Starting phenix.real_space_refine on Fri Aug 7 09:46:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sex_40432/08_2026/8sex_40432.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sex_40432/08_2026/8sex_40432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sex_40432/08_2026/8sex_40432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sex_40432/08_2026/8sex_40432.map" model { file = "/net/cci-nas-00/data/ceres_data/8sex_40432/08_2026/8sex_40432.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sex_40432/08_2026/8sex_40432.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8sex_40432/08_2026/8sex_40432.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sex_40432/08_2026/8sex_40432.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.059 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 4 5.49 5 S 160 5.16 5 C 13344 2.51 5 N 3280 2.21 5 O 3776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20568 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5118 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' ZN': 1} Classifications: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4444 SG CYS A4958 56.003 81.965 85.909 1.00 45.49 S ATOM 4469 SG CYS A4961 58.285 82.520 88.873 1.00 43.92 S Restraints were copied for chains: B, C, D Time building chain proxies: 4.43, per 1000 atoms: 0.22 Number of scatterers: 20568 At special positions: 0 Unit cell: (142.968, 142.968, 130.088, 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 4 15.00 O 3776 8.00 N 3280 7.00 C 13344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.03 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " distance=2.03 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " distance=2.03 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 744.4 milliseconds 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 A4958 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " 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 B4958 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4961 " 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 C4958 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " 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 D4958 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " Number of angles added : 8 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4712 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 8 sheets defined 79.6% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 3950 through 3970 removed outlier: 3.871A pdb=" N ALA A3954 " --> pdb=" O ASN A3950 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3983 Processing helix chain 'A' and resid 3984 through 4006 removed outlier: 3.590A pdb=" N ALA A3988 " --> pdb=" O ARG A3984 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP A4006 " --> pdb=" O LYS A4002 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4031 removed outlier: 3.800A pdb=" N LEU A4019 " --> pdb=" O GLU A4015 " (cutoff:3.500A) removed outlier: 3.519A 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 4056 Processing helix chain 'A' and resid 4198 through 4207 Processing helix chain 'A' and resid 4207 through 4224 Processing helix chain 'A' and resid 4229 through 4252 Processing helix chain 'A' and resid 4543 through 4558 Processing helix chain 'A' and resid 4558 through 4578 removed outlier: 3.507A pdb=" N LEU A4578 " --> pdb=" O ASN A4574 " (cutoff:3.500A) 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 4702 Processing helix chain 'A' and resid 4702 through 4707 removed outlier: 3.915A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN A4707 " --> pdb=" O ARG A4703 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4702 through 4707' Processing helix chain 'A' and resid 4719 through 4733 removed outlier: 5.245A pdb=" N ASP A4730 " --> pdb=" O ASP A4726 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE A4731 " --> pdb=" O LYS A4727 " (cutoff:3.500A) Processing helix chain 'A' and resid 4733 through 4742 Processing helix chain 'A' and resid 4744 through 4749 removed outlier: 3.930A pdb=" N GLU A4749 " --> pdb=" O LEU A4745 " (cutoff:3.500A) Processing helix chain 'A' and resid 4773 through 4785 Processing helix chain 'A' and resid 4786 through 4802 Processing helix chain 'A' and resid 4803 through 4804 No H-bonds generated for 'chain 'A' and resid 4803 through 4804' Processing helix chain 'A' and resid 4805 through 4813 Processing helix chain 'A' and resid 4814 through 4820 removed outlier: 4.173A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) Processing helix chain 'A' and resid 4820 through 4833 removed outlier: 3.690A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) removed outlier: 4.408A 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 4863 removed outlier: 3.577A pdb=" N TYR A4863 " --> pdb=" O ARG A4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4860 through 4863' Processing helix chain 'A' and resid 4878 through 4893 removed outlier: 4.209A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) Processing helix chain 'A' and resid 4896 through 4900 removed outlier: 3.608A pdb=" N ASP A4899 " --> pdb=" O GLY A4896 " (cutoff:3.500A) Processing helix chain 'A' and resid 4909 through 4924 Processing helix chain 'A' and resid 4926 through 4957 Processing helix chain 'A' and resid 4964 through 4969 removed outlier: 3.895A 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 5037 removed outlier: 5.845A pdb=" N ASP A5034 " --> pdb=" O LYS A5030 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN A5035 " --> pdb=" O GLN A5031 " (cutoff:3.500A) Processing helix chain 'B' and resid 3951 through 3970 Processing helix chain 'B' and resid 3973 through 3983 Processing helix chain 'B' and resid 3984 through 4006 removed outlier: 3.590A pdb=" N ALA B3988 " --> pdb=" O ARG B3984 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET B4001 " --> pdb=" O ALA B3997 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP B4006 " --> pdb=" O LYS B4002 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4031 removed outlier: 3.800A pdb=" N LEU B4019 " --> pdb=" O GLU B4015 " (cutoff:3.500A) removed outlier: 3.519A 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 4056 Processing helix chain 'B' and resid 4198 through 4207 Processing helix chain 'B' and resid 4207 through 4224 Processing helix chain 'B' and resid 4229 through 4252 Processing helix chain 'B' and resid 4543 through 4558 Processing helix chain 'B' and resid 4558 through 4578 removed outlier: 3.507A pdb=" N LEU B4578 " --> pdb=" O ASN B4574 " (cutoff:3.500A) 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 4702 Processing helix chain 'B' and resid 4702 through 4707 removed outlier: 3.915A pdb=" N LEU B4706 " --> pdb=" O ASP B4702 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN B4707 " --> pdb=" O ARG B4703 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4702 through 4707' Processing helix chain 'B' and resid 4719 through 4733 removed outlier: 5.245A pdb=" N ASP B4730 " --> pdb=" O ASP B4726 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE B4731 " --> pdb=" O LYS B4727 " (cutoff:3.500A) Processing helix chain 'B' and resid 4733 through 4742 Processing helix chain 'B' and resid 4744 through 4749 removed outlier: 3.930A pdb=" N GLU B4749 " --> pdb=" O LEU B4745 " (cutoff:3.500A) Processing helix chain 'B' and resid 4773 through 4785 Processing helix chain 'B' and resid 4786 through 4802 Processing helix chain 'B' and resid 4803 through 4804 No H-bonds generated for 'chain 'B' and resid 4803 through 4804' Processing helix chain 'B' and resid 4805 through 4813 Processing helix chain 'B' and resid 4814 through 4820 removed outlier: 4.173A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) Processing helix chain 'B' and resid 4820 through 4833 removed outlier: 3.690A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) removed outlier: 4.408A 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 4863 removed outlier: 3.577A pdb=" N TYR B4863 " --> pdb=" O ARG B4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4860 through 4863' Processing helix chain 'B' and resid 4878 through 4893 removed outlier: 4.209A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) Processing helix chain 'B' and resid 4896 through 4900 removed outlier: 3.608A pdb=" N ASP B4899 " --> pdb=" O GLY B4896 " (cutoff:3.500A) Processing helix chain 'B' and resid 4909 through 4924 Processing helix chain 'B' and resid 4926 through 4957 Processing helix chain 'B' and resid 4964 through 4969 removed outlier: 3.895A 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 5037 removed outlier: 5.845A pdb=" N ASP B5034 " --> pdb=" O LYS B5030 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN B5035 " --> pdb=" O GLN B5031 " (cutoff:3.500A) Processing helix chain 'C' and resid 3951 through 3970 Processing helix chain 'C' and resid 3973 through 3983 Processing helix chain 'C' and resid 3984 through 4006 removed outlier: 3.590A pdb=" N ALA C3988 " --> pdb=" O ARG C3984 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP C4006 " --> pdb=" O LYS C4002 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4031 removed outlier: 3.800A pdb=" N LEU C4019 " --> pdb=" O GLU C4015 " (cutoff:3.500A) removed outlier: 3.519A 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 4056 Processing helix chain 'C' and resid 4198 through 4207 Processing helix chain 'C' and resid 4207 through 4224 Processing helix chain 'C' and resid 4229 through 4252 Processing helix chain 'C' and resid 4543 through 4558 Processing helix chain 'C' and resid 4558 through 4578 removed outlier: 3.507A pdb=" N LEU C4578 " --> pdb=" O ASN C4574 " (cutoff:3.500A) 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 4702 Processing helix chain 'C' and resid 4702 through 4707 removed outlier: 3.915A pdb=" N LEU C4706 " --> pdb=" O ASP C4702 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN C4707 " --> pdb=" O ARG C4703 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4702 through 4707' Processing helix chain 'C' and resid 4719 through 4733 removed outlier: 5.245A pdb=" N ASP C4730 " --> pdb=" O ASP C4726 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE C4731 " --> pdb=" O LYS C4727 " (cutoff:3.500A) Processing helix chain 'C' and resid 4733 through 4742 Processing helix chain 'C' and resid 4744 through 4749 removed outlier: 3.930A pdb=" N GLU C4749 " --> pdb=" O LEU C4745 " (cutoff:3.500A) Processing helix chain 'C' and resid 4773 through 4785 Processing helix chain 'C' and resid 4786 through 4802 Processing helix chain 'C' and resid 4803 through 4804 No H-bonds generated for 'chain 'C' and resid 4803 through 4804' Processing helix chain 'C' and resid 4805 through 4813 Processing helix chain 'C' and resid 4814 through 4820 removed outlier: 4.173A pdb=" N MET C4818 " --> pdb=" O LEU C4814 " (cutoff:3.500A) Processing helix chain 'C' and resid 4820 through 4833 removed outlier: 3.690A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) removed outlier: 4.408A 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 4863 removed outlier: 3.577A pdb=" N TYR C4863 " --> pdb=" O ARG C4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4860 through 4863' Processing helix chain 'C' and resid 4878 through 4893 removed outlier: 4.209A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) Processing helix chain 'C' and resid 4896 through 4900 removed outlier: 3.608A pdb=" N ASP C4899 " --> pdb=" O GLY C4896 " (cutoff:3.500A) Processing helix chain 'C' and resid 4909 through 4924 Processing helix chain 'C' and resid 4926 through 4957 Processing helix chain 'C' and resid 4964 through 4969 removed outlier: 3.895A 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 5037 removed outlier: 5.845A pdb=" N ASP C5034 " --> pdb=" O LYS C5030 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN C5035 " --> pdb=" O GLN C5031 " (cutoff:3.500A) Processing helix chain 'D' and resid 3951 through 3970 Processing helix chain 'D' and resid 3973 through 3983 Processing helix chain 'D' and resid 3984 through 4006 removed outlier: 3.590A pdb=" N ALA D3988 " --> pdb=" O ARG D3984 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP D4006 " --> pdb=" O LYS D4002 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4031 removed outlier: 3.800A pdb=" N LEU D4019 " --> pdb=" O GLU D4015 " (cutoff:3.500A) removed outlier: 3.519A 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 4056 Processing helix chain 'D' and resid 4198 through 4207 Processing helix chain 'D' and resid 4207 through 4224 Processing helix chain 'D' and resid 4229 through 4252 Processing helix chain 'D' and resid 4543 through 4558 Processing helix chain 'D' and resid 4558 through 4578 removed outlier: 3.507A pdb=" N LEU D4578 " --> pdb=" O ASN D4574 " (cutoff:3.500A) 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 4702 Processing helix chain 'D' and resid 4702 through 4707 removed outlier: 3.915A pdb=" N LEU D4706 " --> pdb=" O ASP D4702 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN D4707 " --> pdb=" O ARG D4703 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4702 through 4707' Processing helix chain 'D' and resid 4719 through 4733 removed outlier: 5.245A pdb=" N ASP D4730 " --> pdb=" O ASP D4726 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE D4731 " --> pdb=" O LYS D4727 " (cutoff:3.500A) Processing helix chain 'D' and resid 4733 through 4742 Processing helix chain 'D' and resid 4744 through 4749 removed outlier: 3.930A pdb=" N GLU D4749 " --> pdb=" O LEU D4745 " (cutoff:3.500A) Processing helix chain 'D' and resid 4773 through 4785 Processing helix chain 'D' and resid 4786 through 4802 Processing helix chain 'D' and resid 4803 through 4804 No H-bonds generated for 'chain 'D' and resid 4803 through 4804' Processing helix chain 'D' and resid 4805 through 4813 Processing helix chain 'D' and resid 4814 through 4820 removed outlier: 4.173A pdb=" N MET D4818 " --> pdb=" O LEU D4814 " (cutoff:3.500A) Processing helix chain 'D' and resid 4820 through 4833 removed outlier: 3.690A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) removed outlier: 4.408A 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 4863 removed outlier: 3.577A pdb=" N TYR D4863 " --> pdb=" O ARG D4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4860 through 4863' Processing helix chain 'D' and resid 4878 through 4893 removed outlier: 4.209A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) Processing helix chain 'D' and resid 4896 through 4900 removed outlier: 3.608A pdb=" N ASP D4899 " --> pdb=" O GLY D4896 " (cutoff:3.500A) Processing helix chain 'D' and resid 4909 through 4924 Processing helix chain 'D' and resid 4926 through 4957 Processing helix chain 'D' and resid 4964 through 4969 removed outlier: 3.895A 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 5037 removed outlier: 5.845A pdb=" N ASP D5034 " --> pdb=" O LYS D5030 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN D5035 " --> pdb=" O GLN D5031 " (cutoff:3.500A) 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 1396 hydrogen bonds defined for protein. 4068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.11 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6484 1.34 - 1.46: 4196 1.46 - 1.57: 10088 1.57 - 1.69: 4 1.69 - 1.81: 276 Bond restraints: 21048 Sorted by residual: bond pdb=" C4 AMP C5101 " pdb=" C5 AMP C5101 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 AMP D5101 " pdb=" C5 AMP D5101 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 AMP A5101 " pdb=" C5 AMP A5101 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 AMP B5101 " pdb=" C5 AMP B5101 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C5 AMP A5101 " pdb=" C6 AMP A5101 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.81e+01 ... (remaining 21043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 28152 2.29 - 4.58: 200 4.58 - 6.87: 32 6.87 - 9.16: 24 9.16 - 11.44: 8 Bond angle restraints: 28416 Sorted by residual: angle pdb=" C LYS D4665 " pdb=" N VAL D4666 " pdb=" CA VAL D4666 " ideal model delta sigma weight residual 120.24 122.66 -2.42 6.30e-01 2.52e+00 1.47e+01 angle pdb=" C LYS C4665 " pdb=" N VAL C4666 " pdb=" CA VAL C4666 " ideal model delta sigma weight residual 120.24 122.66 -2.42 6.30e-01 2.52e+00 1.47e+01 angle pdb=" C LYS A4665 " pdb=" N VAL A4666 " pdb=" CA VAL A4666 " ideal model delta sigma weight residual 120.24 122.66 -2.42 6.30e-01 2.52e+00 1.47e+01 angle pdb=" C LYS B4665 " pdb=" N VAL B4666 " pdb=" CA VAL B4666 " ideal model delta sigma weight residual 120.24 122.66 -2.42 6.30e-01 2.52e+00 1.47e+01 angle pdb=" C1' AMP D5101 " pdb=" C2' AMP D5101 " pdb=" C3' AMP D5101 " ideal model delta sigma weight residual 111.00 99.56 11.44 3.00e+00 1.11e-01 1.46e+01 ... (remaining 28411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.78: 12100 30.78 - 61.57: 280 61.57 - 92.35: 8 92.35 - 123.13: 0 123.13 - 153.92: 4 Dihedral angle restraints: 12392 sinusoidal: 5080 harmonic: 7312 Sorted by residual: dihedral pdb=" C2' AMP C5101 " pdb=" C1' AMP C5101 " pdb=" N9 AMP C5101 " pdb=" C4 AMP C5101 " ideal model delta sinusoidal sigma weight residual 91.55 -62.36 153.92 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" C2' AMP B5101 " pdb=" C1' AMP B5101 " pdb=" N9 AMP B5101 " pdb=" C4 AMP B5101 " ideal model delta sinusoidal sigma weight residual 91.55 -62.36 153.92 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" C2' AMP A5101 " pdb=" C1' AMP A5101 " pdb=" N9 AMP A5101 " pdb=" C4 AMP A5101 " ideal model delta sinusoidal sigma weight residual 91.55 -62.36 153.92 1 2.00e+01 2.50e-03 4.56e+01 ... (remaining 12389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2008 0.036 - 0.073: 900 0.073 - 0.109: 140 0.109 - 0.145: 24 0.145 - 0.182: 8 Chirality restraints: 3080 Sorted by residual: chirality pdb=" C3' AMP D5101 " pdb=" C2' AMP D5101 " pdb=" C4' AMP D5101 " pdb=" O3' AMP D5101 " both_signs ideal model delta sigma weight residual False -2.51 -2.69 0.18 2.00e-01 2.50e+01 8.26e-01 chirality pdb=" C3' AMP C5101 " pdb=" C2' AMP C5101 " pdb=" C4' AMP C5101 " pdb=" O3' AMP C5101 " both_signs ideal model delta sigma weight residual False -2.51 -2.69 0.18 2.00e-01 2.50e+01 8.26e-01 chirality pdb=" C3' AMP A5101 " pdb=" C2' AMP A5101 " pdb=" C4' AMP A5101 " pdb=" O3' AMP A5101 " both_signs ideal model delta sigma weight residual False -2.51 -2.69 0.18 2.00e-01 2.50e+01 8.26e-01 ... (remaining 3077 not shown) Planarity restraints: 3592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A3971 " 0.083 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO A3972 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO A3972 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO A3972 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B3971 " 0.083 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO B3972 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO B3972 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO B3972 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C3971 " -0.083 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO C3972 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO C3972 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO C3972 " -0.065 5.00e-02 4.00e+02 ... (remaining 3589 not shown) Histogram of nonbonded interaction distances: 0.42 - 1.31: 16 1.31 - 2.21: 28 2.21 - 3.11: 15256 3.11 - 4.00: 54528 4.00 - 4.90: 101440 Warning: very small nonbonded interaction distances. Nonbonded interactions: 171268 Sorted by model distance: nonbonded pdb=" NH2 ARG A4944 " pdb=" OD1 ASP B4938 " model vdw 0.419 3.120 nonbonded pdb=" NH2 ARG B4944 " pdb=" OD1 ASP C4938 " model vdw 0.419 3.120 nonbonded pdb=" OD1 ASP A4938 " pdb=" NH2 ARG D4944 " model vdw 0.419 3.120 nonbonded pdb=" NH2 ARG C4944 " pdb=" OD1 ASP D4938 " model vdw 