4726 ASP cc_start: 0.7346 (m-30) cc_final: 0.7082 (m-30) REVERT: C 4879 MET cc_start: 0.7375 (tpt) cc_final: 0.7090 (tpt) REVERT: C 4992 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8459 (mt) REVERT: D 3986 TRP cc_start: 0.8377 (m100) cc_final: 0.7812 (m100) REVERT: D 4042 ARG cc_start: 0.6525 (mtm110) cc_final: 0.5801 (mtm180) REVERT: D 4196 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6179 (tp30) REVERT: D 4199 GLU cc_start: 0.7854 (pm20) cc_final: 0.7368 (tp30) REVERT: D 4209 GLN cc_start: 0.7970 (pt0) cc_final: 0.7501 (pm20) REVERT: D 4212 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: D 4580 TYR cc_start: 0.6739 (t80) cc_final: 0.6228 (t80) REVERT: D 4584 ASP cc_start: 0.6667 (t0) cc_final: 0.6354 (p0) REVERT: D 4644 TRP cc_start: 0.7638 (t60) cc_final: 0.7315 (t-100) REVERT: D 4726 ASP cc_start: 0.7355 (m-30) cc_final: 0.7090 (m-30) REVERT: D 4879 MET cc_start: 0.7380 (tpt) cc_final: 0.7094 (tpt) REVERT: D 4992 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8474 (mt) outliers start: 43 outliers final: 30 residues processed: 400 average time/residue: 0.5410 time to fit residues: 246.2670 Evaluate side-chains 408 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 366 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4045 VAL Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4212 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 4045 VAL Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4212 GLU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4976 GLU Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 4045 VAL Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4212 GLU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4976 GLU Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 4045 VAL Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4212 GLU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4976 GLU Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 92 optimal weight: 0.8980 chunk 211 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 217 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 245 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4034 ASN A4973 HIS B4034 ASN B4973 HIS C4034 ASN C4973 HIS D4034 ASN D4973 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.176134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.142754 restraints weight = 24711.819| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.15 r_work: 0.3357 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21232 Z= 0.128 Angle : 0.614 11.593 28660 Z= 0.299 Chirality : 0.038 0.244 3096 Planarity : 0.005 0.082 3612 Dihedral : 8.998 150.122 2768 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.14 % Allowed : 19.65 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.17), residues: 2476 helix: 2.07 (0.12), residues: 1696 sheet: 0.18 (0.69), residues: 64 loop : -0.26 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D4736 TYR 0.017 0.001 TYR A4687 PHE 0.027 0.001 PHE A4922 TRP 0.006 0.001 TRP B5019 HIS 0.003 0.001 HIS A3994 Details of bonding type rmsd covalent geometry : bond 0.00290 (21208) covalent geometry : angle 0.61057 (28644) SS BOND : bond 0.00033 ( 4) SS BOND : angle 1.38803 ( 8) hydrogen bonds : bond 0.04028 ( 1388) hydrogen bonds : angle 4.30434 ( 4068) metal coordination : bond 0.00294 ( 16) metal coordination : angle 3.71452 ( 8) Misc. bond : bond 0.00768 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 377 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3955 MET cc_start: 0.7543 (mmm) cc_final: 0.7308 (mmm) REVERT: A 3986 TRP cc_start: 0.8390 (m100) cc_final: 0.7807 (m100) REVERT: A 4042 ARG cc_start: 0.6513 (mtm110) cc_final: 0.5795 (mtm180) REVERT: A 4196 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6138 (tp30) REVERT: A 4199 GLU cc_start: 0.7860 (pm20) cc_final: 0.7347 (tp30) REVERT: A 4209 GLN cc_start: 0.7973 (pt0) cc_final: 0.7498 (pm20) REVERT: A 4212 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: A 4580 TYR cc_start: 0.6699 (t80) cc_final: 0.6235 (t80) REVERT: A 4584 ASP cc_start: 0.6653 (t0) cc_final: 0.6322 (p0) REVERT: A 4644 TRP cc_start: 0.7611 (t60) cc_final: 0.7298 (t-100) REVERT: A 4726 ASP cc_start: 0.7369 (m-30) cc_final: 0.7126 (m-30) REVERT: A 4992 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8456 (mt) REVERT: B 3955 MET cc_start: 0.7376 (mmm) cc_final: 0.7125 (mmm) REVERT: B 3959 LYS cc_start: 0.6200 (mmtt) cc_final: 0.5998 (mmtm) REVERT: B 3986 TRP cc_start: 0.8379 (m100) cc_final: 0.7769 (m100) REVERT: B 4042 ARG cc_start: 0.6512 (mtm110) cc_final: 0.5794 (mtm180) REVERT: B 4196 