Starting phenix.real_space_refine on Wed May 21 06:22:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sew_40431/05_2025/8sew_40431.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sew_40431/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sew_40431/05_2025/8sew_40431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sew_40431/05_2025/8sew_40431.map" model { file = "/net/cci-nas-00/data/ceres_data/8sew_40431/05_2025/8sew_40431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sew_40431/05_2025/8sew_40431.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B, D Time building chain proxies: 12.22, per 1000 atoms: 0.59 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 C4876 " - pdb=" SG CYS C4882 " distance=2.03 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " 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: 5.17 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.28 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: 6.67 Time building geometry restraints manager: 6.01 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 48.960 Find NCS groups from input model: 0.410 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:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (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 TRP 0.009 0.001 TRP C5019 HIS 0.005 0.001 HIS D4886 PHE 0.020 0.002 PHE C4916 TYR 0.012 0.001 TYR C4994 ARG 0.003 0.001 ARG C4913 Details of bonding type rmsd hydrogen bonds : bond 0.14631 ( 1388) hydrogen bonds : angle 4.68462 ( 4068) metal coordination : bond 0.01221 ( 16) metal coordination : angle 4.26074 ( 8) SS BOND : bond 0.00104 ( 4) SS BOND : angle 0.90757 ( 8) covalent geometry : bond 0.00432 (21208) covalent geometry : angle 0.59063 (28644) 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 : 2.130 Fit side-chains REVERT: A 3992 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7633 (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: 0.7628 (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: 0.8095 (tp) REVERT: C 3992 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7628 (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: 0.8091 (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: 1.2245 time to fit residues: 706.6216 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 : 2.922 ------------------------------------------------------------------------------- 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 209 optimal weight: 2.9990 chunk 187 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 75 optimal weight: 0.0870 chunk 118 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4973 HIS ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4973 HIS ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4973 HIS ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4973 HIS ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.174666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.140970 restraints weight = 24362.064| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.97 r_work: 0.3339 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21232 Z= 0.131 Angle : 0.604 13.044 28660 Z= 0.300 Chirality : 0.038 0.141 3096 Planarity : 0.004 0.049 3612 Dihedral : 10.045 144.124 2812 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.55 % Rotamer: Outliers : 3.39 % Allowed : 12.83 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.17), residues: 2476 helix: 2.14 (0.12), residues: 1704 sheet: 0.07 (0.49), residues: 112 loop : 0.05 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D3986 HIS 0.004 0.001 HIS C3994 PHE 0.018 0.001 PHE D4916 TYR 0.010 0.001 TYR D5032 ARG 0.008 0.001 ARG D4189 Details of bonding type rmsd hydrogen bonds : bond 0.04926 ( 1388) hydrogen bonds : angle 4.10234 ( 4068) metal coordination : bond 0.00307 ( 16) metal coordination : angle 3.67136 ( 8) SS BOND : bond 0.00075 ( 4) SS BOND : angle 0.92929 ( 8) covalent geometry : bond 0.00274 (21208) covalent geometry : angle 0.60046 (28644) Misc. bond : bond 0.00217 ( 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 472 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 396 time to evaluate : 2.183 Fit side-chains REVERT: A 4023 MET cc_start: 0.7536 (ttp) cc_final: 0.6936 (tpp) REVERT: A 4042 ARG cc_start: 0.6713 (mtm110) cc_final: 0.6163 (mtm180) REVERT: A 4184 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.8023 (ttp) REVERT: A 4196 GLU cc_start: 0.6456 (OUTLIER) cc_final: 0.5935 (tp30) REVERT: A 4580 TYR cc_start: 0.7654 (OUTLIER) cc_final: 0.6498 (t80) REVERT: A 4584 ASP cc_start: 0.6700 (t0) cc_final: 0.6472 (p0) REVERT: A 4644 TRP cc_start: 0.7703 (t60) cc_final: 0.7417 (t-100) REVERT: A 4726 ASP cc_start: 0.7324 (m-30) cc_final: 0.7060 (m-30) REVERT: A 4992 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8374 (mt) REVERT: B 4023 MET cc_start: 0.7514 (ttp) cc_final: 0.6909 (tpp) REVERT: B 4042 ARG cc_start: 0.6725 (mtm110) cc_final: 0.6172 (mtm180) REVERT: B 4184 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.8010 (ttp) REVERT: B 4196 GLU cc_start: 0.6456 (OUTLIER) cc_final: 0.5933 (tp30) REVERT: B 4580 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.6504 (t80) REVERT: B 4584 ASP cc_start: 0.6708 (t0) cc_final: 0.6483 (p0) REVERT: B 4644 TRP cc_start: 0.7696 (t60) cc_final: 0.7411 (t-100) REVERT: B 4726 ASP cc_start: 0.7323 (m-30) cc_final: 0.7060 (m-30) REVERT: B 4992 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8375 (mt) REVERT: C 4023 MET cc_start: 0.7505 (ttp) cc_final: 0.6906 (tpp) REVERT: C 4042 ARG cc_start: 0.6734 (mtm110) cc_final: 0.6178 (mtm180) REVERT: C 4184 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.8005 (ttp) REVERT: C 4196 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.5938 (tp30) REVERT: C 4580 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.6505 (t80) REVERT: C 4584 ASP cc_start: 0.6703 (t0) cc_final: 0.6476 (p0) REVERT: C 4644 TRP cc_start: 0.7699 (t60) cc_final: 0.7410 (t-100) REVERT: C 4726 ASP cc_start: 0.7323 (m-30) cc_final: 0.7061 (m-30) REVERT: C 4992 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8365 (mt) REVERT: D 4023 MET cc_start: 0.7516 (ttp) cc_final: 0.6912 (tpp) REVERT: D 4042 ARG cc_start: 0.6731 (mtm110) cc_final: 0.6178 (mtm180) REVERT: D 4184 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.8001 (ttp) REVERT: D 4196 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.5933 (tp30) REVERT: D 4580 TYR cc_start: 0.7664 (OUTLIER) cc_final: 0.6511 (t80) REVERT: D 4584 ASP cc_start: 0.6697 (t0) cc_final: 0.6471 (p0) REVERT: D 4644 TRP cc_start: 0.7706 (t60) cc_final: 0.7415 (t-100) REVERT: D 4726 ASP cc_start: 0.7316 (m-30) cc_final: 0.7054 (m-30) REVERT: D 4992 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8369 (mt) outliers start: 76 outliers final: 16 residues processed: 432 average time/residue: 1.2402 time to fit residues: 606.9840 Evaluate side-chains 404 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 372 time to evaluate : 2.292 ------------------------------------------------------------------------------- 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 4580 TYR Chi-restraints excluded: chain A residue 4666 VAL 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 4183 ILE Chi-restraints excluded: chain B residue 4184 MET Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4666 VAL 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 4183 ILE Chi-restraints excluded: chain C residue 4184 MET Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4666 VAL 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 4183 ILE Chi-restraints excluded: chain D residue 4184 MET Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4666 VAL 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 185 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 235 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 223 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 chunk 228 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 D4973 HIS D5031 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.173017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.139325 restraints weight = 