0.419 3.120 nonbonded pdb=" NH2 ARG A4944 " pdb=" CG ASP B4938 " model vdw 1.035 3.350 ... (remaining 171263 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 19.070 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 : 0.005 0.110 21068 Z= 0.230 Angle : 0.605 11.445 28432 Z= 0.300 Chirality : 0.039 0.182 3080 Planarity : 0.005 0.126 3592 Dihedral : 12.773 153.916 7668 Min Nonbonded Distance : 0.419 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.76 % Favored : 97.08 % Rotamer: Outliers : 2.15 % Allowed : 6.45 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.17), residues: 2464 helix: 1.56 (0.12), residues: 1664 sheet: -0.11 (0.54), residues: 104 loop : 0.20 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D4673 TYR 0.017 0.002 TYR D4994 PHE 0.020 0.002 PHE D4916 TRP 0.011 0.002 TRP A4716 HIS 0.003 0.001 HIS C4650 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.23 (21048) covalent geometry : angle 0.59330 / 0.30 (28416) SS BOND : bond 0.00093 / 0.05 ( 4) SS BOND : angle 1.26743 / 0.85 ( 8) hydrogen bonds : bond 0.15115 / 10.30 ( 1396) hydrogen bonds : angle 5.18237 / 3.75 ( 4068) metal coordination : bond 0.00711 / 0.44 ( 16) metal coordination : angle 7.00607 / 4.70 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 392 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4047 MET cc_start: 0.6927 (tmm) cc_final: 0.6382 (tmm) REVERT: A 4580 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.6265 (t80) REVERT: A 4629 TYR cc_start: 0.7423 (m-80) cc_final: 0.7091 (m-80) REVERT: A 4949 GLN cc_start: 0.8113 (tp40) cc_final: 0.7647 (mp10) REVERT: A 5006 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7461 (pt0) REVERT: A 5030 LYS cc_start: 0.8295 (ttmt) cc_final: 0.7527 (ttpt) REVERT: B 4047 MET cc_start: 0.6926 (tmm) cc_final: 0.6382 (tmm) REVERT: B 4580 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.6263 (t80) REVERT: B 4629 TYR cc_start: 0.7419 (m-80) cc_final: 0.7089 (m-80) REVERT: B 4949 GLN cc_start: 0.8112 (tp40) cc_final: 0.7646 (mp10) REVERT: B 5006 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7459 (pt0) REVERT: B 5030 LYS cc_start: 0.8302 (ttmt) cc_final: 0.7532 (ttpt) REVERT: C 4047 MET cc_start: 0.6927 (tmm) cc_final: 0.6380 (tmm) REVERT: C 4580 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.6269 (t80) REVERT: C 4629 TYR cc_start: 0.7422 (m-80) cc_final: 0.7093 (m-80) REVERT: C 4949 GLN cc_start: 0.8110 (tp40) cc_final: 0.7646 (mp10) REVERT: C 5006 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7458 (pt0) REVERT: C 5030 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7528 (ttpt) REVERT: D 4047 MET cc_start: 0.6924 (tmm) cc_final: 0.6380 (tmm) REVERT: D 4580 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.6266 (t80) REVERT: D 4629 TYR cc_start: 0.7426 (m-80) cc_final: 0.7095 (m-80) REVERT: D 4949 GLN cc_start: 0.8113 (tp40) cc_final: 0.7650 (mp10) REVERT: D 5006 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7456 (pt0) REVERT: D 5030 LYS cc_start: 0.8293 (ttmt) cc_final: 0.7528 (ttpt) outliers start: 48 outliers final: 24 residues processed: 436 average time/residue: 0.5841 time to fit residues: 287.6237 Evaluate side-chains 332 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 300 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 5004 THR Chi-restraints excluded: chain A residue 5006 GLN Chi-restraints excluded: chain A residue 5034 ASP Chi-restraints excluded: chain B residue 4027 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 5004 THR Chi-restraints excluded: chain B residue 5006 GLN Chi-restraints excluded: chain B residue 5034 ASP Chi-restraints excluded: chain C residue 4027 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 5004 THR Chi-restraints excluded: chain C residue 5006 GLN Chi-restraints excluded: chain C residue 5034 ASP Chi-restraints excluded: chain D residue 4027 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 5004 THR Chi-restraints excluded: chain D residue 5006 GLN Chi-restraints excluded: chain D residue 5034 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.0050 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3963 ASN A3978 GLN A4020 GLN A4997 ASN B3963 ASN B3978 GLN B4020 GLN B4997 ASN C3963 ASN C3978 GLN C4020 GLN C4997 ASN D3963 ASN D3978 GLN D4020 GLN D4997 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.176608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.141929 restraints weight = 23375.300| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.62 r_work: 0.3251 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21068 Z= 0.195 Angle : 0.600 8.402 28432 Z= 0.308 Chirality : 0.041 0.173 3080 Planarity : 0.006 0.126 3592 Dihedral : 8.314 153.338 2784 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.60 % Favored : 97.24 % Rotamer: Outliers : 4.12 % Allowed : 11.47 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.16), residues: 2464 helix: 1.66 (0.12), residues: 1700 sheet: -0.66 (0.49), residues: 104 loop : 0.15 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B4188 TYR 0.017 0.002 TYR C4687 PHE 0.020 0.002 PHE B4916 TRP 0.010 0.002 TRP B4716 HIS 0.004 0.001 HIS A3998 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (21048) covalent geometry : angle 0.59363 / 0.31 (28416) SS BOND : bond 0.00027 / 0.01 ( 4) SS BOND : angle 1.57833 / 1.07 ( 8) hydrogen bonds : bond 0.05252 / 3.49 ( 1396) hydrogen bonds : angle 4.43436 / 3.21 ( 4068) metal coordination : bond 0.01253 / 0.70 ( 16) metal coordination : angle 5.11526 / 3.50 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 324 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4022 ASP cc_start: 0.6949 (m-30) cc_final: 0.6621 (m-30) REVERT: A 4047 MET cc_start: 0.6579 (tmm) cc_final: 0.5843 (tmm) REVERT: A 4580 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.6810 (t80) REVERT: A 4933 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7812 (mt0) REVERT: A 5006 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7530 (pt0) REVERT: A 5030 LYS cc_start: 0.8439 (ttmt) cc_final: 0.7689 (ttpt) REVERT: B 4022 ASP cc_start: 0.6925 (m-30) cc_final: 0.6570 (m-30) REVERT: B 4047 MET cc_start: 0.6570 (tmm) cc_final: 0.5835 (tmm) REVERT: B 4580 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.6815 (t80) REVERT: B 4933 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7783 (mt0) REVERT: B 5006 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7523 (pt0) REVERT: B 5030 LYS cc_start: 0.8454 (ttmt) cc_final: 0.7702 (ttpt) REVERT: C 4022 ASP cc_start: 0.6916 (m-30) cc_final: 0.6564 (m-30) REVERT: C 4047 MET cc_start: 0.6571 (tmm) cc_final: 0.5840 (tmm) REVERT: C 4580 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.6815 (t80) REVERT: C 4933 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7790 (mt0) REVERT: C 5006 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7586 (pt0) REVERT: C 5030 LYS cc_start: 0.8444 (ttmt) cc_final: 0.7698 (ttpt) REVERT: D 4022 ASP cc_start: 0.6939 (m-30) cc_final: 0.6588 (m-30) REVERT: D 4047 MET cc_start: 0.6569 (tmm) cc_final: 0.5834 (tmm) REVERT: D 4580 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.6804 (t80) REVERT: D 4933 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7804 (mt0) REVERT: D 5006 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7529 (pt0) REVERT: D 5030 LYS cc_start: 0.8447 (ttmt) cc_final: 0.7704 (ttpt) outliers start: 92 outliers final: 40 residues processed: 380 average time/residue: 0.5871 time to fit residues: 253.3680 Evaluate side-chains 352 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 300 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4951 LYS Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4953 ASP Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5006 GLN Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4951 LYS Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4953 ASP Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5006 GLN Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4951 LYS Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4953 ASP Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5006 GLN Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4951 LYS Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4953 ASP Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5006 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 46 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 224 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A5031 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.177928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.142796 restraints weight = 23485.060| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.45 r_work: 0.3291 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21068 Z= 0.139 Angle : 0.530 7.555 28432 Z= 0.269 Chirality : 0.038 0.175 3080 Planarity : 0.005 0.121 3592 Dihedral : 7.756 151.108 2764 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.60 % Favored : 97.24 % Rotamer: Outliers : 3.94 % Allowed : 14.11 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.17), residues: 2464 helix: 2.11 (0.12), residues: 1680 sheet: -0.93 (0.49), residues: 104 loop : 0.10 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D4188 TYR 0.014 0.001 TYR C5032 PHE 0.016 0.001 PHE D4916 TRP 0.012 0.002 TRP B5011 HIS 0.003 0.001 HIS A4886 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (21048) covalent geometry : angle 0.52335 / 0.27 (28416) SS BOND : bond 0.00022 / 0.01 ( 4) SS BOND : angle 1.23988 / 0.85 ( 8) hydrogen bonds : bond 0.04479 / 2.98 ( 1396) hydrogen bonds : angle 4.16720 / 3.01 ( 4068) metal coordination : bond 0.00492 / 0.28 ( 16) metal coordination : angle 4.84440 / 3.32 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 320 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4022 ASP cc_start: 0.6701 (m-30) cc_final: 0.6464 (m-30) REVERT: A 4047 MET cc_start: 0.6587 (tmm) cc_final: 0.5923 (tmm) REVERT: A 4188 ARG cc_start: 0.7986 (mmm160) cc_final: 0.7187 (tpt170) REVERT: A 4580 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.6655 (t80) REVERT: A 4639 MET cc_start: 0.8166 (mmm) cc_final: 0.7621 (mtm) REVERT: A 4821 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7817 (mmtp) REVERT: A 4844 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8479 (tp) REVERT: A 4933 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7720 (mt0) REVERT: A 5030 LYS cc_start: 0.8360 (ttmt) cc_final: 0.7879 (ttmt) REVERT: B 4022 ASP cc_start: 0.6702 (m-30) cc_final: 0.6463 (m-30) REVERT: B 4047 MET cc_start: 0.6595 (tmm) cc_final: 0.5932 (tmm) REVERT: B 4188 ARG cc_start: 0.7975 (mmm160) cc_final: 0.7175 (tpt170) REVERT: B 4580 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.6650 (t80) REVERT: B 4639 MET cc_start: 0.8176 (mmm) cc_final: 0.7628 (mtm) REVERT: B 4821 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7804 (mmtp) REVERT: B 4844 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8482 (tp) REVERT: B 4933 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7716 (mt0) REVERT: B 5030 LYS cc_start: 0.8372 (ttmt) cc_final: 0.7894 (ttmt) REVERT: C 4022 ASP cc_start: 0.6701 (m-30) cc_final: 0.6461 (m-30) REVERT: C 4047 MET cc_start: 0.6592 (tmm) cc_final: 0.5929 (tmm) REVERT: C 4188 ARG cc_start: 0.7974 (mmm160) cc_final: 0.7175 (tpt170) REVERT: C 4580 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.6650 (t80) REVERT: C 4639 MET cc_start: 0.8177 (mmm) cc_final: 0.7632 (mtm) REVERT: C 4821 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7794 (mmtp) REVERT: C 4844 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8486 (tp) REVERT: C 4933 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7715 (mt0) REVERT: C 5030 LYS cc_start: 0.8366 (ttmt) cc_final: 0.7891 (ttmt) REVERT: D 4022 ASP cc_start: 0.6710 (m-30) cc_final: 0.6471 (m-30) REVERT: D 4047 MET cc_start: 0.6594 (tmm) cc_final: 0.5927 (tmm) REVERT: D 4188 ARG cc_start: 0.7991 (mmm160) cc_final: 0.7187 (tpt170) REVERT: D 4580 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.6638 (t80) REVERT: D 4639 MET cc_start: 0.8176 (mmm) cc_final: 0.7627 (mtm) REVERT: D 4821 LYS cc_start: 0.8268 (mmtt) cc_final: 0.7810 (mmtp) REVERT: D 4844 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8480 (tp) REVERT: D 4933 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7727 (mt0) REVERT: D 5030 LYS cc_start: 0.8355 (ttmt) cc_final: 0.7880 (ttmt) outliers start: 88 outliers final: 36 residues processed: 376 average time/residue: 0.5917 time to fit residues: 253.7869 Evaluate side-chains 336 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 288 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4737 ILE Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4951 LYS Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4953 ASP Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain B residue 4221 VAL Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4951 LYS Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4953 ASP Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain C residue 4221 VAL Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4951 LYS Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4953 ASP Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4951 LYS Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4953 ASP Chi-restraints excluded: chain D residue 4980 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 128 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 213 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 242 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3963 ASN A3998 HIS B3998 HIS ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3998 HIS ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3998 HIS ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.177919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.140694 restraints weight = 23655.408| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.77 r_work: 0.3257 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21068 Z= 0.143 Angle : 0.523 7.118 28432 Z= 0.266 Chirality : 0.037 0.173 3080 Planarity : 0.005 0.118 3592 Dihedral : 7.546 149.436 2748 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.11 % Favored : 97.73 % Rotamer: Outliers : 4.48 % Allowed : 14.52 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.17), residues: 2464 helix: 2.18 (0.12), residues: 1680 sheet: -1.07 (0.49), residues: 104 loop : 0.03 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A4189 TYR 0.013 0.001 TYR A4687 PHE 0.017 0.001 PHE C4916 TRP 0.008 0.001 TRP B4716 HIS 0.003 0.001 HIS D4803 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (21048) covalent geometry : angle 0.51766 / 0.27 (28416) SS BOND : bond 0.00012 / 0.01 ( 4) SS BOND : angle 1.34454 / 0.91 ( 8) hydrogen bonds : bond 0.04329 / 2.87 ( 1396) hydrogen bonds : angle 4.18384 / 3.03 ( 4068) metal coordination : bond 0.00457 / 0.26 ( 16) metal coordination : angle 4.46268 / 3.10 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 312 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4047 MET cc_start: 0.6549 (tmm) cc_final: 0.5872 (tmm) REVERT: A 4188 ARG cc_start: 0.8104 (mmm160) cc_final: 0.7282 (tpt170) REVERT: A 4207 MET cc_start: 0.8487 (mmm) cc_final: 0.8256 (mtp) REVERT: A 4580 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.6677 (t80) REVERT: A 4639 MET cc_start: 0.8184 (mmm) cc_final: 0.7629 (mtm) REVERT: A 4725 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6611 (tp) REVERT: A 4844 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8501 (tp) REVERT: A 4933 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7938 (mp10) REVERT: A 4956 THR cc_start: 0.8906 (p) cc_final: 0.8693 (p) REVERT: B 4022 ASP cc_start: 0.6495 (m-30) cc_final: 0.6246 (m-30) REVERT: B 4047 MET cc_start: 0.6552 (tmm) cc_final: 0.5872 (tmm) REVERT: B 4188 ARG cc_start: 0.8097 (mmm160) cc_final: 0.7273 (tpt170) REVERT: B 4207 MET cc_start: 0.8498 (mmm) cc_final: 0.8268 (mtp) REVERT: B 4580 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.6672 (t80) REVERT: B 4639 MET cc_start: 0.8185 (mmm) cc_final: 0.7626 (mtm) REVERT: B 4725 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6599 (tp) REVERT: B 4821 LYS cc_start: 0.8279 (mmtt) cc_final: 0.8075 (mmmt) REVERT: B 4844 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8501 (tp) REVERT: B 4933 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7940 (mp10) REVERT: B 4956 THR cc_start: 0.8901 (p) cc_final: 0.8691 (p) REVERT: C 4022 ASP cc_start: 0.6498 (m-30) cc_final: 0.6250 (m-30) REVERT: C 4047 MET cc_start: 0.6554 (tmm) cc_final: 0.5878 (tmm) REVERT: C 4188 ARG cc_start: 0.8096 (mmm160) cc_final: 0.7271 (tpt170) REVERT: C 4207 MET cc_start: 0.8488 (mmm) cc_final: 0.8254 (mtp) REVERT: C 4580 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.6669 (t80) REVERT: C 4639 MET cc_start: 0.8199 (mmm) cc_final: 0.7647 (mtm) REVERT: C 4725 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6598 (tp) REVERT: C 4821 LYS cc_start: 0.8277 (mmtt) cc_final: 0.8067 (mmmt) REVERT: C 4844 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8504 (tp) REVERT: C 4933 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7928 (mp10) REVERT: C 4956 THR cc_start: 0.8898 (p) cc_final: 0.8685 (p) REVERT: D 4022 ASP cc_start: 0.6516 (m-30) cc_final: 0.6271 (m-30) REVERT: D 4047 MET cc_start: 0.6548 (tmm) cc_final: 0.5867 (tmm) REVERT: D 4188 ARG cc_start: 0.8106 (mmm160) cc_final: 0.7280 (tpt170) REVERT: D 4207 MET cc_start: 0.8502 (mmm) cc_final: 0.8272 (mtp) REVERT: D 4580 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.6660 (t80) REVERT: D 4639 MET cc_start: 0.8194 (mmm) cc_final: 0.7639 (mtm) REVERT: D 4725 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6596 (tp) REVERT: D 4821 LYS cc_start: 0.8277 (mmtt) cc_final: 0.8072 (mmmt) REVERT: D 4844 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8501 (tp) REVERT: D 4933 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7938 (mp10) REVERT: D 4956 THR cc_start: 0.8907 (p) cc_final: 0.8694 (p) outliers start: 100 outliers final: 48 residues processed: 384 average time/residue: 0.5644 time to fit residues: 248.3434 Evaluate side-chains 355 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 291 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4036 VAL Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4676 GLU Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4725 LEU Chi-restraints excluded: chain A residue 4737 ILE Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4953 ASP Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5004 THR Chi-restraints excluded: chain B residue 4036 VAL Chi-restraints excluded: chain B residue 4221 VAL Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4676 GLU Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4725 LEU Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4953 ASP Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5004 THR Chi-restraints excluded: chain C residue 4036 VAL Chi-restraints excluded: chain C residue 4221 VAL Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4676 GLU Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4725 LEU Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4953 ASP Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5004 THR Chi-restraints excluded: chain D residue 4036 VAL Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4676 GLU Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4953 ASP Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5004 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 208 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 212 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.177616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.139528 restraints weight = 23492.474| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.52 