Starting phenix.real_space_refine on Sat Jul 4 12:46:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sex_40432/07_2026/8sex_40432.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sex_40432/07_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_40432/07_2026/8sex_40432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sex_40432/07_2026/8sex_40432.map" model { file = "/net/cci-nas-00/data/ceres_data/8sex_40432/07_2026/8sex_40432.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sex_40432/07_2026/8sex_40432.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8sex_40432/07_2026/8sex_40432.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sex_40432/07_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-dev-6108/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: {'RNA': 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: 5.13, per 1000 atoms: 0.25 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: 2.12 Conformation dependent library (CDL) restraints added in 988.4 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: 0.58 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: 3.75 Time building geometry restraints manager: 2.76 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 - 1.87: 28056 1.87 - 3.73: 284 3.73 - 5.60: 48 5.60 - 7.46: 16 7.46 - 9.33: 12 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=" N1 AMP A5101 " pdb=" C2 AMP A5101 " pdb=" N3 AMP A5101 " ideal model delta sigma weight residual 120.00 129.33 -9.33 3.00e+00 1.11e-01 9.66e+00 ... (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 - 0.035: 1952 0.035 - 0.070: 928 0.070 - 0.104: 160 0.104 - 0.139: 36 0.139 - 0.174: 4 Chirality restraints: 3080 Sorted by residual: chirality pdb=" CA PRO A3972 " pdb=" N PRO A3972 " pdb=" C PRO A3972 " pdb=" CB PRO A3972 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CA PRO B3972 " pdb=" N PRO B3972 " pdb=" C PRO B3972 " pdb=" CB PRO B3972 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CA PRO D3972 " pdb=" N PRO D3972 " pdb=" C PRO D3972 " pdb=" CB PRO D3972 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.57e-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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.360 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.910 ------------------------------------------------------------------------------- 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= 0.229 Angle : 0.569 9.326 28432 Z= 0.295 Chirality : 0.038 0.174 3080 Planarity : 0.005 0.126 3592 Dihedral : 12.782 153.916 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 0.00517 / 0.23 (21048) covalent geometry : angle 0.55599 / 0.29 (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 : 0.788 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: 0.6429 time to fit residues: 316.4492 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 : 0.759 ------------------------------------------------------------------------------- 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 B3982 HIS 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.176635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.140921 restraints weight = 23386.648| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.61 r_work: 0.3214 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1385 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= 0.196 Angle : 0.583 8.321 28432 Z= 0.304 Chirality : 0.040 0.174 3080 Planarity : 0.006 0.126 3592 Dihedral : 8.475 149.537 2784 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.44 % Favored : 97.40 % Rotamer: Outliers : 4.30 % Allowed : 11.65 % Favored : 84.05 % 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: 1.70 (0.16), residues: 2464 helix: 1.67 (0.12), residues: 1700 sheet: -0.67 (0.49), residues: 104 loop : 0.14 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C4188 TYR 0.016 0.002 TYR D4687 PHE 0.020 0.002 PHE B4916 TRP 0.012 0.002 TRP A5011 HIS 0.004 0.001 HIS A3998 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (21048) covalent geometry : angle 0.57651 / 0.30 (28416) SS BOND : bond 0.00029 / 0.01 ( 4) SS BOND : angle 1.62204 / 1.09 ( 8) hydrogen bonds : bond 0.05320 / 3.53 ( 1396) hydrogen