24242.953| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.03 r_work: 0.3316 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21232 Z= 0.155 Angle : 0.590 13.207 28660 Z= 0.294 Chirality : 0.038 0.137 3096 Planarity : 0.004 0.059 3612 Dihedral : 9.564 145.974 2784 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 4.46 % Allowed : 13.55 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.17), residues: 2476 helix: 2.11 (0.12), residues: 1704 sheet: -0.30 (0.48), residues: 112 loop : 0.04 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B5019 HIS 0.004 0.001 HIS A3994 PHE 0.020 0.001 PHE D4916 TYR 0.013 0.001 TYR B5032 ARG 0.008 0.001 ARG C4736 Details of bonding type rmsd hydrogen bonds : bond 0.04786 ( 1388) hydrogen bonds : angle 4.15716 ( 4068) metal coordination : bond 0.00865 ( 16) metal coordination : angle 4.23094 ( 8) SS BOND : bond 0.00182 ( 4) SS BOND : angle 1.28336 ( 8) covalent geometry : bond 0.00354 (21208) covalent geometry : angle 0.58552 (28644) Misc. bond : bond 0.00257 ( 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 472 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 372 time to evaluate : 2.220 Fit side-chains REVERT: A 3955 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7044 (mtm) REVERT: A 3959 LYS cc_start: 0.6279 (tttp) cc_final: 0.6032 (tttp) REVERT: A 3980 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.7894 (mm) REVERT: A 3992 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.7179 (m-80) REVERT: A 4023 MET cc_start: 0.7530 (ttp) cc_final: 0.7018 (tpp) REVERT: A 4042 ARG cc_start: 0.6603 (mtm110) cc_final: 0.5950 (mtm180) REVERT: A 4184 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8103 (ttp) REVERT: A 4196 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.6071 (tp30) REVERT: A 4209 GLN cc_start: 0.8017 (pt0) cc_final: 0.7508 (pm20) REVERT: A 4212 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: A 4224 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7584 (pt0) REVERT: A 4580 TYR cc_start: 0.7812 (OUTLIER) cc_final: 0.6590 (t80) REVERT: A 4584 ASP cc_start: 0.6845 (t0) cc_final: 0.6568 (p0) REVERT: A 4644 TRP cc_start: 0.7740 (t60) cc_final: 0.7453 (t-100) REVERT: A 4726 ASP cc_start: 0.7313 (m-30) cc_final: 0.7091 (m-30) REVERT: A 4911 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7620 (mm) REVERT: A 4992 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8429 (mt) REVERT: B 3955 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7059 (mtm) REVERT: B 3959 LYS cc_start: 0.6273 (tttp) cc_final: 0.6022 (tttp) REVERT: B 3980 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.7892 (mm) REVERT: B 3992 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7176 (m-80) REVERT: B 4023 MET cc_start: 0.7531 (ttp) cc_final: 0.7014 (tpp) REVERT: B 4042 ARG cc_start: 0.6605 (mtm110) cc_final: 0.5949 (mtm180) REVERT: B 4184 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8114 (ttp) REVERT: B 4196 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.6071 (tp30) REVERT: B 4209 GLN cc_start: 0.8022 (pt0) cc_final: 0.7518 (pm20) REVERT: B 4212 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: B 4224 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7598 (pt0) REVERT: B 4580 TYR cc_start: 0.7812 (OUTLIER) cc_final: 0.6587 (t80) REVERT: B 4584 ASP cc_start: 0.6842 (t0) cc_final: 0.6571 (p0) REVERT: B 4644 TRP cc_start: 0.7742 (t60) cc_final: 0.7453 (t-100) REVERT: B 4726 ASP cc_start: 0.7310 (m-30) cc_final: 0.7088 (m-30) REVERT: B 4911 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7631 (mm) REVERT: B 4992 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8432 (mt) REVERT: C 3955 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7059 (mtm) REVERT: C 3959 LYS cc_start: 0.6269 (tttp) cc_final: 0.6023 (tttp) REVERT: C 3980 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.7891 (mm) REVERT: C 3992 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7176 (m-80) REVERT: C 4023 MET cc_start: 0.7513 (ttp) cc_final: 0.6998 (tpp) REVERT: C 4042 ARG cc_start: 0.6625 (mtm110) cc_final: 0.5968 (mtm180) REVERT: C 4184 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8119 (ttp) REVERT: C 4196 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6074 (tp30) REVERT: C 4209 GLN cc_start: 0.8022 (pt0) cc_final: 0.7514 (pm20) REVERT: C 4212 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: C 4224 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7609 (pt0) REVERT: C 4580 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.6594 (t80) REVERT: C 4584 ASP cc_start: 0.6850 (t0) cc_final: 0.6577 (p0) REVERT: C 4644 TRP cc_start: 0.7739 (t60) cc_final: 0.7451 (t-100) REVERT: C 4726 ASP cc_start: 0.7306 (m-30) cc_final: 0.7084 (m-30) REVERT: C 4911 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7620 (mm) REVERT: C 4992 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8425 (mt) REVERT: D 3955 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7060 (mtm) REVERT: D 3959 LYS cc_start: 0.6283 (tttp) cc_final: 0.6038 (tttp) REVERT: D 3980 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.7891 (mm) REVERT: D 3992 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7181 (m-80) REVERT: D 4023 MET cc_start: 0.7525 (ttp) cc_final: 0.7010 (tpp) REVERT: D 4042 ARG cc_start: 0.6624 (mtm110) cc_final: 0.5971 (mtm180) REVERT: D 4184 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8097 (ttp) REVERT: D 4196 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.6055 (tp30) REVERT: D 4209 GLN cc_start: 0.8011 (pt0) cc_final: 0.7494 (pm20) REVERT: D 4212 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: D 4224 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7589 (pt0) REVERT: D 4580 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.6596 (t80) REVERT: D 4584 ASP cc_start: 0.6847 (t0) cc_final: 0.6575 (p0) REVERT: D 4644 TRP cc_start: 0.7747 (t60) cc_final: 0.7456 (t-100) REVERT: D 4726 ASP cc_start: 0.7316 (m-30) cc_final: 0.7093 (m-30) REVERT: D 4911 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7631 (mm) REVERT: D 4992 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8422 (mt) outliers start: 100 outliers final: 24 residues processed: 420 average time/residue: 1.2261 time to fit residues: 584.1552 Evaluate side-chains 416 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 352 time to evaluate : 2.180 ------------------------------------------------------------------------------- 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 3992 PHE 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 4212 GLU Chi-restraints excluded: chain A residue 4224 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 4911 LEU 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 4184 MET Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4212 GLU Chi-restraints excluded: chain B residue 4224 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 4911 LEU 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 4184 MET Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4212 GLU Chi-restraints excluded: chain C residue 4224 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 4911 LEU 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 4184 MET Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4212 GLU Chi-restraints excluded: chain D residue 4224 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 4911 LEU 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 165 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 237 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 124 optimal weight: 20.0000 chunk 158 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4973 HIS B4973 HIS C4973 HIS D4973 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.171763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138401 restraints weight = 24574.169| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.21 r_work: 0.3302 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21232 Z= 0.198 Angle : 0.615 8.912 28660 Z= 0.308 Chirality : 0.040 0.144 3096 Planarity : 0.004 0.068 3612 Dihedral : 9.524 148.429 2784 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.86 % Favored : 97.98 % Rotamer: Outliers : 4.81 % Allowed : 13.90 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.17), residues: 2476 helix: 1.91 (0.12), residues: 1704 sheet: 0.65 (0.67), residues: 64 loop : -0.10 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C5019 HIS 0.004 0.001 HIS D3994 PHE 0.022 0.002 PHE A4916 TYR 0.011 0.002 TYR B4994 ARG 0.010 0.001 ARG D4189 Details of bonding type rmsd hydrogen bonds : bond 0.04978 ( 1388) hydrogen bonds : angle 4.32465 ( 4068) metal coordination : bond 0.01291 ( 16) metal coordination : angle 4.70324 ( 8) SS BOND : bond 0.00307 ( 4) SS BOND : angle 1.37881 ( 8) covalent geometry : bond 0.00465 (21208) covalent geometry : angle 0.60953 (28644) Misc. bond : bond 0.00328 ( 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 472 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 364 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3955 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7047 (mtm) REVERT: A 3980 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.7764 (mm) REVERT: A 4023 MET cc_start: 0.7532 (ttp) cc_final: 0.7177 (tpp) REVERT: A 4039 MET cc_start: 0.7787 (mtp) cc_final: 0.7351 (ttm) REVERT: A 4042 ARG cc_start: 0.6533 (mtm110) cc_final: 0.5878 (mtm180) REVERT: A 4196 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6140 (tp30) REVERT: A 4209 GLN cc_start: 0.8064 (pt0) cc_final: 0.7541 (pm20) REVERT: A 4212 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: A 4580 TYR cc_start: 0.7781 (OUTLIER) cc_final: 0.6666 (t80) REVERT: A 4584 ASP cc_start: 0.6904 (t0) cc_final: 0.6689 (p0) REVERT: A 4644 TRP cc_start: 0.7582 (t60) cc_final: 0.7274 (t-100) REVERT: A 4726 ASP cc_start: 0.7304 (m-30) cc_final: 0.7078 (m-30) REVERT: A 4887 MET cc_start: 0.8374 (mmm) cc_final: 0.8065 (tpt) REVERT: A 4911 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7665 (mm) REVERT: B 3955 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7096 (mtm) REVERT: B 3980 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.7762 (mm) REVERT: B 4023 MET cc_start: 0.7523 (ttp) cc_final: 0.7165 (tpp) REVERT: B 4039 MET cc_start: 0.7789 (mtp) cc_final: 0.7352 (ttm) REVERT: B 4042 ARG cc_start: 0.6532 (mtm110) cc_final: 0.5875 (mtm180) REVERT: B 4196 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6152 (tp30) REVERT: B 4209 GLN cc_start: 0.8077 (pt0) cc_final: 0.7553 (pm20) REVERT: B 4212 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: B 4580 TYR cc_start: 0.7781 (OUTLIER) cc_final: 0.6672 (t80) REVERT: B 4584 ASP cc_start: 0.6905 (t0) cc_final: 0.6687 (p0) REVERT: B 4644 TRP cc_start: 0.7580 (t60) cc_final: 0.7273 (t-100) REVERT: B 4726 ASP cc_start: 0.7307 (m-30) cc_final: 0.7078 (m-30) REVERT: B 4887 MET cc_start: 0.8360 (mmm) cc_final: 0.8053 (tpt) REVERT: B 4911 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7668 (mm) REVERT: C 3955 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7094 (mtm) REVERT: C 3980 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.7762 (mm) REVERT: C 4023 MET cc_start: 0.7499 (ttp) cc_final: 0.7142 (tpp) REVERT: C 4039 MET cc_start: 0.7768 (mtp) cc_final: 0.7347 (ttm) REVERT: C 4042 ARG cc_start: 0.6535 (mtm110) cc_final: 0.5877 (mtm180) REVERT: C 4196 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6143 (tp30) REVERT: C 4209 GLN cc_start: 0.8080 (pt0) cc_final: 0.7552 (pm20) REVERT: C 4212 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: C 4580 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.6672 (t80) REVERT: C 4584 ASP cc_start: 0.6907 (t0) cc_final: 0.6688 (p0) REVERT: C 4644 TRP cc_start: 0.7583 (t60) cc_final: 0.7272 (t-100) REVERT: C 4726 ASP cc_start: 0.7296 (m-30) cc_final: 0.7068 (m-30) REVERT: C 4887 MET cc_start: 0.8353 (mmm) cc_final: 0.8051 (tpt) REVERT: C 4911 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7662 (mm) REVERT: D 3955 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7089 (mtm) REVERT: D 3980 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.7767 (mm) REVERT: D 4023 MET cc_start: 0.7512 (ttp) cc_final: 0.7158 (tpp) REVERT: D 4039 MET cc_start: 0.7784 (mtp) cc_final: 0.7354 (ttm) REVERT: D 4042 ARG cc_start: 0.6552 (mtm110) cc_final: 0.5896 (mtm180) REVERT: D 4196 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6128 (tp30) REVERT: D 4209 GLN cc_start: 0.8061 (pt0) cc_final: 0.7529 (pm20) REVERT: D 4212 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: D 4580 TYR cc_start: 0.7783 (OUTLIER) cc_final: 0.6680 (t80) REVERT: D 4584 ASP cc_start: 0.6898 (t0) cc_final: 0.6680 (p0) REVERT: D 4644 TRP cc_start: 0.7584 (t60) cc_final: 0.7273 (t-100) REVERT: D 4726 ASP cc_start: 0.7304 (m-30) cc_final: 0.7075 (m-30) REVERT: D 4887 MET cc_start: 0.8372 (mmm) cc_final: 0.8067 (tpt) REVERT: D 4911 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7674 (mm) outliers start: 108 outliers final: 32 residues processed: 424 average time/residue: 1.2244 time to fit residues: 590.7561 Evaluate side-chains 416 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 360 time to evaluate : 2.142 ------------------------------------------------------------------------------- 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 4773 VAL Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4911 LEU 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 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 4773 VAL Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4911 LEU 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 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 4773 VAL Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4911 LEU 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 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 4773 VAL Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4911 LEU 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 18 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 178 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 chunk 161 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4034 ASN A4043 GLN A4973 HIS B4034 ASN B4043 GLN B4973 HIS C4034 ASN C4043 GLN C4973 HIS D4034 ASN D4043 GLN D4973 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.174536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.141301 restraints weight = 24715.882| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.12 r_work: 0.3342 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21232 Z= 0.126 Angle : 0.565 8.975 28660 Z= 0.281 Chirality : 0.037 0.133 3096 Planarity : 0.004 0.078 3612 Dihedral : 9.232 148.307 2776 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 3.03 % Allowed : 16.58 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.17), residues: 2476 helix: 2.09 (0.12), residues: 1720 sheet: 0.54 (0.67), residues: 64 loop : -0.14 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B5019 HIS 0.003 0.001 HIS D4803 PHE 0.019 0.001 PHE C4916 TYR 0.009 0.001 TYR D4994 ARG 0.011 0.001 ARG D4736 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 1388) hydrogen bonds : angle 4.17228 ( 4068) metal coordination : bond 0.00319 ( 16) metal coordination : angle 3.82824 ( 8) SS BOND : bond 0.00210 ( 4) SS BOND : angle 1.07812 ( 8) covalent geometry : bond 0.00279 (21208) covalent geometry : angle 0.56166 (28644) Misc. bond : bond 0.00380 ( 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 449 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 381 time to evaluate : 2.412 Fit side-chains REVERT: A 3955 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.7072 (mtm) REVERT: A 3959 LYS cc_start: 0.6299 (tttp) cc_final: 0.5968 (tttp) REVERT: A 3986 TRP cc_start: 0.8453 (m100) cc_final: 0.7700 (m100) REVERT: A 3999 MET cc_start: 0.8177 (mmm) cc_final: 0.7780 (tpt) REVERT: A 4023 MET cc_start: 0.7505 (ttp) cc_final: 0.7120 (tpp) REVERT: A 4042 ARG cc_start: 0.6525 (mtm110) cc_final: 0.5797 (mtm180) REVERT: A 4054 ASN cc_start: 0.7330 (m110) cc_final: 0.7119 (m-40) REVERT: A 4196 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.5845 (tp30) REVERT: A 4209 GLN cc_start: 0.8016 (pt0) cc_final: 0.7508 (pm20) REVERT: A 4212 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: A 