r_work: 0.3253 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21068 Z= 0.154 Angle : 0.533 6.752 28432 Z= 0.270 Chirality : 0.038 0.175 3080 Planarity : 0.005 0.115 3592 Dihedral : 7.484 147.919 2748 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.44 % Favored : 97.40 % Rotamer: Outliers : 4.84 % Allowed : 15.05 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.17), residues: 2464 helix: 2.14 (0.12), residues: 1680 sheet: -1.22 (0.47), residues: 104 loop : 0.04 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D4189 TYR 0.013 0.001 TYR D4994 PHE 0.017 0.002 PHE B4916 TRP 0.008 0.001 TRP B4716 HIS 0.003 0.001 HIS A4803 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (21048) covalent geometry : angle 0.52699 / 0.27 (28416) SS BOND : bond 0.00018 / 0.01 ( 4) SS BOND : angle 1.43410 / 0.97 ( 8) hydrogen bonds : bond 0.04338 / 2.87 ( 1396) hydrogen bonds : angle 4.17625 / 3.02 ( 4068) metal coordination : bond 0.00531 / 0.31 ( 16) metal coordination : angle 4.47075 / 3.13 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 299 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4000 MET cc_start: 0.4573 (tpt) cc_final: 0.3926 (mmm) REVERT: A 4047 MET cc_start: 0.6510 (tmm) cc_final: 0.5833 (tmm) REVERT: A 4188 ARG cc_start: 0.8089 (mmm160) cc_final: 0.7227 (tpt170) REVERT: A 4199 GLU cc_start: 0.7806 (mp0) cc_final: 0.7571 (tm-30) REVERT: A 4223 ASN cc_start: 0.8276 (t0) cc_final: 0.7956 (t0) REVERT: A 4580 TYR cc_start: 0.8729 (OUTLIER) cc_final: 0.6551 (t80) REVERT: A 4725 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6451 (tp) REVERT: A 4821 LYS cc_start: 0.8277 (mmmt) cc_final: 0.8024 (mmmm) REVERT: A 4844 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8427 (tp) REVERT: A 4933 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7812 (mp10) REVERT: A 5006 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7425 (pt0) REVERT: B 4000 MET cc_start: 0.4567 (tpt) cc_final: 0.3924 (mmm) REVERT: B 4022 ASP cc_start: 0.6419 (m-30) cc_final: 0.6161 (m-30) REVERT: B 4047 MET cc_start: 0.6509 (tmm) cc_final: 0.5851 (tmm) REVERT: B 4188 ARG cc_start: 0.8087 (mmm160) cc_final: 0.7223 (tpt170) REVERT: B 4199 GLU cc_start: 0.7806 (mp0) cc_final: 0.7567 (tm-30) REVERT: B 4223 ASN cc_start: 0.8276 (t0) cc_final: 0.7956 (t0) REVERT: B 4580 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.6532 (t80) REVERT: B 4725 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6449 (tp) REVERT: B 4821 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7965 (mmmt) REVERT: B 4844 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8425 (tp) REVERT: B 4933 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7824 (mp10) REVERT: B 5006 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7424 (pt0) REVERT: C 4000 MET cc_start: 0.4575 (tpt) cc_final: 0.3926 (mmm) REVERT: C 4022 ASP cc_start: 0.6431 (m-30) cc_final: 0.6175 (m-30) REVERT: C 4047 MET cc_start: 0.6511 (tmm) cc_final: 0.5855 (tmm) REVERT: C 4188 ARG cc_start: 0.8079 (mmm160) cc_final: 0.7218 (tpt170) REVERT: C 4199 GLU cc_start: 0.7824 (mp0) cc_final: 0.7583 (tm-30) REVERT: C 4223 ASN cc_start: 0.8268 (t0) cc_final: 0.7947 (t0) REVERT: C 4580 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.6542 (t80) REVERT: C 4725 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6429 (tp) REVERT: C 4821 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7962 (mmmt) REVERT: C 4844 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8428 (tp) REVERT: C 4933 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7811 (mp10) REVERT: C 5006 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: D 4000 MET cc_start: 0.4568 (tpt) cc_final: 0.3923 (mmm) REVERT: D 4022 ASP cc_start: 0.6439 (m-30) cc_final: 0.6184 (m-30) REVERT: D 4047 MET cc_start: 0.6511 (tmm) cc_final: 0.5853 (tmm) REVERT: D 4188 ARG cc_start: 0.8085 (mmm160) cc_final: 0.7225 (tpt170) REVERT: D 4199 GLU cc_start: 0.7823 (mp0) cc_final: 0.7592 (tm-30) REVERT: D 4223 ASN cc_start: 0.8265 (t0) cc_final: 0.7942 (t0) REVERT: D 4580 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.6528 (t80) REVERT: D 4725 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6443 (tp) REVERT: D 4821 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7965 (mmmt) REVERT: D 4844 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8428 (tp) REVERT: D 4933 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7812 (mp10) REVERT: D 5006 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7423 (pt0) outliers start: 108 outliers final: 56 residues processed: 371 average time/residue: 0.5562 time to fit residues: 236.9725 Evaluate side-chains 367 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 291 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4036 VAL Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4676 GLU Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4725 LEU Chi-restraints excluded: chain A residue 4737 ILE Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4951 LYS Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4953 ASP Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5004 THR Chi-restraints excluded: chain A residue 5006 GLN Chi-restraints excluded: chain B residue 4036 VAL Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4221 VAL Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4676 GLU Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4725 LEU Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4951 LYS Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4953 ASP Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5004 THR Chi-restraints excluded: chain B residue 5006 GLN Chi-restraints excluded: chain C residue 4036 VAL Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4221 VAL Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4676 GLU Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4725 LEU Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4951 LYS Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4953 ASP Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5004 THR Chi-restraints excluded: chain C residue 5006 GLN Chi-restraints excluded: chain D residue 4036 VAL Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4676 GLU Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4951 LYS Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4953 ASP Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5004 THR Chi-restraints excluded: chain D residue 5006 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 102 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 178 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 154 optimal weight: 0.0070 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B3963 ASN B5031 GLN C3963 ASN C5031 GLN D3963 ASN D5031 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.178736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.141773 restraints weight = 23464.257| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.46 r_work: 0.3296 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21068 Z= 0.120 Angle : 0.502 6.147 28432 Z= 0.255 Chirality : 0.036 0.179 3080 Planarity : 0.005 0.111 3592 Dihedral : 7.361 146.331 2748 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.23 % Favored : 97.61 % Rotamer: Outliers : 4.12 % Allowed : 16.44 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.17), residues: 2464 helix: 2.33 (0.12), residues: 1680 sheet: -1.13 (0.49), residues: 104 loop : 0.10 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B4189 TYR 0.011 0.001 TYR A4994 PHE 0.015 0.001 PHE B4916 TRP 0.008 0.001 TRP D4716 HIS 0.003 0.001 HIS A3998 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (21048) covalent geometry : angle 0.49716 / 0.25 (28416) SS BOND : bond 0.00016 / 0.01 ( 4) SS BOND : angle 1.16671 / 0.80 ( 8) hydrogen bonds : bond 0.03995 / 2.65 ( 1396) hydrogen bonds : angle 4.09047 / 2.96 ( 4068) metal coordination : bond 0.00266 / 0.16 ( 16) metal coordination : angle 4.04031 / 2.82 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 299 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4000 MET cc_start: 0.4631 (tpt) cc_final: 0.3976 (mmm) REVERT: A 4047 MET cc_start: 0.6441 (tmm) cc_final: 0.5777 (tmm) REVERT: A 4188 ARG cc_start: 0.8077 (mmm160) cc_final: 0.7224 (tpt170) REVERT: A 4207 MET cc_start: 0.8260 (mmm) cc_final: 0.8033 (mtp) REVERT: A 4580 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.6565 (t80) REVERT: A 4725 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6253 (tp) REVERT: A 4735 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6431 (pm20) REVERT: A 4821 LYS cc_start: 0.8105 (mmmt) cc_final: 0.7802 (mmmm) REVERT: A 4844 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8376 (tp) REVERT: A 4933 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7791 (mp10) REVERT: B 4000 MET cc_start: 0.4629 (tpt) cc_final: 0.3975 (mmm) REVERT: B 4020 GLN cc_start: 0.7018 (tt0) cc_final: 0.6748 (tp40) REVERT: B 4047 MET cc_start: 0.6430 (tmm) cc_final: 0.5767 (tmm) REVERT: B 4188 ARG cc_start: 0.8076 (mmm160) cc_final: 0.7220 (tpt170) REVERT: B 4207 MET cc_start: 0.8273 (mmm) cc_final: 0.8050 (mtp) REVERT: B 4580 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.6554 (t80) REVERT: B 4725 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6246 (tp) REVERT: B 4735 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6426 (pm20) REVERT: B 4821 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7949 (mmmt) REVERT: B 4844 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8385 (tp) REVERT: B 4933 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7793 (mp10) REVERT: C 4000 MET cc_start: 0.4635 (tpt) cc_final: 0.3978 (mmm) REVERT: C 4020 GLN cc_start: 0.7020 (tt0) cc_final: 0.6751 (tp40) REVERT: C 4047 MET cc_start: 0.6438 (tmm) cc_final: 0.5776 (tmm) REVERT: C 4188 ARG cc_start: 0.8071 (mmm160) cc_final: 0.7222 (tpt170) REVERT: C 4207 MET cc_start: 0.8261 (mmm) cc_final: 0.8031 (mtp) REVERT: C 4580 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.6549 (t80) REVERT: C 4725 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6236 (tp) REVERT: C 4735 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6432 (pm20) REVERT: C 4821 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7956 (mmmt) REVERT: C 4844 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8381 (tp) REVERT: C 4933 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7785 (mp10) REVERT: D 4000 MET cc_start: 0.4627 (tpt) cc_final: 0.3971 (mmm) REVERT: D 4020 GLN cc_start: 0.7022 (tt0) cc_final: 0.6750 (tp40) REVERT: D 4047 MET cc_start: 0.6440 (tmm) cc_final: 0.5775 (tmm) REVERT: D 4188 ARG cc_start: 0.8073 (mmm160) cc_final: 0.7224 (tpt170) REVERT: D 4207 MET cc_start: 0.8267 (mmm) cc_final: 0.8042 (mtp) REVERT: D 4580 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.6549 (t80) REVERT: D 4725 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.6236 (tp) REVERT: D 4735 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6431 (pm20) REVERT: D 4821 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7954 (mmmt) REVERT: D 4844 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8376 (tp) REVERT: D 4933 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7791 (mp10) outliers start: 92 outliers final: 48 residues processed: 371 average time/residue: 0.5854 time to fit residues: 247.1072 Evaluate side-chains 339 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 275 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4036 VAL Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4676 GLU Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4725 LEU Chi-restraints excluded: chain A residue 4737 ILE Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4951 LYS Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4953 ASP Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain B residue 4036 VAL Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4221 VAL Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4676 GLU Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4725 LEU Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4951 LYS Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4953 ASP Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain C residue 4036 VAL Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4221 VAL Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4676 GLU Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4725 LEU Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4951 LYS Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4953 ASP Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain D residue 4036 VAL Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4676 GLU Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4951 LYS Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4953 ASP Chi-restraints excluded: chain D residue 4980 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 207 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 101 optimal weight: 0.0980 chunk 200 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 206 optimal weight: 0.9990 chunk 188 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.178911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.140594 restraints weight = 23578.427| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.58 r_work: 0.3263 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21068 Z= 0.122 Angle : 0.515 7.365 28432 Z= 0.259 Chirality : 0.036 0.180 3080 Planarity : 0.005 0.108 3592 Dihedral : 7.300 145.306 2748 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.56 % Rotamer: Outliers : 3.58 % Allowed : 17.43 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.17), residues: 2464 helix: 2.39 (0.12), residues: 1680 sheet: -1.20 (0.48), residues: 104 loop : 0.13 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A4189 TYR 0.010 0.001 TYR A4994 PHE 0.015 0.001 PHE D4916 TRP 0.007 0.001 TRP B5011 HIS 0.003 0.001 HIS A3998 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (21048) covalent geometry : angle 0.51014 / 0.26 (28416) SS BOND : bond 0.00036 / 0.02 ( 4) SS BOND : angle 1.14938 / 0.78 ( 8) hydrogen bonds : bond 0.03929 / 2.60 ( 1396) hydrogen bonds : angle 4.06019 / 2.94 ( 4068) metal coordination : bond 0.00246 / 0.15 ( 16) metal coordination : angle 3.94214 / 2.74 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 287 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4000 MET cc_start: 0.4542 (tpt) cc_final: 0.3832 (mmm) REVERT: A 4020 GLN cc_start: 0.7017 (tt0) cc_final: 0.6745 (tp40) REVERT: A 4047 MET cc_start: 0.6558 (tmm) cc_final: 0.5870 (tmm) REVERT: A 4188 ARG cc_start: 0.8007 (mmm160) cc_final: 0.7249 (tpt170) REVERT: A 4207 MET cc_start: 0.8444 (mmm) cc_final: 0.8212 (mtp) REVERT: A 4580 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.6516 (t80) REVERT: A 4725 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6426 (tp) REVERT: A 4735 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6485 (pm20) REVERT: A 4821 LYS cc_start: 0.8080 (mmmt) cc_final: 0.7858 (mmmm) REVERT: A 4844 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8445 (tp) REVERT: B 4000 MET cc_start: 0.4542 (tpt) cc_final: 0.3832 (mmm) REVERT: B 4020 GLN cc_start: 0.7070 (tt0) cc_final: 0.6813 (tp40) REVERT: B 4047 MET cc_start: 0.6543 (tmm) cc_final: 0.5863 (tmm) REVERT: B 4188 ARG cc_start: 0.8003 (mmm160) cc_final: 0.7233 (tpt170) REVERT: B 4207 MET cc_start: 0.8456 (mmm) cc_final: 0.8224 (mtp) REVERT: B 4580 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.6518 (t80) REVERT: B 4725 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6423 (tp) REVERT: B 4735 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6479 (pm20) REVERT: B 4821 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7955 (mmmm) REVERT: B 4844 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8454 (tp) REVERT: C 4000 MET cc_start: 0.4537 (tpt) cc_final: 0.3829 (mmm) REVERT: C 4020 GLN cc_start: 0.7067 (tt0) cc_final: 0.6808 (tp40) REVERT: C 4047 MET cc_start: 0.6568 (tmm) cc_final: 0.5882 (tmm) REVERT: C 4188 ARG cc_start: 0.8006 (mmm160) cc_final: 0.7237 (tpt170) REVERT: C 4207 MET cc_start: 0.8436 (mmm) cc_final: 0.8199 (mtp) REVERT: C 4580 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.6485 (t80) REVERT: C 4725 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6419 (tp) REVERT: C 4735 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6488 (pm20) REVERT: C 4821 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7957 (mmmm) REVERT: C 4844 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8459 (tp) REVERT: D 4000 MET cc_start: 0.4535 (tpt) cc_final: 0.3823 (mmm) REVERT: D 4020 GLN cc_start: 0.7070 (tt0) cc_final: 0.6812 (tp40) REVERT: D 4047 MET cc_start: 0.6554 (tmm) cc_final: 0.5867 (tmm) REVERT: D 4188 ARG cc_start: 0.8001 (mmm160) cc_final: 0.7233 (tpt170) REVERT: D 4207 MET cc_start: 0.8441 (mmm) cc_final: 0.8204 (mtp) REVERT: D 4580 TYR cc_start: 0.8661 (OUTLIER) cc_final: 0.6513 (t80) REVERT: D 4725 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6411 (tp) REVERT: D 4735 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6476 (pm20) REVERT: D 4821 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7958 (mmmm) REVERT: D 4844 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8456 (tp) outliers start: 80 outliers final: 48 residues processed: 351 average time/residue: 0.5154 time to fit residues: 208.4426 Evaluate side-chains 347 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 287 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4030 LEU Chi-restraints excluded: chain A residue 4036 VAL Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4676 GLU Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4725 LEU Chi-restraints excluded: chain A residue 4737 ILE Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain B residue 4030 LEU Chi-restraints excluded: chain B residue 4036 VAL Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4221 VAL Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4676 GLU Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4725 LEU Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain C residue 4030 LEU Chi-restraints excluded: chain C residue 4036 VAL Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4221 VAL Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4676 GLU Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4725 LEU Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain D residue 4030 LEU Chi-restraints excluded: chain D residue 4036 VAL Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4676 GLU Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4980 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 202 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 246 optimal weight: 0.9980 chunk 174 optimal weight: 0.5980 chunk 16 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.179310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.143195 restraints weight = 23709.146| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.80 r_work: 0.3298 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21068 Z= 0.118 Angle : 0.503 6.512 28432 Z= 0.254 Chirality : 0.036 0.182 3080 Planarity : 0.005 0.106 3592 Dihedral : 7.246 144.362 2748 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.99 % Favored : 97.85 % Rotamer: Outliers : 4.48 % Allowed : 15.99 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.17), residues: 2464 helix: 2.43 (0.12), residues: 1680 sheet: -1.20 (0.49), residues: 104 loop : 0.13 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D4189 TYR 0.010 0.001 TYR B4994 PHE 0.015 0.001 PHE C4916 TRP 0.007 0.001 TRP A5011 HIS 0.003 0.001 HIS A3998 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (21048) covalent geometry : angle 0.49871 / 0.25 (28416) SS BOND : bond 0.00031 / 0.02 ( 4) SS