bonds : angle 4.43757 / 3.21 ( 4068) metal coordination : bond 0.01250 / 0.70 ( 16) metal coordination : angle 5.14610 / 3.52 ( 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 420 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 324 time to evaluate : 0.808 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: 0.6983 (m-30) cc_final: 0.6661 (m-30) REVERT: A 4047 MET cc_start: 0.6571 (tmm) cc_final: 0.5849 (tmm) REVERT: A 4580 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.6863 (t80) REVERT: A 4933 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7897 (mt0) REVERT: A 5006 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7631 (pt0) REVERT: A 5030 LYS cc_start: 0.8466 (ttmt) cc_final: 0.7717 (ttpt) REVERT: B 4022 ASP cc_start: 0.6947 (m-30) cc_final: 0.6619 (m-30) REVERT: B 4047 MET cc_start: 0.6566 (tmm) cc_final: 0.5844 (tmm) REVERT: B 4580 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.6860 (t80) REVERT: B 4933 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7868 (mt0) REVERT: B 5006 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7621 (pt0) REVERT: B 5030 LYS cc_start: 0.8484 (ttmt) cc_final: 0.7737 (ttpt) REVERT: C 4022 ASP cc_start: 0.6942 (m-30) cc_final: 0.6618 (m-30) REVERT: C 4047 MET cc_start: 0.6568 (tmm) cc_final: 0.5849 (tmm) REVERT: C 4580 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.6867 (t80) REVERT: C 4933 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7872 (mt0) REVERT: C 5006 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7625 (pt0) REVERT: C 5030 LYS cc_start: 0.8473 (ttmt) cc_final: 0.7728 (ttpt) REVERT: D 4022 ASP cc_start: 0.6965 (m-30) cc_final: 0.6641 (m-30) REVERT: D 4047 MET cc_start: 0.6569 (tmm) cc_final: 0.5847 (tmm) REVERT: D 4580 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.6853 (t80) REVERT: D 4933 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7888 (mt0) REVERT: D 5006 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7627 (pt0) REVERT: D 5030 LYS cc_start: 0.8470 (ttmt) cc_final: 0.7728 (ttpt) outliers start: 96 outliers final: 40 residues processed: 384 average time/residue: 0.6201 time to fit residues: 270.3076 Evaluate side-chains 348 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 296 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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: 0.5980 chunk 83 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 49)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.143202 restraints weight = 23472.180| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.60 r_work: 0.3272 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21068 Z= 0.135 Angle : 0.517 7.541 28432 Z= 0.266 Chirality : 0.037 0.173 3080 Planarity : 0.005 0.121 3592 Dihedral : 7.979 145.079 2764 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.44 % Favored : 97.40 % Rotamer: Outliers : 3.94 % Allowed : 14.16 % Favored : 81.90 % 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: 2.11 (0.12), residues: 1680 sheet: -0.90 (0.49), residues: 104 loop : 0.09 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A4188 TYR 0.014 0.001 TYR D4687 PHE 0.016 0.001 PHE C4916 TRP 0.008 0.001 TRP A4716 HIS 0.002 0.001 HIS D4886 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (21048) covalent geometry : angle 0.51058 / 0.27 (28416) SS BOND : bond 0.00004 / 0.00 ( 4) SS BOND : angle 1.23197 / 0.84 ( 8) hydrogen bonds : bond 0.04483 / 2.98 ( 1396) hydrogen bonds : angle 4.16168 / 3.01 ( 4068) metal coordination : bond 0.00531 / 0.30 ( 16) metal coordination : angle 4.71271 / 3.22 ( 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 404 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 316 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4022 ASP cc_start: 0.6720 (m-30) cc_final: 0.6502 (m-30) REVERT: A 4047 MET cc_start: 0.6559 (tmm) cc_final: 0.5897 (tmm) REVERT: A 4188 ARG cc_start: 0.8047 (mmm160) cc_final: 0.7251 (tpt170) REVERT: A 4580 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.6686 (t80) REVERT: A 4639 MET cc_start: 0.8187 (mmm) cc_final: 0.7640 (mtm) REVERT: A 4821 LYS cc_start: 0.8281 (mmtt) cc_final: 0.7844 (mmtp) REVERT: A 4844 