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6066 (tp30) REVERT: B 4199 GLU cc_start: 0.7833 (pm20) cc_final: 0.7346 (tp30) REVERT: B 4209 GLN cc_start: 0.8002 (pt0) cc_final: 0.7524 (pm20) REVERT: B 4212 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: B 4580 TYR cc_start: 0.6612 (t80) cc_final: 0.6142 (t80) REVERT: B 4584 ASP cc_start: 0.6626 (t0) cc_final: 0.6299 (p0) REVERT: B 4644 TRP cc_start: 0.7609 (t60) cc_final: 0.7294 (t-100) REVERT: B 4726 ASP cc_start: 0.7355 (m-30) cc_final: 0.7113 (m-30) REVERT: B 4992 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8468 (mt) REVERT: C 3955 MET cc_start: 0.7381 (mmm) cc_final: 0.7129 (mmm) REVERT: C 3959 LYS cc_start: 0.6200 (mmtt) cc_final: 0.5997 (mmtm) REVERT: C 3986 TRP cc_start: 0.8369 (m100) cc_final: 0.7721 (m100) REVERT: C 4042 ARG cc_start: 0.6553 (mtm110) cc_final: 0.5831 (mtm180) REVERT: C 4196 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6067 (tp30) REVERT: C 4199 GLU cc_start: 0.7857 (pm20) cc_final: 0.7348 (tp30) REVERT: C 4209 GLN cc_start: 0.7993 (pt0) cc_final: 0.7505 (pm20) REVERT: C 4212 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: C 4580 TYR cc_start: 0.6612 (t80) cc_final: 0.6142 (t80) REVERT: C 4584 ASP cc_start: 0.6641 (t0) cc_final: 0.6309 (p0) REVERT: C 4644 TRP cc_start: 0.7604 (t60) cc_final: 0.7291 (t-100) REVERT: C 4726 ASP cc_start: 0.7360 (m-30) cc_final: 0.7117 (m-30) REVERT: C 4992 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8449 (mt) REVERT: D 3955 MET cc_start: 0.7362 (mmm) cc_final: 0.7112 (mmm) REVERT: D 3986 TRP cc_start: 0.8376 (m100) cc_final: 0.7804 (m100) REVERT: D 4042 ARG cc_start: 0.6525 (mtm110) cc_final: 0.5808 (mtm180) REVERT: D 4196 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6139 (tp30) REVERT: D 4199 GLU cc_start: 0.7838 (pm20) cc_final: 0.7349 (tp30) REVERT: D 4209 GLN cc_start: 0.7985 (pt0) cc_final: 0.7495 (pm20) REVERT: D 4212 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: D 4580 TYR cc_start: 0.6612 (t80) cc_final: 0.6144 (t80) REVERT: D 4584 ASP cc_start: 0.6656 (t0) cc_final: 0.6329 (p0) REVERT: D 4644 TRP cc_start: 0.7605 (t60) cc_final: 0.7291 (t-100) REVERT: D 4726 ASP cc_start: 0.7365 (m-30) cc_final: 0.7123 (m-30) REVERT: D 4992 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8463 (mt) outliers start: 48 outliers final: 35 residues processed: 408 average time/residue: 0.5243 time to fit residues: 243.2524 Evaluate side-chains 401 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 354 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4045 VAL Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4212 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 4045 VAL Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4212 GLU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4976 GLU Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 4045 VAL Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4212 GLU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4976 GLU Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 4045 VAL Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4212 GLU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4976 GLU Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 59 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4034 ASN B4034 ASN C4034 ASN C4707 ASN D4034 ASN D4707 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.175093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.142071 restraints weight = 24695.715| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.12 r_work: 0.3353 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21232 Z= 0.148 Angle : 0.627 11.652 28660 Z= 0.306 Chirality : 0.039 0.287 3096 Planarity : 0.005 0.085 3612 Dihedral : 9.019 150.694 2768 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.72 % Allowed : 19.25 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.17), residues: 2476 helix: 1.86 (0.12), residues: 1720 sheet: 0.22 (0.70), residues: 64 loop : -0.28 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C4736 TYR 0.011 0.001 TYR D4629 PHE 0.032 0.001 PHE A4922 TRP 0.006 0.001 TRP C5019 HIS 0.004 0.001 HIS B4886 Details of bonding type rmsd covalent geometry : bond 0.00343 (21208) covalent geometry : angle 0.62289 (28644) SS BOND : bond 0.00043 ( 4) SS BOND : angle 1.54676 ( 8) hydrogen bonds : bond 0.04244 ( 1388) hydrogen bonds : angle 4.35506 ( 4068) metal coordination : bond 0.00641 ( 16) metal coordination : angle 3.98617 ( 8) Misc. bond : bond 0.00776 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7666.04 seconds wall clock time: 130 minutes 52.78 seconds (7852.78 seconds total)