4580 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.6504 (t80) REVERT: A 4584 ASP cc_start: 0.6964 (t0) cc_final: 0.6724 (p0) REVERT: A 4644 TRP cc_start: 0.7669 (t60) cc_final: 0.7346 (t-100) REVERT: A 4704 LEU cc_start: 0.8961 (tp) cc_final: 0.8357 (mm) REVERT: A 4726 ASP cc_start: 0.7315 (m-30) cc_final: 0.7070 (m-30) REVERT: A 4887 MET cc_start: 0.8433 (mmm) cc_final: 0.8124 (tpt) REVERT: A 4911 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7655 (mm) REVERT: A 4992 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8453 (mt) REVERT: B 3955 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.7084 (mtm) REVERT: B 3959 LYS cc_start: 0.6275 (tttp) cc_final: 0.5947 (tttp) REVERT: B 3986 TRP cc_start: 0.8459 (m100) cc_final: 0.7699 (m100) REVERT: B 3999 MET cc_start: 0.8226 (mmm) cc_final: 0.7851 (tpt) REVERT: B 4022 ASP cc_start: 0.6015 (m-30) cc_final: 0.5812 (m-30) REVERT: B 4023 MET cc_start: 0.7493 (ttp) cc_final: 0.7102 (tpp) REVERT: B 4042 ARG cc_start: 0.6529 (mtm110) cc_final: 0.5799 (mtm180) REVERT: B 4054 ASN cc_start: 0.7328 (m110) cc_final: 0.7120 (m-40) REVERT: B 4196 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.5848 (tp30) REVERT: B 4209 GLN cc_start: 0.8018 (pt0) cc_final: 0.7511 (pm20) REVERT: B 4212 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: B 4580 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.6505 (t80) REVERT: B 4584 ASP cc_start: 0.6969 (t0) cc_final: 0.6730 (p0) REVERT: B 4644 TRP cc_start: 0.7670 (t60) cc_final: 0.7348 (t-100) REVERT: B 4704 LEU cc_start: 0.8963 (tp) cc_final: 0.8362 (mm) REVERT: B 4726 ASP cc_start: 0.7324 (m-30) cc_final: 0.7075 (m-30) REVERT: B 4887 MET cc_start: 0.8413 (mmm) cc_final: 0.8102 (tpt) REVERT: B 4911 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7647 (mm) REVERT: B 4992 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8459 (mt) REVERT: C 3955 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7094 (mtm) REVERT: C 3959 LYS cc_start: 0.6277 (tttp) cc_final: 0.5951 (tttp) REVERT: C 3986 TRP cc_start: 0.8454 (m100) cc_final: 0.7700 (m100) REVERT: C 3999 MET cc_start: 0.8224 (mmm) cc_final: 0.7845 (tpt) REVERT: C 4023 MET cc_start: 0.7473 (ttp) cc_final: 0.7083 (tpp) REVERT: C 4042 ARG cc_start: 0.6534 (mtm110) cc_final: 0.5805 (mtm180) REVERT: C 4054 ASN cc_start: 0.7330 (m110) cc_final: 0.7121 (m-40) REVERT: C 4196 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.5849 (tp30) REVERT: C 4209 GLN cc_start: 0.8023 (pt0) cc_final: 0.7504 (pm20) REVERT: C 4212 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: C 4580 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.6500 (t80) REVERT: C 4584 ASP cc_start: 0.6961 (t0) cc_final: 0.6731 (p0) REVERT: C 4644 TRP cc_start: 0.7670 (t60) cc_final: 0.7346 (t-100) REVERT: C 4704 LEU cc_start: 0.8966 (tp) cc_final: 0.8371 (mm) REVERT: C 4726 ASP cc_start: 0.7308 (m-30) cc_final: 0.7067 (m-30) REVERT: C 4887 MET cc_start: 0.8417 (mmm) cc_final: 0.8111 (tpt) REVERT: C 4911 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7654 (mm) REVERT: C 4992 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8449 (mt) REVERT: D 3955 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7097 (mtm) REVERT: D 3959 LYS cc_start: 0.6290 (tttp) cc_final: 0.5962 (tttp) REVERT: D 3986 TRP cc_start: 0.8450 (m100) cc_final: 0.7698 (m100) REVERT: D 3999 MET cc_start: 0.8226 (mmm) cc_final: 0.7845 (tpt) REVERT: D 4023 MET cc_start: 0.7489 (ttp) cc_final: 0.7098 (tpp) REVERT: D 4042 ARG cc_start: 0.6531 (mtm110) cc_final: 0.5804 (mtm180) REVERT: D 4054 ASN cc_start: 0.7328 (m110) cc_final: 0.7115 (m-40) REVERT: D 4196 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.5870 (tp30) REVERT: D 4209 GLN cc_start: 0.8008 (pt0) cc_final: 0.7491 (pm20) REVERT: D 4212 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: D 4580 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.6505 (t80) REVERT: D 4584 ASP cc_start: 0.6948 (t0) cc_final: 0.6715 (p0) REVERT: D 4644 TRP cc_start: 0.7671 (t60) cc_final: 0.7344 (t-100) REVERT: D 4704 LEU cc_start: 0.8966 (tp) cc_final: 0.8367 (mm) REVERT: D 4726 ASP cc_start: 0.7312 (m-30) cc_final: 0.7068 (m-30) REVERT: D 4887 MET cc_start: 0.8435 (mmm) cc_final: 0.8129 (tpt) REVERT: D 4911 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7646 (mm) REVERT: D 4992 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8445 (mt) outliers start: 68 outliers final: 17 residues processed: 428 average time/residue: 1.2404 time to fit residues: 602.6374 Evaluate side-chains 404 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 363 time to evaluate : 2.257 ------------------------------------------------------------------------------- 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 4580 TYR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4911 LEU 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 4196 GLU Chi-restraints excluded: chain B residue 4212 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 4844 LEU Chi-restraints excluded: chain B residue 4911 LEU 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 4196 GLU Chi-restraints excluded: chain C residue 4212 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 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 3955 MET Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4212 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 4844 LEU Chi-restraints excluded: chain D residue 4911 LEU 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 205 optimal weight: 0.4980 chunk 98 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 178 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 243 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.174562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.141145 restraints weight = 24431.865| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.92 r_work: 0.3359 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21232 Z= 0.132 Angle : 0.602 12.197 28660 Z= 0.294 Chirality : 0.037 0.142 3096 Planarity : 0.004 0.081 3612 Dihedral : 9.146 148.879 2776 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 3.25 % Allowed : 16.35 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.17), residues: 2476 helix: 2.16 (0.12), residues: 1720 sheet: 0.42 (0.68), residues: 64 loop : -0.23 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B5019 HIS 0.003 0.001 HIS A3994 PHE 0.021 0.001 PHE A4922 TYR 0.012 0.001 TYR A4580 ARG 0.011 0.001 ARG A4736 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 1388) hydrogen bonds : angle 4.15864 ( 4068) metal coordination : bond 0.00457 ( 16) metal coordination : angle 3.85143 ( 8) SS BOND : bond 0.00136 ( 4) SS BOND : angle 1.36485 ( 8) covalent geometry : bond 0.00296 (21208) covalent geometry : angle 0.59817 (28644) Misc. bond : bond 0.00816 ( 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 459 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 386 time to evaluate : 2.434 Fit side-chains REVERT: A 3955 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7103 (mtm) REVERT: A 3959 LYS cc_start: 0.6240 (tttp) cc_final: 0.5936 (tttp) REVERT: A 3986 TRP cc_start: 0.8307 (m100) cc_final: 0.7692 (m100) REVERT: A 4023 MET cc_start: 0.7447 (ttp) cc_final: 0.6900 (tpp) REVERT: A 4042 ARG cc_start: 0.6513 (mtm110) cc_final: 0.5798 (mtm180) REVERT: A 4196 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.5983 (tp30) REVERT: A 4199 GLU cc_start: 0.7475 (pm20) cc_final: 0.7090 (tp30) REVERT: A 4209 GLN cc_start: 0.7976 (pt0) cc_final: 0.7471 (pm20) REVERT: A 4212 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: A 4580 TYR cc_start: 0.6899 (t80) cc_final: 0.6406 (t80) REVERT: A 4584 ASP cc_start: 0.6736 (t0) cc_final: 0.6449 (p0) REVERT: A 4644 TRP cc_start: 0.7638 (t60) cc_final: 0.7301 (t-100) REVERT: A 4726 ASP cc_start: 0.7314 (m-30) cc_final: 0.7061 (m-30) REVERT: A 4743 MET cc_start: 0.7267 (ptm) cc_final: 0.6954 (ptm) REVERT: A 4887 MET cc_start: 0.8401 (mmm) cc_final: 0.8110 (tpt) REVERT: A 4911 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7626 (mm) REVERT: A 4992 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8423 (mt) REVERT: B 3955 