BOND : angle 1.11068 / 0.75 ( 8) hydrogen bonds : bond 0.03849 / 2.55 ( 1396) hydrogen bonds : angle 4.03981 / 2.92 ( 4068) metal coordination : bond 0.00291 / 0.18 ( 16) metal coordination : angle 3.74941 / 2.62 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 287 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4000 MET cc_start: 0.4712 (tpt) cc_final: 0.4015 (mmm) REVERT: A 4020 GLN cc_start: 0.7062 (tt0) cc_final: 0.6813 (tp40) REVERT: A 4047 MET cc_start: 0.6535 (tmm) cc_final: 0.5844 (tmm) REVERT: A 4188 ARG cc_start: 0.8149 (mmm160) cc_final: 0.7354 (tpt170) REVERT: A 4207 MET cc_start: 0.8455 (mmm) cc_final: 0.8192 (mtp) REVERT: A 4580 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.6633 (t80) REVERT: A 4725 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6433 (tp) REVERT: A 4735 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6542 (pm20) REVERT: A 4821 LYS cc_start: 0.8150 (mmmt) cc_final: 0.7904 (mmmm) REVERT: A 4844 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8460 (tp) REVERT: A 5006 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7532 (pt0) REVERT: A 5016 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8304 (mp0) REVERT: B 4000 MET cc_start: 0.4718 (tpt) cc_final: 0.4027 (mmm) REVERT: B 4020 GLN cc_start: 0.7065 (tt0) cc_final: 0.6832 (tp40) REVERT: B 4047 MET cc_start: 0.6517 (tmm) cc_final: 0.5828 (tmm) REVERT: B 4188 ARG cc_start: 0.8121 (mmm160) cc_final: 0.7338 (tpt170) REVERT: B 4207 MET cc_start: 0.8473 (mmm) cc_final: 0.8210 (mtp) REVERT: B 4580 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.6637 (t80) REVERT: B 4725 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6441 (tp) REVERT: B 4735 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6535 (pm20) REVERT: B 4821 LYS cc_start: 0.8275 (mmtt) cc_final: 0.8004 (mmmm) REVERT: B 4844 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8468 (tp) REVERT: B 5006 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7528 (pt0) REVERT: B 5016 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8329 (mp0) REVERT: C 4000 MET cc_start: 0.4716 (tpt) cc_final: 0.4028 (mmm) REVERT: C 4020 GLN cc_start: 0.7053 (tt0) cc_final: 0.6822 (tp40) REVERT: C 4047 MET cc_start: 0.6529 (tmm) cc_final: 0.5837 (tmm) REVERT: C 4188 ARG cc_start: 0.8132 (mmm160) cc_final: 0.7349 (tpt170) REVERT: C 4207 MET cc_start: 0.8443 (mmm) cc_final: 0.8178 (mtp) REVERT: C 4580 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.6635 (t80) REVERT: C 4725 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6434 (tp) REVERT: C 4735 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6544 (pm20) REVERT: C 4821 LYS cc_start: 0.8276 (mmtt) cc_final: 0.8011 (mmmm) REVERT: C 4844 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8470 (tp) REVERT: C 5006 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7523 (pt0) REVERT: C 5016 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8311 (mp0) REVERT: D 4000 MET cc_start: 0.4715 (tpt) cc_final: 0.4016 (mmm) REVERT: D 4020 GLN cc_start: 0.7071 (tt0) cc_final: 0.6835 (tp40) REVERT: D 4047 MET cc_start: 0.6518 (tmm) cc_final: 0.5827 (tmm) REVERT: D 4188 ARG cc_start: 0.8132 (mmm160) cc_final: 0.7351 (tpt170) REVERT: D 4207 MET cc_start: 0.8462 (mmm) cc_final: 0.8197 (mtp) REVERT: D 4580 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.6628 (t80) REVERT: D 4725 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6429 (tp) REVERT: D 4735 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6547 (pm20) REVERT: D 4821 LYS cc_start: 0.8276 (mmtt) cc_final: 0.8008 (mmmm) REVERT: D 4844 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8467 (tp) REVERT: D 5006 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7523 (pt0) REVERT: D 5016 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8299 (mp0) outliers start: 100 outliers final: 44 residues processed: 359 average time/residue: 0.5666 time to fit residues: 232.8448 Evaluate side-chains 343 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 279 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4036 VAL Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4676 GLU Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4725 LEU Chi-restraints excluded: chain A residue 4737 ILE Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5004 THR Chi-restraints excluded: chain A residue 5006 GLN Chi-restraints excluded: chain A residue 5016 GLU Chi-restraints excluded: chain B residue 4036 VAL Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4221 VAL Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4676 GLU Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4725 LEU Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5004 THR Chi-restraints excluded: chain B residue 5006 GLN Chi-restraints excluded: chain B residue 5016 GLU Chi-restraints excluded: chain C residue 4036 VAL Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4221 VAL Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4676 GLU Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4725 LEU Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5004 THR Chi-restraints excluded: chain C residue 5006 GLN Chi-restraints excluded: chain C residue 5016 GLU Chi-restraints excluded: chain D residue 4036 VAL Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4676 GLU Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5004 THR Chi-restraints excluded: chain D residue 5006 GLN Chi-restraints excluded: chain D residue 5016 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 96 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 205 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.177636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.140701 restraints weight = 23573.142| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.03 r_work: 0.3238 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21068 Z= 0.158 Angle : 0.537 6.542 28432 Z= 0.271 Chirality : 0.038 0.181 3080 Planarity : 0.005 0.105 3592 Dihedral : 7.322 144.242 2748 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.03 % Favored : 97.81 % Rotamer: Outliers : 3.14 % Allowed : 17.34 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.17), residues: 2464 helix: 2.20 (0.12), residues: 1680 sheet: -1.20 (0.49), residues: 104 loop : 0.07 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C4189 TYR 0.013 0.001 TYR B4994 PHE 0.017 0.002 PHE A4916 TRP 0.010 0.001 TRP A5011 HIS 0.003 0.001 HIS B4803 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (21048) covalent geometry : angle 0.53195 / 0.27 (28416) SS BOND : bond 0.00042 / 0.02 ( 4) SS BOND : angle 1.47011 / 1.00 ( 8) hydrogen bonds : bond 0.04176 / 2.76 ( 1396) hydrogen bonds : angle 4.14901 / 3.00 ( 4068) metal coordination : bond 0.00669 / 0.39 ( 16) metal coordination : angle 4.09777 / 2.89 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 288 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4000 MET cc_start: 0.4725 (tpt) cc_final: 0.4028 (mmm) REVERT: A 4020 GLN cc_start: 0.7058 (tt0) cc_final: 0.6789 (tp40) REVERT: A 4047 MET cc_start: 0.6424 (tmm) cc_final: 0.5804 (tmm) REVERT: A 4207 MET cc_start: 0.8494 (mmm) cc_final: 0.8229 (mtp) REVERT: A 4580 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.6719 (t80) REVERT: A 4725 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6669 (tp) REVERT: A 4821 LYS cc_start: 0.8177 (mmmt) cc_final: 0.7914 (mmmm) REVERT: A 4844 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8479 (tp) REVERT: A 4933 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7179 (mt0) REVERT: A 5006 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7563 (pt0) REVERT: B 4000 MET cc_start: 0.4726 (tpt) cc_final: 0.4043 (mmm) REVERT: B 4020 GLN cc_start: 0.7072 (tt0) cc_final: 0.6803 (tp40) REVERT: B 4047 MET cc_start: 0.6404 (tmm) cc_final: 0.5782 (tmm) REVERT: B 4207 MET cc_start: 0.8507 (mmm) cc_final: 0.8246 (mtp) REVERT: B 4580 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.6724 (t80) REVERT: B 4725 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6661 (tp) REVERT: B 4844 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8515 (tp) REVERT: B 4933 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7202 (mt0) REVERT: B 5006 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7563 (pt0) REVERT: C 4000 MET cc_start: 0.4735 (tpt) cc_final: 0.4046 (mmm) REVERT: C 4020 GLN cc_start: 0.7066 (tt0) cc_final: 0.6797 (tp40) REVERT: C 4047 MET cc_start: 0.6429 (tmm) cc_final: 0.5801 (tmm) REVERT: C 4207 MET cc_start: 0.8494 (mmm) cc_final: 0.8229 (mtp) REVERT: C 4580 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.6730 (t80) REVERT: C 4725 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6665 (tp) REVERT: C 4844 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8523 (tp) REVERT: C 4933 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7193 (mt0) REVERT: C 5006 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7560 (pt0) REVERT: D 4000 MET cc_start: 0.4729 (tpt) cc_final: 0.4035 (mmm) REVERT: D 4020 GLN cc_start: 0.7069 (tt0) cc_final: 0.6799 (tp40) REVERT: D 4047 MET cc_start: 0.6421 (tmm) cc_final: 0.5794 (tmm) REVERT: D 4207 MET cc_start: 0.8517 (mmm) cc_final: 0.8255 (mtp) REVERT: D 4580 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.6726 (t80) REVERT: D 4725 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6657 (tp) REVERT: D 4844 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8481 (tp) REVERT: D 4933 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7198 (mt0) REVERT: D 5006 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7563 (pt0) outliers start: 70 outliers final: 40 residues processed: 350 average time/residue: 0.5259 time to fit residues: 211.4432 Evaluate side-chains 344 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 284 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4036 VAL Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4725 