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8491 (tp) REVERT: A 4933 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7758 (mt0) REVERT: A 5030 LYS cc_start: 0.8394 (ttmt) cc_final: 0.7920 (ttmt) REVERT: B 4022 ASP cc_start: 0.6720 (m-30) cc_final: 0.6503 (m-30) REVERT: B 4047 MET cc_start: 0.6563 (tmm) cc_final: 0.5900 (tmm) REVERT: B 4188 ARG cc_start: 0.8033 (mmm160) cc_final: 0.7241 (tpt170) REVERT: B 4580 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.6684 (t80) REVERT: B 4639 MET cc_start: 0.8196 (mmm) cc_final: 0.7647 (mtm) REVERT: B 4821 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7832 (mmtp) REVERT: B 4844 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8495 (tp) REVERT: B 4933 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7747 (mt0) REVERT: B 5030 LYS cc_start: 0.8403 (ttmt) cc_final: 0.7931 (ttmt) REVERT: C 4022 ASP cc_start: 0.6716 (m-30) cc_final: 0.6497 (m-30) REVERT: C 4047 MET cc_start: 0.6569 (tmm) cc_final: 0.5907 (tmm) REVERT: C 4188 ARG cc_start: 0.8042 (mmm160) cc_final: 0.7245 (tpt170) REVERT: C 4580 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.6691 (t80) REVERT: C 4639 MET cc_start: 0.8203 (mmm) cc_final: 0.7656 (mtm) REVERT: C 4821 LYS cc_start: 0.8272 (mmtt) cc_final: 0.7822 (mmtp) REVERT: C 4844 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8498 (tp) REVERT: C 4933 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7754 (mt0) REVERT: C 5030 LYS cc_start: 0.8400 (ttmt) cc_final: 0.7932 (ttmt) REVERT: D 4022 ASP cc_start: 0.6726 (m-30) cc_final: 0.6509 (m-30) REVERT: D 4047 MET cc_start: 0.6564 (tmm) cc_final: 0.5899 (tmm) REVERT: D 4188 ARG cc_start: 0.8054 (mmm160) cc_final: 0.7255 (tpt170) REVERT: D 4580 TYR cc_start: 0.8714 (OUTLIER) cc_final: 0.6678 (t80) REVERT: D 4639 MET cc_start: 0.8195 (mmm) cc_final: 0.7647 (mtm) REVERT: D 4821 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7840 (mmtp) REVERT: D 4844 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8494 (tp) REVERT: D 4933 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7761 (mt0) REVERT: D 5030 LYS cc_start: 0.8397 (ttmt) cc_final: 0.7927 (ttmt) outliers start: 88 outliers final: 36 residues processed: 372 average time/residue: 0.5941 time to fit residues: 252.4006 Evaluate side-chains 332 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 284 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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: 0.7980 chunk 203 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3998 HIS B3998 HIS C3998 HIS D3998 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.177195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.139654 restraints weight = 23688.102| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.94 r_work: 0.3218 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21068 Z= 0.168 Angle : 0.530 7.325 28432 Z= 0.273 Chirality : 0.038 0.175 3080 Planarity : 0.005 0.119 3592 Dihedral : 7.805 143.388 2748 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.56 % Rotamer: Outliers : 4.48 % Allowed : 14.70 % Favored : 80.82 % 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: 2.02 (0.17), residues: 2464 helix: 2.07 (0.12), residues: 1680 sheet: -1.12 (0.47), residues: 104 loop : -0.02 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D4189 TYR 0.014 0.002 TYR B4994 PHE 0.018 0.002 PHE A4916 TRP 0.008 0.002 TRP A4716 HIS 0.003 0.001 HIS C4650 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (21048) covalent geometry : angle 0.52337 / 0.27 (28416) SS BOND : bond 0.00016 / 0.01 ( 4) SS BOND : angle 1.55408 / 1.05 ( 8) hydrogen bonds : bond 0.04549 / 3.01 ( 1396) hydrogen bonds : angle 4.23568 / 3.07 ( 4068) metal coordination : bond 0.00700 / 0.40 ( 16) metal coordination : angle 4.61151 / 3.20 ( 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 396 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 296 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4022 ASP cc_start: 0.6655 (m-30) cc_final: 0.6423 (m-30) REVERT: A 4047 MET cc_start: 0.6615 (tmm) cc_final: 0.5949 (tmm) REVERT: A 4188 ARG cc_start: 0.8035 (mmm160) cc_final: 0.7229 (tpt170) REVERT: A 4207 MET cc_start: 0.8510 (mmm) cc_final: 