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7087 (mtm) REVERT: B 3959 LYS cc_start: 0.6265 (tttp) cc_final: 0.5914 (tttp) REVERT: B 3986 TRP cc_start: 0.8312 (m100) cc_final: 0.7695 (m100) REVERT: B 3999 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7916 (tpt) REVERT: B 4023 MET cc_start: 0.7438 (ttp) cc_final: 0.6875 (tpp) REVERT: B 4042 ARG cc_start: 0.6521 (mtm110) cc_final: 0.5802 (mtm180) REVERT: B 4196 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.5972 (tp30) REVERT: B 4199 GLU cc_start: 0.7475 (pm20) cc_final: 0.7087 (tp30) REVERT: B 4209 GLN cc_start: 0.7982 (pt0) cc_final: 0.7479 (pm20) REVERT: B 4212 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: B 4580 TYR cc_start: 0.6896 (t80) cc_final: 0.6399 (t80) REVERT: B 4584 ASP cc_start: 0.6753 (t0) cc_final: 0.6459 (p0) REVERT: B 4644 TRP cc_start: 0.7637 (t60) cc_final: 0.7298 (t-100) REVERT: B 4726 ASP cc_start: 0.7316 (m-30) cc_final: 0.7063 (m-30) REVERT: B 4743 MET cc_start: 0.7260 (ptm) cc_final: 0.6947 (ptm) REVERT: B 4887 MET cc_start: 0.8384 (mmm) cc_final: 0.8098 (tpt) REVERT: B 4911 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7621 (mm) REVERT: B 4992 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8420 (mt) REVERT: C 3955 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7091 (mtm) REVERT: C 3959 LYS cc_start: 0.6230 (tttp) cc_final: 0.5929 (tttp) REVERT: C 3986 TRP cc_start: 0.8308 (m100) cc_final: 0.7699 (m100) REVERT: C 3999 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7919 (tpt) REVERT: C 4023 MET cc_start: 0.7418 (ttp) cc_final: 0.6865 (tpp) REVERT: C 4042 ARG cc_start: 0.6521 (mtm110) cc_final: 0.5805 (mtm180) REVERT: C 4196 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.5968 (tp30) REVERT: C 4199 GLU cc_start: 0.7461 (pm20) cc_final: 0.7090 (tp30) REVERT: C 4209 GLN cc_start: 0.7993 (pt0) cc_final: 0.7479 (pm20) REVERT: C 4212 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: C 4580 TYR cc_start: 0.6889 (t80) cc_final: 0.6401 (t80) REVERT: C 4584 ASP cc_start: 0.6747 (t0) cc_final: 0.6457 (p0) REVERT: C 4644 TRP cc_start: 0.7636 (t60) cc_final: 0.7295 (t-100) REVERT: C 4726 ASP cc_start: 0.7301 (m-30) cc_final: 0.7052 (m-30) REVERT: C 4743 MET cc_start: 0.7283 (ptm) cc_final: 0.6969 (ptm) REVERT: C 4887 MET cc_start: 0.8389 (mmm) cc_final: 0.8107 (tpt) REVERT: C 4911 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7619 (mm) REVERT: C 4992 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8417 (mt) REVERT: D 3955 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.7089 (mtm) REVERT: D 3959 LYS cc_start: 0.6232 (tttp) cc_final: 0.5928 (tttp) REVERT: D 3986 TRP cc_start: 0.8307 (m100) cc_final: 0.7693 (m100) REVERT: D 3999 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7913 (tpt) REVERT: D 4023 MET cc_start: 0.7437 (ttp) cc_final: 0.6885 (tpp) REVERT: D 4042 ARG cc_start: 0.6516 (mtm110) cc_final: 0.5798 (mtm180) REVERT: D 4196 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.5965 (tp30) REVERT: D 4199 GLU cc_start: 0.7462 (pm20) cc_final: 0.7084 (tp30) REVERT: D 4209 GLN cc_start: 0.7978 (pt0) cc_final: 0.7461 (pm20) REVERT: D 4212 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: D 4580 TYR cc_start: 0.6892 (t80) cc_final: 0.6406 (t80) REVERT: D 4584 ASP cc_start: 0.6734 (t0) cc_final: 0.6444 (p0) REVERT: D 4644 TRP cc_start: 0.7638 (t60) cc_final: 0.7297 (t-100) REVERT: D 4726 ASP cc_start: 0.7301 (m-30) cc_final: 0.7050 (m-30) REVERT: D 4743 MET cc_start: 0.7278 (ptm) cc_final: 0.6964 (ptm) REVERT: D 4887 MET cc_start: 0.8402 (mmm) cc_final: 0.8114 (tpt) REVERT: D 4911 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7616 (mm) REVERT: D 4992 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8408 (mt) outliers start: 73 outliers final: 28 residues processed: 427 average time/residue: 1.2413 time to fit residues: 602.3624 Evaluate side-chains 426 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 375 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3955 MET 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 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 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 3955 MET Chi-restraints excluded: chain B residue 3999 MET 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 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 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 3955 MET Chi-restraints excluded: chain C residue 3999 MET 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 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 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 3955 MET Chi-restraints excluded: chain D residue 3999 MET 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 92 optimal weight: 0.1980 chunk 226 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 247 optimal weight: 0.9980 chunk 170 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.175212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.141391 restraints weight = 24602.588| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.07 r_work: 0.3370 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21232 Z= 0.134 Angle : 0.610 18.239 28660 Z= 0.293 Chirality : 0.038 0.199 3096 Planarity : 0.004 0.081 3612 Dihedral : 9.017 149.194 2768 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.02 % Favored : 97.82 % Rotamer: Outliers : 3.03 % Allowed : 16.89 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.17), residues: 2476 helix: 2.26 (0.12), residues: 1700 sheet: 0.43 (0.69), residues: 64 loop : -0.14 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D5019 HIS 0.002 0.001 HIS C4886 PHE 0.022 0.001 PHE D4922 TYR 0.008 0.001 TYR C5014 ARG 0.013 0.001 ARG A4736 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 1388) hydrogen bonds : angle 4.15150 ( 4068) metal coordination : bond 0.00311 ( 16) metal coordination : angle 3.62493 ( 8) SS BOND : bond 0.00066 ( 4) SS BOND : angle 1.46398 ( 8) covalent geometry : bond 0.00301 (21208) covalent geometry : angle 0.60708 (28644) Misc. bond : bond 0.01541 ( 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 451 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 383 time to evaluate : 2.228 Fit side-chains REVERT: A 3955 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7115 (mtm) REVERT: A 3959 LYS cc_start: 0.6268 (tttp) cc_final: 0.5980 (tttp) REVERT: A 3986 TRP cc_start: 0.8342 (m100) cc_final: 0.7732 (m100) REVERT: A 3999 MET cc_start: 0.8298 (mmm) cc_final: 0.7877 (tpt) REVERT: A 4023 MET cc_start: 0.7378 (ttp) cc_final: 0.6977 (tpp) REVERT: A 4042 ARG cc_start: 0.6507 (mtm110) cc_final: 0.5799 (mtm180) REVERT: A 4196 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.5889 (tp30) REVERT: A 4209 GLN cc_start: 0.7971 (pt0) cc_final: 0.7474 (pm20) REVERT: A 4212 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: A 4580 TYR cc_start: 0.6581 (t80) cc_final: 0.6103 (t80) REVERT: A 4584 ASP cc_start: 0.6647 (t0) cc_final: 0.6376 (p0) REVERT: A 4644 TRP cc_start: 0.7622 (t60) cc_final: 0.7292 (t-100) REVERT: A 4704 LEU cc_start: 0.8927 (tp) cc_final: 0.8327 (mm) REVERT: A 4726 ASP cc_start: 0.7323 (m-30) cc_final: 0.7047 (m-30) REVERT: A 4743 MET cc_start: 0.7202 (ptm) cc_final: 0.6875 (ptm) REVERT: A 4887 MET cc_start: 0.8384 (mmm) cc_final: 0.8096 (tpt) REVERT: A 4992 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8409 (mt) REVERT: B 3959 LYS cc_start: 0.6260 (tttp) cc_final: 0.5976 (tttp) REVERT: B 3986 TRP cc_start: 0.8347 (m100) cc_final: 0.7742 (m100) REVERT: B 3999 MET cc_start: 0.8288 (mmm) cc_final: 0.7856 (tpt) REVERT: B 4023 MET cc_start: 0.7372 (ttp) cc_final: 0.6975 (tpp) REVERT: B 4042 ARG cc_start: 0.6513 (mtm110) cc_final: 0.5802 (mtm180) REVERT: B 4196 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.5975 (tp30) REVERT: B 4209 GLN cc_start: 0.7975 (pt0) cc_final: 0.7481 (pm20) REVERT: B 4212 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: B 4580 TYR cc_start: 0.6580 (t80) cc_final: 0.6104 (t80) REVERT: B 4584 ASP cc_start: 0.6666 (t0) cc_final: 0.6383 (p0) REVERT: B 4644 TRP cc_start: 0.7620 (t60) cc_final: 0.7288 (t-100) REVERT: B 4704 LEU cc_start: 