LEU Chi-restraints excluded: chain A residue 4737 ILE Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5004 THR Chi-restraints excluded: chain A residue 5006 GLN Chi-restraints excluded: chain B residue 4036 VAL Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4221 VAL Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4725 LEU Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5004 THR Chi-restraints excluded: chain B residue 5006 GLN Chi-restraints excluded: chain C residue 4036 VAL Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4221 VAL Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4725 LEU Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5004 THR Chi-restraints excluded: chain C residue 5006 GLN Chi-restraints excluded: chain D residue 4036 VAL Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5004 THR Chi-restraints excluded: chain D residue 5006 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 194 optimal weight: 0.9980 chunk 241 optimal weight: 0.0470 chunk 229 optimal weight: 0.5980 chunk 190 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 240 optimal weight: 4.9990 overall best weight: 1.1080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.177921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.142318 restraints weight = 23529.531| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.01 r_work: 0.3256 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21068 Z= 0.149 Angle : 0.548 6.713 28432 Z= 0.277 Chirality : 0.038 0.184 3080 Planarity : 0.005 0.102 3592 Dihedral : 7.334 144.025 2748 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.83 % Favored : 98.01 % Rotamer: Outliers : 3.18 % Allowed : 17.83 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.17), residues: 2464 helix: 2.17 (0.12), residues: 1680 sheet: -1.27 (0.50), residues: 104 loop : 0.04 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A4188 TYR 0.013 0.001 TYR B4994 PHE 0.017 0.001 PHE B4916 TRP 0.009 0.001 TRP B5011 HIS 0.003 0.001 HIS A4803 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (21048) covalent geometry : angle 0.54297 / 0.28 (28416) SS BOND : bond 0.00030 / 0.02 ( 4) SS BOND : angle 1.39734 / 0.95 ( 8) hydrogen bonds : bond 0.04105 / 2.72 ( 1396) hydrogen bonds : angle 4.13367 / 2.99 ( 4068) metal coordination : bond 0.00409 / 0.24 ( 16) metal coordination : angle 4.11213 / 2.89 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 294 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3967 GLU cc_start: 0.8000 (mm-30) cc_final: 0.6962 (tm-30) REVERT: A 4000 MET cc_start: 0.4474 (tpt) cc_final: 0.3822 (mmm) REVERT: A 4020 GLN cc_start: 0.7042 (tt0) cc_final: 0.6794 (tp40) REVERT: A 4047 MET cc_start: 0.6399 (tmm) cc_final: 0.5785 (tmm) REVERT: A 4188 ARG cc_start: 0.8146 (mmm160) cc_final: 0.7255 (tpt170) REVERT: A 4196 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.4592 (tp30) REVERT: A 4207 MET cc_start: 0.8473 (mmm) cc_final: 0.8201 (mtp) REVERT: A 4580 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.6690 (t80) REVERT: A 4725 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6610 (tp) REVERT: A 4735 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6395 (pm20) REVERT: A 4821 LYS cc_start: 0.8147 (mmmt) cc_final: 0.7880 (mmmm) REVERT: A 4844 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8470 (tp) REVERT: A 4933 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7143 (mt0) REVERT: A 5006 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7523 (pt0) REVERT: A 5016 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8321 (mp0) REVERT: B 3959 LYS cc_start: 0.5900 (OUTLIER) cc_final: 0.5401 (tttm) REVERT: B 3967 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7000 (tm-30) REVERT: B 4000 MET cc_start: 0.4486 (tpt) cc_final: 0.3842 (mmm) REVERT: B 4020 GLN cc_start: 0.7045 (tt0) cc_final: 0.6776 (tp40) REVERT: B 4047 MET cc_start: 0.6374 (tmm) cc_final: 0.5765 (tmm) REVERT: B 4188 ARG cc_start: 0.8138 (mmm160) cc_final: 0.7241 (tpt170) REVERT: B 4207 MET cc_start: 0.8488 (mmm) cc_final: 0.8219 (mtp) REVERT: B 4580 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.6698 (t80) REVERT: B 4725 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6604 (tp) REVERT: B 4735 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6394 (pm20) REVERT: B 4844 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8504 (tp) REVERT: B 4933 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7157 (mt0) REVERT: B 5006 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7522 (pt0) REVERT: B 5016 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8336 (mp0) REVERT: C 3959 LYS cc_start: 0.5913 (OUTLIER) cc_final: 0.5415 (tttm) REVERT: C 3967 GLU cc_start: 0.8018 (mm-30) cc_final: 0.6996 (tm-30) REVERT: C 4000 MET cc_start: 0.4492 (tpt) cc_final: 0.3840 (mmm) REVERT: C 4020 GLN cc_start: 0.7038 (tt0) cc_final: 0.6769 (tp40) REVERT: C 4047 MET cc_start: 0.6397 (tmm) cc_final: 0.5782 (tmm) REVERT: C 4188 ARG cc_start: 0.8171 (mmm160) cc_final: 0.7281 (tpt170) REVERT: C 4196 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.4315 (tp30) REVERT: C 4207 MET cc_start: 0.8477 (mmm) cc_final: 0.8206 (mtp) REVERT: C 4580 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.6702 (t80) REVERT: C 4725 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6611 (tp) REVERT: C 4735 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6399 (pm20) REVERT: C 4844 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8507 (tp) REVERT: C 4933 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7156 (mt0) REVERT: C 5006 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7520 (pt0) REVERT: C 5016 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8349 (mp0) REVERT: D 3959 LYS cc_start: 0.5915 (OUTLIER) cc_final: 0.5423 (tttm) REVERT: D 3967 GLU cc_start: 0.8016 (mm-30) cc_final: 0.6995 (tm-30) REVERT: D 4000 MET cc_start: 0.4483 (tpt) cc_final: 0.3832 (mmm) REVERT: D 4020 GLN cc_start: 0.7049 (tt0) cc_final: 0.6776 (tp40) REVERT: D 4047 MET cc_start: 0.6390 (tmm) cc_final: 0.5774 (tmm) REVERT: D 4188 ARG cc_start: 0.8157 (mmm160) cc_final: 0.7260 (tpt170) REVERT: D 4207 MET cc_start: 0.8488 (mmm) cc_final: 0.8219 (mtp) REVERT: D 4580 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.6692 (t80) REVERT: D 4725 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6614 (tp) REVERT: D 4735 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6400 (pm20) REVERT: D 4844 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8468 (tp) REVERT: D 4933 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7152 (mt0) REVERT: D 5006 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7525 (pt0) REVERT: D 5016 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8337 (mp0) outliers start: 71 outliers final: 40 residues processed: 359 average time/residue: 0.5765 time to fit residues: 236.4518 Evaluate side-chains 354 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 285 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4036 VAL Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4725 LEU Chi-restraints excluded: chain A residue 4737 ILE Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5004 THR Chi-restraints excluded: chain A residue 5006 GLN Chi-restraints excluded: chain A residue 5016 GLU Chi-restraints excluded: chain B residue 3959 LYS Chi-restraints excluded: chain B residue 4036 VAL Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4221 VAL Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4725 LEU Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5004 THR Chi-restraints excluded: chain B residue 5006 GLN Chi-restraints excluded: chain B residue 5016 GLU Chi-restraints excluded: chain C residue 3959 LYS Chi-restraints excluded: chain C residue 4036 VAL Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4221 VAL Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4725 LEU Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5004 THR Chi-restraints excluded: chain C residue 5006 GLN Chi-restraints excluded: chain C residue 5016 GLU Chi-restraints excluded: chain D residue 3959 LYS Chi-restraints excluded: chain D residue 4036 VAL Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5004 THR Chi-restraints excluded: chain D residue 5006 GLN Chi-restraints excluded: chain D residue 5016 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 2 optimal weight: 4.9990 chunk 94 optimal weight: 0.0050 chunk 79 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 134 optimal weight: 0.4980 chunk 65 optimal weight: 9.9990 chunk 146 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.179243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.143320 restraints weight = 23583.639| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.80 r_work: 0.3281 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 21068 Z= 0.120 Angle : 0.534 8.037 28432 Z= 0.269 Chirality : 0.036 0.197 3080 Planarity : 0.005 0.098 3592 Dihedral : 7.241 143.363 2748 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.95 % Favored : 97.89 % Rotamer: Outliers : 2.87 % Allowed : 17.97 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.17), residues: 2464 helix: 2.32 (0.12), residues: 1680 sheet: -1.22 (0.50), residues: 104 loop : 0.09 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D4188 TYR 0.011 0.001 TYR D4554 PHE 0.015 0.001 PHE B4916 TRP 0.007 0.001 TRP D4716 HIS 0.003 0.001 HIS A3998 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (21048) covalent geometry : angle 0.53043 / 0.27 (28416) SS BOND : bond 0.00056 / 0.03 ( 4) SS BOND : angle 1.09646 / 0.75 ( 8) hydrogen bonds : bond 0.03808 / 2.53 ( 1396) hydrogen bonds : angle 4.04585 / 2.93 ( 4068) metal coordination : bond 0.00187 / 0.12 ( 16) metal coordination : angle 3.75021 / 2.60 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7971.41 seconds wall clock time: 136 minutes 18.14 seconds (8178.14 seconds total)