0.8932 (tp) cc_final: 0.8330 (mm) REVERT: B 4726 ASP cc_start: 0.7334 (m-30) cc_final: 0.7054 (m-30) REVERT: B 4743 MET cc_start: 0.7188 (ptm) cc_final: 0.6863 (ptm) REVERT: B 4887 MET cc_start: 0.8377 (mmm) cc_final: 0.8087 (tpt) REVERT: B 4911 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7621 (mm) REVERT: B 4992 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8411 (mt) REVERT: C 3959 LYS cc_start: 0.6255 (tttp) cc_final: 0.5970 (tttp) REVERT: C 3986 TRP cc_start: 0.8347 (m100) cc_final: 0.7745 (m100) REVERT: C 3999 MET cc_start: 0.8291 (mmm) cc_final: 0.7856 (tpt) REVERT: C 4023 MET cc_start: 0.7352 (ttp) cc_final: 0.6947 (tpp) REVERT: C 4042 ARG cc_start: 0.6527 (mtm110) cc_final: 0.5819 (mtm180) REVERT: C 4196 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.5885 (tp30) REVERT: C 4209 GLN cc_start: 0.7978 (pt0) cc_final: 0.7479 (pm20) REVERT: C 4212 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: C 4580 TYR cc_start: 0.6581 (t80) cc_final: 0.6104 (t80) REVERT: C 4584 ASP cc_start: 0.6649 (t0) cc_final: 0.6382 (p0) REVERT: C 4644 TRP cc_start: 0.7620 (t60) cc_final: 0.7289 (t-100) REVERT: C 4704 LEU cc_start: 0.8932 (tp) cc_final: 0.8333 (mm) REVERT: C 4726 ASP cc_start: 0.7311 (m-30) cc_final: 0.7038 (m-30) REVERT: C 4743 MET cc_start: 0.7216 (ptm) cc_final: 0.6891 (ptm) REVERT: C 4887 MET cc_start: 0.8378 (mmm) cc_final: 0.8094 (tpt) REVERT: C 4992 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8396 (mt) REVERT: D 3959 LYS cc_start: 0.6268 (tttp) cc_final: 0.5979 (tttp) REVERT: D 3986 TRP cc_start: 0.8335 (m100) cc_final: 0.7735 (m100) REVERT: D 3999 MET cc_start: 0.8283 (mmm) cc_final: 0.7843 (tpt) REVERT: D 4023 MET cc_start: 0.7376 (ttp) cc_final: 0.6974 (tpp) REVERT: D 4042 ARG cc_start: 0.6512 (mtm110) cc_final: 0.5805 (mtm180) REVERT: D 4196 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.5872 (tp30) REVERT: D 4209 GLN cc_start: 0.7965 (pt0) cc_final: 0.7463 (pm20) REVERT: D 4212 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: D 4580 TYR cc_start: 0.6577 (t80) cc_final: 0.6106 (t80) REVERT: D 4584 ASP cc_start: 0.6636 (t0) cc_final: 0.6369 (p0) REVERT: D 4644 TRP cc_start: 0.7626 (t60) cc_final: 0.7292 (t-100) REVERT: D 4704 LEU cc_start: 0.8929 (tp) cc_final: 0.8330 (mm) REVERT: D 4726 ASP cc_start: 0.7326 (m-30) cc_final: 0.7050 (m-30) REVERT: D 4743 MET cc_start: 0.7207 (ptm) cc_final: 0.6882 (ptm) REVERT: D 4887 MET cc_start: 0.8384 (mmm) cc_final: 0.8096 (tpt) REVERT: D 4911 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7616 (mm) REVERT: D 4992 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8405 (mt) outliers start: 68 outliers final: 28 residues processed: 426 average time/residue: 1.2671 time to fit residues: 615.1612 Evaluate side-chains 416 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 373 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3955 MET 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 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 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 4045 VAL 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 4785 THR 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 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 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 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 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 66 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 23 optimal weight: 0.0980 chunk 213 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.176502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.142764 restraints weight = 24526.881| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.98 r_work: 0.3376 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2456 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= 0.133 Angle : 0.663 18.670 28660 Z= 0.317 Chirality : 0.038 0.188 3096 Planarity : 0.004 0.080 3612 Dihedral : 9.055 149.534 2768 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 2.63 % Allowed : 18.54 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.17), residues: 2476 helix: 2.25 (0.12), residues: 1704 sheet: 0.39 (0.70), residues: 64 loop : -0.27 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C5019 HIS 0.002 0.001 HIS D3994 PHE 0.024 0.001 PHE A4922 TYR 0.019 0.001 TYR A4580 ARG 0.014 0.001 ARG B4736 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 1388) hydrogen bonds : angle 4.24466 ( 4068) metal coordination : bond 0.00295 ( 16) metal coordination : angle 3.53965 ( 8) SS BOND : bond 0.00185 ( 4) SS BOND : angle 1.26180 ( 8) covalent geometry : bond 0.00296 (21208) covalent geometry : angle 0.66017 (28644) Misc. bond : bond 0.01191 ( 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 447 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 388 time to evaluate : 2.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3959 LYS cc_start: 0.6221 (tttp) cc_final: 0.5842 (tttp) REVERT: A 3986 TRP cc_start: 0.8316 (m100) cc_final: 0.7892 (m100) REVERT: A 3999 MET cc_start: 0.8351 (mmm) cc_final: 0.7949 (tpt) REVERT: A 4023 MET cc_start: 0.7272 (ttp) cc_final: 0.6845 (ttt) REVERT: A 4042 ARG cc_start: 0.6437 (mtm110) cc_final: 0.5743 (mtm180) REVERT: A 4196 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.5853 (tp30) REVERT: A 4199 GLU cc_start: 0.7665 (pm20) cc_final: 0.7159 (tp30) REVERT: A 4209 GLN cc_start: 0.7942 (pt0) cc_final: 0.7438 (pm20) REVERT: A 4212 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: A 4644 TRP cc_start: 0.7564 (t60) cc_final: 0.7222 (t-100) REVERT: A 4726 ASP cc_start: 0.7311 (m-30) cc_final: 0.7029 (m-30) REVERT: A 4743 MET cc_start: 0.7165 (ptm) cc_final: 0.6836 (ptm) REVERT: A 4887 MET cc_start: 0.8358 (mmm) cc_final: 0.8069 (tpt) REVERT: A 4992 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8419 (mt) REVERT: B 3955 MET cc_start: 0.7456 (mmm) cc_final: 0.7161 (mtm) REVERT: B 3959 LYS cc_start: 0.6212 (tttp) cc_final: 0.5834 (tttp) REVERT: B 3986 TRP cc_start: 0.8310 (m100) cc_final: 0.7870 (m100) REVERT: B 3999 MET cc_start: 0.8339 (mmm) cc_final: 0.7918 (tpt) REVERT: B 4023 MET cc_start: 0.7275 (ttp) cc_final: 0.6850 (ttt) REVERT: B 4042 ARG cc_start: 0.6463 (mtm110) cc_final: 0.5764 (mtm180) REVERT: B 4196 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.5860 (tp30) REVERT: B 4199 GLU cc_start: 0.7659 (pm20) cc_final: 0.7159 (tp30) REVERT: B 4209 GLN cc_start: 0.7963 (pt0) cc_final: 0.7450 (pm20) REVERT: B 4212 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: B 4644 TRP cc_start: 0.7556 (t60) cc_final: 0.7213 (t-100) REVERT: B 4726 ASP cc_start: 0.7293 (m-30) cc_final: 0.7010 (m-30) REVERT: B 4743 MET cc_start: 0.7157 (ptm) cc_final: 0.6829 (ptm) REVERT: B 4887 MET cc_start: 0.8358 (mmm) cc_final: 0.8077 (tpt) REVERT: B 4911 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7658 (mm) REVERT: B 4992 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8423 (mt) REVERT: C 3955 MET cc_start: 0.7459 (mmm) cc_final: 0.7165 (mtm) REVERT: C 3959 LYS cc_start: 0.6224 (tttp) cc_final: 0.5844 (tttp) REVERT: C 3986 TRP cc_start: 0.8307 (m100) cc_final: 0.7872 (m100) REVERT: C 3999 MET cc_start: 0.8331 (mmm) cc_final: 0.7909 (tpt) REVERT: C 4023 MET cc_start: 0.7291 (ttp) cc_final: 0.6861 (ttt) REVERT: C 4042 ARG cc_start: 0.6458 (mtm110) cc_final: 0.5765 (mtm180) REVERT: C 4196 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.5861 (tp30) REVERT: C 4199 GLU cc_start: 0.7651 (pm20) cc_final: 0.7157 (tp30) REVERT: C 4209 GLN cc_start: 0.7950 (pt0) cc_final: 0.7435 (pm20) REVERT: C 4212 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: C 4644 TRP cc_start: 0.7561 (t60) cc_final: 0.7219 (t-100) REVERT: C 4726 ASP cc_start: 0.7305 (m-30) cc_final: 0.7024 (m-30) REVERT: C 4743 MET cc_start: 0.7172 (ptm) cc_final: 0.6846 (ptm) REVERT: C 4887 MET cc_start: 0.8365 (mmm) cc_final: 0.8084 (tpt) REVERT: C 4992 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8412 (mt) REVERT: D 3955 MET cc_start: 0.7446 (mmm) cc_final: 0.7151 (mtm) REVERT: D 3959 LYS cc_start: 0.6213 (tttp) cc_final: 0.5828 (tttp) REVERT: D 3986 TRP cc_start: 0.8306 (m100) cc_final: 0.7874 (m100) REVERT: D 3999 MET cc_start: 0.8341 (mmm) cc_final: 0.7920 (tpt) REVERT: D 4023 MET cc_start: 0.7280 (ttp) cc_final: 0.6853 (ttt) REVERT: D 4042 ARG cc_start: 0.6466 (mtm110) cc_final: 0.5769 (mtm180) REVERT: D 4196 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.5855 (tp30) REVERT: D 4199 GLU cc_start: 0.7658 (pm20) cc_final: 0.7162 (tp30) REVERT: D 4209 GLN cc_start: 0.7938 (pt0) cc_final: 0.7420 (pm20) REVERT: D 4212 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: D 4644 TRP cc_start: 0.7555 (t60) cc_final: 0.7214 (t-100) REVERT: D 4726 ASP cc_start: 0.7301 (m-30) cc_final: 0.7021 (m-30) REVERT: D 4743 MET cc_start: 0.7167 (ptm) cc_final: 0.6834 (ptm) REVERT: D 4887 MET cc_start: 0.8354 (mmm) cc_final: 0.8076 (tpt) REVERT: D 4911 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7659 (mm) REVERT: D 4992 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8422 (mt) outliers start: 59 outliers final: 33 residues processed: 433 average time/residue: 1.1444 time to fit residues: 568.1957 Evaluate side-chains 408 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 361 time to evaluate : 2.406 ------------------------------------------------------------------------------- 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 4785 THR Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4878 ASP 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 4045 VAL 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 4785 THR Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4878 ASP 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 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 C residue 4878 ASP 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 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 Chi-restraints excluded: chain D residue 4878 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 47 optimal weight: 0.5980 chunk 111 optimal weight: 0.0670 chunk 178 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 223 optimal weight: 4.9990 chunk 171 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 D4034 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.177174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.143904 restraints weight = 24632.519| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.98 r_work: 0.3385 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21232 Z= 0.123 Angle : 0.622 13.299 28660 Z= 0.301 Chirality : 0.038 0.178 3096 Planarity : 0.004 0.078 3612 Dihedral : 8.995 149.745 2768 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.86 % Favored : 97.98 % Rotamer: Outliers : 2.14 % Allowed : 18.67 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.17), residues: 2476 helix: 2.29 (0.12), residues: 1700 sheet: 0.38 (0.71), residues: 64 loop : -0.39 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A5019 HIS 0.003 0.001 HIS C3994 PHE 0.025 0.001 PHE D4922 TYR 0.021 0.001 TYR D4580 ARG 0.016 0.001 ARG D4189 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 1388) hydrogen bonds : angle 4.19684 ( 4068) metal coordination : bond 0.00225 ( 16) metal coordination : angle 3.33330 ( 8) SS BOND : bond 0.00062 ( 4) SS BOND : angle 1.38230 ( 8) covalent geometry : bond 0.00266 (21208) covalent geometry : angle 0.61974 (28644) Misc. bond : bond 0.01260 ( 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 416 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 368 time to evaluate : 2.195 Fit side-chains revert: symmetry clash REVERT: A 3959 LYS cc_start: 0.6252 (tttp) cc_final: 0.5906 (tttp) REVERT: A 3980 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7528 (mm) REVERT: A 3986 TRP cc_start: 0.8271 (m100) cc_final: 0.7710 (m100) REVERT: A 3999 MET cc_start: 0.8312 (mmm) cc_final: 0.7911 (tpt) REVERT: A 4023 MET cc_start: 0.6987 (ttp) cc_final: 0.6696 (ttt) REVERT: A 4042 ARG cc_start: 0.6421 (mtm110) cc_final: 0.5730 (mtm180) REVERT: A 4184 MET cc_start: 0.8058 (tpp) cc_final: 0.7819 (ttp) REVERT: A 4196 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.5820 (tp30) REVERT: A 4199 GLU cc_start: 0.7624 (pm20) cc_final: 0.7109 (tp30) REVERT: A 4212 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: A 4644 TRP cc_start: 0.7620 (t60) cc_final: 0.7263 (t-100) REVERT: A 4704 LEU cc_start: 0.8937 (tp) cc_final: 0.8319 (mm) REVERT: A 4726 ASP cc_start: 0.7315 (m-30) cc_final: 0.7036 (m-30) REVERT: A 4736 ARG cc_start: 0.6975 (ttp-110) cc_final: 0.6593 (ttp-110) REVERT: A 4743 MET cc_start: 0.7180 (ptm) cc_final: 0.6861 (ptm) REVERT: A 4887 MET cc_start: 0.8356 (mmm) cc_final: 0.8075 (tpt) REVERT: A 4992 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8390 (mt) REVERT: B 3959 LYS cc_start: 0.6262 (tttp) cc_final: 0.5921 (tttp) REVERT: B 3986 TRP cc_start: 0.8247 (m100) cc_final: 0.7827 (m100) REVERT: B 3999 MET cc_start: 0.8324 (mmm) cc_final: 0.7909 (tpt) REVERT: B 4023 MET cc_start: 0.6999 (ttp) cc_final: 0.6649 (tpp) REVERT: B 4042 ARG cc_start: 0.6433 (mtm110) cc_final: 0.5736 (mtm180) REVERT: B 4184 MET cc_start: 0.8068 (tpp) cc_final: 0.7833 (ttp) REVERT: B 4196 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.5822 (tp30) REVERT: B 4199 GLU cc_start: 0.7623 (pm20) cc_final: 0.7106 (tp30) REVERT: B 4212 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: B 4644 TRP cc_start: 0.7615 (t60) cc_final: 0.7261 (t-100) REVERT: B 4704 LEU cc_start: 0.8939 (tp) cc_final: 0.8325 (mm) REVERT: B 4726 ASP cc_start: 0.7306 (m-30) cc_final: 0.7027 (m-30) REVERT: B 4736 ARG cc_start: 0.6969 (ttp-110) cc_final: 0.6587 (ttp-110) REVERT: B 4743 MET cc_start: 0.7182 (ptm) cc_final: 0.6863 (ptm) REVERT: B 4887 MET cc_start: 0.8360 (mmm) cc_final: 0.8081 (tpt) REVERT: B 4911 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7639 (mm) REVERT: B 4992 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8393 (mt) REVERT: C 3959 LYS cc_start: 0.6272 (tttp) cc_final: 0.5927 (tttp) REVERT: C 3986 TRP cc_start: 0.8242 (m100) cc_final: 0.7830 (m100) REVERT: C 3999 MET cc_start: 0.8326 (mmm) cc_final: 0.7910 (tpt) REVERT: C 4023 MET cc_start: 0.7009 (ttp) cc_final: 0.6662 (tpp) REVERT: C 4042 ARG cc_start: 0.6434 (mtm110) cc_final: 0.5740 (mtm180) REVERT: C 4184 MET cc_start: 0.8071 (tpp) cc_final: 0.7835 (ttp) REVERT: C 4196 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.5830 (tp30) REVERT: C 4199 GLU cc_start: 0.7622 (pm20) cc_final: 0.7110 (tp30) REVERT: C 4212 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: C 4644 TRP cc_start: 0.7606 (t60) cc_final: 0.7252 (t-100) REVERT: C 4704 LEU cc_start: 0.8939 (tp) cc_final: 0.8325 (mm) REVERT: C 4726 ASP cc_start: 0.7315 (m-30) cc_final: 0.7036 (m-30) REVERT: C 4736 ARG cc_start: 0.6970 (ttp-110) cc_final: 0.6590 (ttp-110) REVERT: C 4743 MET cc_start: 0.7196 (ptm) cc_final: 0.6881 (ptm) REVERT: C 4887 MET cc_start: 0.8361 (mmm) cc_final: 0.8083 (tpt) REVERT: C 4992 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8381 (mt) REVERT: D 3959 LYS cc_start: 0.6251 (tttp) cc_final: 0.5903 (tttp) REVERT: D 3986 TRP cc_start: 0.8243 (m100) cc_final: 0.7830 (m100) REVERT: D 3999 MET cc_start: 0.8337 (mmm) cc_final: 0.7921 (tpt) REVERT: D 4023 MET cc_start: 0.6991 (ttp) cc_final: 0.6644 (tpp) REVERT: D 4042 ARG cc_start: 0.6433 (mtm110) cc_final: 0.5738 (mtm180) REVERT: D 4184 MET cc_start: 0.8059 (tpp) cc_final: 0.7816 (ttp) REVERT: D 4196 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.5825 (tp30) REVERT: D 4199 GLU cc_start: 0.7609 (pm20) cc_final: 0.7114 (tp30) REVERT: D 4212 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: D 4644 TRP cc_start: 0.7603 (t60) cc_final: 0.7247 (t-100) REVERT: D 4704 LEU cc_start: 0.8942 (tp) cc_final: 0.8328 (mm) REVERT: D 4726 ASP cc_start: 0.7308 (m-30) cc_final: 0.7029 (m-30) REVERT: D 4736 ARG cc_start: 0.6963 (ttp-110) cc_final: 0.6581 (ttp-110) REVERT: D 4743 MET cc_start: 0.7189 (ptm) cc_final: 0.6871 (ptm) REVERT: D 4887 MET cc_start: 0.8360 (mmm) cc_final: 0.8082 (tpt) REVERT: D 4911 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7633 (mm) REVERT: D 4992 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8390 (mt) outliers start: 48 outliers final: 26 residues processed: 405 average time/residue: 1.1884 time to fit residues: 549.2253 Evaluate side-chains 397 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 356 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3980 LEU 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 4785 THR Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4878 ASP 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 4561 THR 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 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 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 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 4785 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 142 optimal weight: 0.0870 chunk 138 optimal weight: 2.9990 chunk 208 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- 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 D4034 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.175565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.142310 restraints weight = 24556.541| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.15 r_work: 0.3355 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21232 Z= 0.151 Angle : 0.729 28.543 28660 Z= 0.336 Chirality : 0.039 0.190 3096 Planarity : 0.004 0.084 3612 Dihedral : 9.039 150.594 2768 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 2.18 % Allowed : 18.45 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.17), residues: 2476 helix: 2.15 (0.12), residues: 1700 sheet: 0.38 (0.70), residues: 64 loop : -0.45 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C5019 HIS 0.003 0.001 HIS D4886 PHE 0.029 0.002 PHE C4922 TYR 0.014 0.001 TYR C4580 ARG 0.014 0.001 ARG C4189 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 1388) hydrogen bonds : angle 4.31661 ( 4068) metal coordination : bond 0.00546 ( 16) metal coordination : angle 3.94017 ( 8) SS BOND : bond 0.00017 ( 4) SS BOND : angle 1.72443 ( 8) covalent geometry : bond 0.00344 (21208) covalent geometry : angle 0.72569 (28644) Misc. bond : bond 0.01533 ( 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 410 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 361 time to evaluate : 2.418 Fit side-chains REVERT: A 3986 TRP cc_start: 0.8267 (m100) cc_final: 0.7872 (m100) REVERT: A 3999 MET cc_start: 0.8313 (mmm) cc_final: 0.7916 (tpt) REVERT: A 4023 MET cc_start: 0.7155 (ttp) cc_final: 0.6763 (ttp) REVERT: A 4042 ARG cc_start: 0.6455 (mtm110) cc_final: 0.5756 (mtm180) REVERT: A 4196 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.5852 (tp30) REVERT: A 4199 GLU cc_start: 0.7823 (pm20) cc_final: 0.7331 (tp30) REVERT: A 4209 GLN cc_start: 0.7992 (pt0) cc_final: 0.7471 (pm20) REVERT: A 4212 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: A 4644 TRP cc_start: 0.7624 (t60) cc_final: 0.7276 (t-100) REVERT: A 4686 LEU cc_start: 0.7616 (tp) cc_final: 0.7394 (tm) REVERT: A 4726 ASP cc_start: 0.7321 (m-30) cc_final: 0.7086 (m-30) REVERT: A 4887 MET cc_start: 0.8258 (mmm) cc_final: 0.7979 (tpt) REVERT: A 4992 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8444 (mt) REVERT: B 3980 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7602 (mm) REVERT: B 3986 TRP cc_start: 0.8297 (m100) cc_final: 0.7712 (m100) REVERT: B 3999 MET cc_start: 0.8329 (mmm) cc_final: 0.7913 (tpt) REVERT: B 4023 MET cc_start: 0.7212 (ttp) cc_final: 0.6836 (ttp) REVERT: B 4042 ARG cc_start: 0.6444 (mtm110) cc_final: 0.5744 (mtm180) REVERT: B 4196 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.5857 (tp30) REVERT: B 4199 GLU cc_start: 0.7829 (pm20) cc_final: 0.7335 (tp30) REVERT: B 4209 GLN cc_start: 0.8003 (pt0) cc_final: 0.7477 (pm20) REVERT: B 4212 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: B 4644 TRP cc_start: 0.7614 (t60) cc_final: 0.7268 (t-100) REVERT: B 4686 LEU cc_start: 0.7612 (tp) cc_final: 0.7389 (tm) REVERT: B 4726 ASP cc_start: 0.7314 (m-30) cc_final: 0.7078 (m-30) REVERT: B 4887 MET cc_start: 0.8262 (mmm) cc_final: 0.7989 (tpt) REVERT: B 4911 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7670 (mm) REVERT: B 4992 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8439 (mt) REVERT: C 3980 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7606 (mm) REVERT: C 3986 TRP cc_start: 0.8293 (m100) cc_final: 0.7713 (m100) REVERT: C 3999 MET cc_start: 0.8326 (mmm) cc_final: 0.7907 (tpt) REVERT: C 4023 MET cc_start: 0.7172 (ttp) cc_final: 0.6790 (ttp) REVERT: C 4042 ARG cc_start: 0.6447 (mtm110) cc_final: 0.5752 (mtm180) REVERT: C 4196 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.5872 (tp30) REVERT: C 4199 GLU cc_start: 0.7826 (pm20) cc_final: 0.7330 (tp30) REVERT: C 4209 GLN cc_start: 0.7999 (pt0) cc_final: 0.7468 (pm20) REVERT: C 4212 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: C 4644 TRP cc_start: 0.7613 (t60) cc_final: 0.7266 (t-100) REVERT: C 4686 LEU cc_start: 0.7620 (tp) cc_final: 0.7396 (tm) REVERT: C 4726 ASP cc_start: 0.7316 (m-30) cc_final: 0.7084 (m-30) REVERT: C 4887 MET cc_start: 0.8260 (mmm) cc_final: 0.7986 (tpt) REVERT: C 4992 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8428 (mt) REVERT: D 3980 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7606 (mm) REVERT: D 3986 TRP cc_start: 0.8289 (m100) cc_final: 0.7710 (m100) REVERT: D 3999 MET cc_start: 0.8342 (mmm) cc_final: 0.7923 (tpt) REVERT: D 4023 MET cc_start: 0.7164 (ttp) cc_final: 0.6783 (ttp) REVERT: D 4042 ARG cc_start: 0.6457 (mtm110) cc_final: 0.5759 (mtm180) REVERT: D 4196 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.5863 (tp30) REVERT: D 4199 GLU cc_start: 0.7824 (pm20) cc_final: 0.7331 (tp30) REVERT: D 4209 GLN cc_start: 0.7989 (pt0) cc_final: 0.7457 (pm20) REVERT: D 4212 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7409 (mp0) REVERT: D 4644 TRP cc_start: 0.7611 (t60) cc_final: 0.7265 (t-100) REVERT: D 4686 LEU cc_start: 0.7617 (tp) cc_final: 0.7402 (tm) REVERT: D 4726 ASP cc_start: 0.7323 (m-30) cc_final: 0.7089 (m-30) REVERT: D 4887 MET cc_start: 0.8256 (mmm) cc_final: 0.7983 (tpt) REVERT: D 4911 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7666 (mm) REVERT: D 4992 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8443 (mt) outliers start: 49 outliers final: 32 residues processed: 393 average time/residue: 1.2147 time to fit residues: 545.2901 Evaluate side-chains 406 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 357 time to evaluate : 2.178 ------------------------------------------------------------------------------- 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 4785 THR 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 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 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 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 3980 LEU 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 239 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 D4034 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.175732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.142334 restraints weight = 24719.459| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.17 r_work: 0.3362 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21232 Z= 0.145 Angle : 0.724 27.238 28660 Z= 0.336 Chirality : 0.039 0.183 3096 Planarity : 0.004 0.082 3612 Dihedral : 9.025 150.567 2768 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.70 % Favored : 98.18 % Rotamer: Outliers : 2.23 % Allowed : 18.32 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.17), residues: 2476 helix: 2.03 (0.12), residues: 1724 sheet: 0.33 (0.71), residues: 64 loop : -0.49 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A5019 HIS 0.003 0.001 HIS C4886 PHE 0.029 0.001 PHE A4922 TYR 0.015 0.001 TYR A4580 ARG 0.016 0.001 ARG D4189 Details of bonding type rmsd hydrogen bonds : bond 0.04128 ( 1388) hydrogen bonds : angle 4.32412 ( 4068) metal coordination : bond 0.00460 ( 16) metal coordination : angle 4.09821 ( 8) SS BOND : bond 0.00023 ( 4) SS BOND : angle 1.66553 ( 8) covalent geometry : bond 0.00328 (21208) covalent geometry : angle 0.72042 (28644) Misc. bond : bond 0.01465 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17159.46 seconds wall clock time: 295 minutes 4.94 seconds (17704.94 seconds total)