0.8288 (mtp) REVERT: A 4580 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.6656 (t80) REVERT: A 4725 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6652 (tp) REVERT: A 4844 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8475 (tp) REVERT: A 4933 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7580 (mt0) REVERT: A 4956 THR cc_start: 0.8908 (p) cc_final: 0.8703 (p) REVERT: A 5030 LYS cc_start: 0.8363 (ttmt) cc_final: 0.7516 (ttpt) REVERT: B 4022 ASP cc_start: 0.6658 (m-30) cc_final: 0.6419 (m-30) REVERT: B 4047 MET cc_start: 0.6611 (tmm) cc_final: 0.5947 (tmm) REVERT: B 4188 ARG cc_start: 0.8031 (mmm160) cc_final: 0.7222 (tpt170) REVERT: B 4207 MET cc_start: 0.8518 (mmm) cc_final: 0.8298 (mtp) REVERT: B 4580 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.6651 (t80) REVERT: B 4725 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6641 (tp) REVERT: B 4844 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8477 (tp) REVERT: B 4933 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7572 (mt0) REVERT: B 4956 THR cc_start: 0.8903 (p) cc_final: 0.8701 (p) REVERT: B 5030 LYS cc_start: 0.8366 (ttmt) cc_final: 0.7519 (ttpt) REVERT: C 4022 ASP cc_start: 0.6643 (m-30) cc_final: 0.6405 (m-30) REVERT: C 4047 MET cc_start: 0.6617 (tmm) cc_final: 0.5954 (tmm) REVERT: C 4188 ARG cc_start: 0.8021 (mmm160) cc_final: 0.7214 (tpt170) REVERT: C 4207 MET cc_start: 0.8509 (mmm) cc_final: 0.8287 (mtp) REVERT: C 4580 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.6650 (t80) REVERT: C 4725 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6636 (tp) REVERT: C 4844 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8483 (tp) REVERT: C 4933 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: C 4956 THR cc_start: 0.8899 (p) cc_final: 0.8692 (p) REVERT: C 5030 LYS cc_start: 0.8354 (ttmt) cc_final: 0.7511 (ttpt) REVERT: D 4022 ASP cc_start: 0.6656 (m-30) cc_final: 0.6422 (m-30) REVERT: D 4047 MET cc_start: 0.6610 (tmm) cc_final: 0.5943 (tmm) REVERT: D 4188 ARG cc_start: 0.8033 (mmm160) cc_final: 0.7227 (tpt170) REVERT: D 4207 MET cc_start: 0.8510 (mmm) cc_final: 0.8289 (mtp) REVERT: D 4580 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.6642 (t80) REVERT: D 4725 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6645 (tp) REVERT: D 4844 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8479 (tp) REVERT: D 4933 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7588 (mt0) REVERT: D 4956 THR cc_start: 0.8910 (p) cc_final: 0.8703 (p) REVERT: D 5030 LYS cc_start: 0.8357 (ttmt) cc_final: 0.7513 (ttpt) outliers start: 100 outliers final: 46 residues processed: 364 average time/residue: 0.5619 time to fit residues: 235.3159 Evaluate side-chains 356 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 294 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 4951 LYS 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 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 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 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 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 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 4951 LYS Chi-restraints excluded: chain D residue 4952 GLU 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: 0.0050 chunk 173 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 174 optimal weight: 0.5980 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3963 ASN B5031 GLN C5031 GLN D5031 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.178405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.142125 restraints weight = 23270.383| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.57 r_work: 0.3276 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2027 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= 0.126 Angle : 0.492 6.589 28432 Z= 0.253 Chirality : 0.036 0.176 3080 Planarity : 0.005 0.114 3592 Dihedral : 7.660 141.990 2748 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.56 % Rotamer: Outliers : 4.84 % Allowed : 14.65 % Favored : 80.51 % 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: 2.24 (0.17), residues: 2464 helix: 2.25 (0.12), residues: 1680 sheet: -1.24 (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 C4189 TYR 0.012 0.001 TYR A4687 PHE 0.016 0.001 PHE C4916 TRP 0.008 0.001 TRP B4716 HIS 0.002 0.001 HIS C3998 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (21048) covalent geometry : angle 0.48671 / 0.25 (28416) SS BOND : bond 0.00009 / 0.00 ( 4) SS BOND : angle 1.22175 / 0.84 ( 8) hydrogen bonds : bond 0.04122 / 2.73 ( 1396) hydrogen bonds : angle 4.09319 / 2.96 ( 4068) metal coordination : bond 0.00280 / 0.17 ( 16) metal coordination : angle 4.19036 / 2.91 ( 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 420 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 312 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3959 LYS cc_start: 0.6384 (OUTLIER) cc_final: 0.6044 (tttm) REVERT: A 4020 GLN cc_start: 0.7119 (tt0) cc_final: 0.6824 (tp40) REVERT: A 4047 MET cc_start: 0.6592 (tmm) cc_final: 0.5929 (tmm) REVERT: A 4188 ARG cc_start: 0.8150 (mmm160) cc_final: 0.7359 (tpt170) REVERT: A 4580 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.6744 (t80) REVERT: A 4725 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6725 (tp) REVERT: A 4735 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6552 (pm20) REVERT: A 4745 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5758 (pp) REVERT: A 4821 LYS cc_start: 0.8235 (mmmt) cc_final: 0.8015 (mmmm) REVERT: A 4844 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8515 (tp) REVERT: A 4933 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7937 (mp10) REVERT: A 5006 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7528 (pt0) REVERT: A 5030 LYS cc_start: 0.8464 (ttmt) cc_final: 0.7618 (ttpt) REVERT: B 4020 GLN cc_start: 0.7123 (tt0) cc_final: 0.6829 (tp40) REVERT: B 4022 ASP cc_start: 0.6570 (m-30) cc_final: 0.6343 (m-30) REVERT: B 4047 MET cc_start: 0.6595 (tmm) cc_final: 0.5930 (tmm) REVERT: B 4188 ARG cc_start: 0.8141 (mmm160) cc_final: 0.7345 (tpt170) REVERT: B 4580 TYR cc_start: 0.8714 (OUTLIER) cc_final: 0.6736 (t80) REVERT: B 4725 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6716 (tp) REVERT: B 4735 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6551 (pm20) REVERT: B 4745 LEU cc_start: 0.6119 (OUTLIER) cc_final: 0.5767 (pp) REVERT: B 4821 LYS cc_start: 0.8231 (mmmt) cc_final: 0.8010 (mmmm) REVERT: B 4844 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8516 (tp) REVERT: B 4933 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7931 (mp10) REVERT: B 5006 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7522 (pt0) REVERT: B 5030 LYS cc_start: 0.8474 (ttmt) cc_final: 0.7629 (ttpt) REVERT: C 4020 GLN cc_start: 0.7124 (tt0) cc_final: 0.6830 (tp40) REVERT: C 4022 ASP cc_start: 0.6575 (m-30) cc_final: 0.6344 (m-30) REVERT: C 4047 MET cc_start: 0.6594 (tmm) cc_final: 0.5934 (tmm) REVERT: C 4188 ARG cc_start: 0.8131 (mmm160) cc_final: 0.7338 (tpt170) REVERT: C 4580 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.6726 (t80) REVERT: C 4725 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6709 (tp) REVERT: C 4735 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6557 (pm20) REVERT: C 4745 LEU cc_start: 0.6110 (OUTLIER) cc_final: 0.5754 (pp) REVERT: C 4821 LYS cc_start: 0.8225 (mmmt) cc_final: 0.8006 (mmmm) REVERT: C 4844 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8520 (tp) REVERT: C 4933 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7916 (mp10) REVERT: C 5006 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7522 (pt0) REVERT: C 5030 LYS cc_start: 0.8468 (ttmt) cc_final: 0.7622 (ttpt) REVERT: D 4020 GLN cc_start: 0.7128 (tt0) cc_final: 0.6832 (tp40) REVERT: D 4022 ASP cc_start: 0.6579 (m-30) cc_final: 0.6351 (m-30) REVERT: D 4047 MET cc_start: 0.6592 (tmm) cc_final: 0.5926 (tmm) REVERT: D 4188 ARG cc_start: 0.8144 (mmm160) cc_final: 0.7351 (tpt170) REVERT: D 4580 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.6720 (t80) REVERT: D 4725 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6708 (tp) REVERT: D 4735 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6554 (pm20) REVERT: D 4745 LEU cc_start: 0.6108 (OUTLIER) cc_final: 0.5756 (pp) REVERT: D 4821 LYS cc_start: 0.8231 (mmmt) cc_final: 0.8006 (mmmm) REVERT: D 4844 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8515 (tp) REVERT: D 4933 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7940 (mp10) REVERT: D 5006 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7516 (pt0) REVERT: D 5030 LYS cc_start: 0.8465 (ttmt) cc_final: 0.7615 (ttpt) outliers start: 108 outliers final: 48 residues processed: 392 average time/residue: 0.6045 time to fit residues: 269.5031 Evaluate side-chains 356 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 283 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3959 LYS 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 4745 LEU 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 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 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 4745 LEU 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 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 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 4745 LEU 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 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 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 4745 LEU 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 5006 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 102 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 154 optimal weight: 0.0000 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B3963 ASN D3963 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.179154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.141564 restraints weight = 23472.884| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.53 r_work: 0.3270 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21068 Z= 0.115 Angle : 0.483 6.183 28432 Z= 0.249 Chirality : 0.036 0.179 3080 Planarity : 0.005 0.111 3592 Dihedral : 7.569 140.897 2748 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.11 % Favored : 97.73 % Rotamer: Outliers : 4.61 % Allowed : 15.41 % Favored : 79.97 % 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: 2.39 (0.17), residues: 2464 helix: 2.37 (0.12), residues: 1680 sheet: -1.24 (0.47), residues: 104 loop : 0.09 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C4189 TYR 0.011 0.001 TYR A4687 PHE 0.015 0.001 PHE A4916 TRP 0.007 0.001 TRP D4716 HIS 0.003 0.001 HIS A3998 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (21048) covalent geometry : angle 0.47833 / 0.25 (28416) SS BOND : bond 0.00025 / 0.01 ( 4) SS BOND : angle 1.13293 / 0.78 ( 8) hydrogen bonds : bond 0.03945 / 2.62 ( 1396) hydrogen bonds : angle 4.04862 / 2.93 ( 4068) metal coordination : bond 0.00239 / 0.14 ( 16) metal coordination : angle 3.88650 / 2.70 ( 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 395 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 292 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4020 GLN cc_start: 0.7039 (tt0) cc_final: 0.6746 (tp40) REVERT: A 4047 MET cc_start: 0.6484 (tmm) cc_final: 0.5825 (tmm) REVERT: A 4188 ARG cc_start: 0.8118 (mmm160) cc_final: 0.7294 (tpt170) REVERT: A 4207 MET cc_start: 0.8379 (mmm) cc_final: 0.8156 (mtp) REVERT: A 4223 ASN cc_start: 0.8324 (t0) cc_final: 0.8030 (t0) REVERT: A 4580 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.6567 (t80) REVERT: A 4639 MET cc_start: 0.8191 (mmm) cc_final: 0.7629 (mtm) REVERT: A 4725 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6350 (tp) REVERT: A 4821 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7858 (mmmm) REVERT: A 4844 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8436 (tp) REVERT: A 4933 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: A 5006 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7479 (pt0) REVERT: A 5030 LYS cc_start: 0.8360 (ttmt) cc_final: 0.7429 (ttpt) REVERT: B 4020 GLN cc_start: 0.7051 (tt0) cc_final: 0.6737 (tp40) REVERT: B 4047 MET cc_start: 0.6480 (tmm) cc_final: 0.5818 (tmm) REVERT: B 4188 ARG cc_start: 0.8111 (mmm160) cc_final: 0.7285 (tpt170) REVERT: B 4207 MET cc_start: 0.8394 (mmm) cc_final: 0.8175 (mtp) REVERT: B 4223 ASN cc_start: 0.8321 (t0) cc_final: 0.8025 (t0) REVERT: B 4580 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.6566 (t80) REVERT: B 4639 MET cc_start: 0.8192 (mmm) cc_final: 0.7624 (mtm) REVERT: B 4725 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6342 (tp) REVERT: B 4821 LYS cc_start: 0.8138 (mmmt) cc_final: 0.7853 (mmmm) REVERT: B 4844 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8445 (tp) REVERT: B 4933 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7893 (mp10) REVERT: B 5006 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7469 (pt0) REVERT: B 5030 LYS cc_start: 0.8360 (ttmt) cc_final: 0.7429 (ttpt) REVERT: C 4020 GLN cc_start: 0.7052 (tt0) cc_final: 0.6738 (tp40) REVERT: C 4022 ASP cc_start: 0.6202 (m-30) cc_final: 0.5956 (m-30) REVERT: C 4047 MET cc_start: 0.6477 (tmm) cc_final: 0.5821 (tmm) REVERT: C 4188 ARG cc_start: 0.8105 (mmm160) cc_final: 0.7280 (tpt170) REVERT: C 4207 MET cc_start: 0.8369 (mmm) cc_final: 0.8143 (mtp) REVERT: C 4223 ASN cc_start: 0.8316 (t0) cc_final: 0.8020 (t0) REVERT: C 4580 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.6558 (t80) REVERT: C 4639 MET cc_start: 0.8197 (mmm) cc_final: 0.7633 (mtm) REVERT: C 4725 LEU cc_start: 0.6791 (OUTLIER) cc_final: 0.6324 (tp) REVERT: C 4821 LYS cc_start: 0.8141 (mmmt) cc_final: 0.7859 (mmmm) REVERT: C 4844 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8437 (tp) REVERT: C 4933 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7887 (mp10) REVERT: C 5006 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7480 (pt0) REVERT: C 5030 LYS cc_start: 0.8346 (ttmt) cc_final: 0.7414 (ttpt) REVERT: D 4020 GLN cc_start: 0.7055 (tt0) cc_final: 0.6741 (tp40) REVERT: D 4047 MET cc_start: 0.6480 (tmm) cc_final: 0.5818 (tmm) REVERT: D 4188 ARG cc_start: 0.8112 (mmm160) cc_final: 0.7290 (tpt170) REVERT: D 4207 MET cc_start: 0.8395 (mmm) cc_final: 0.8174 (mtp) REVERT: D 4223 ASN cc_start: 0.8311 (t0) cc_final: 0.8020 (t0) REVERT: D 4580 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.6555 (t80) REVERT: D 4639 MET cc_start: 0.8196 (mmm) cc_final: 0.7632 (mtm) REVERT: D 4725 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6332 (tp) REVERT: D 4821 LYS cc_start: 0.8147 (mmmt) cc_final: 0.7863 (mmmm) REVERT: D 4844 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8435 (tp) REVERT: D 4933 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7896 (mp10) REVERT: D 5006 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7465 (pt0) REVERT: D 5030 LYS cc_start: 0.8354 (ttmt) cc_final: 0.7418 (ttpt) outliers start: 103 outliers final: 54 residues processed: 379 average time/residue: 0.5711 time to fit residues: 247.7551 Evaluate side-chains 355 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 281 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 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 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=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: 0.6980 chunk 200 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 110 optimal weight: 5.9990 chunk 70 optimal weight: 0.0070 chunk 102 optimal weight: 0.7980 chunk 197 optimal weight: 10.0000 chunk 206 optimal weight: 0.6980 chunk 188 optimal weight: 7.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C3963 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.179721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.142419 restraints weight = 23601.332| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.55 r_work: 0.3222 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2170 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= 0.110 Angle : 0.484 7.447 28432 Z= 0.246 Chirality : 0.036 0.182 3080 Planarity : 0.005 0.108 3592 Dihedral : 7.495 140.009 2748 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.79 % Favored : 98.05 % Rotamer: Outliers : 4.12 % Allowed : 16.26 % Favored : 79.61 % 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: 2.54 (0.17), residues: 2464 helix: 2.49 (0.12), residues: 1680 sheet: -1.20 (0.48), residues: 104 loop : 0.15 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B4189 TYR 0.009 0.001 TYR D4994 PHE 0.015 0.001 PHE D4916 TRP 0.006 0.001 TRP D4716 HIS 0.003 0.001 HIS D3998 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (21048) covalent geometry : angle 0.47940 / 0.25 (28416) SS BOND : bond 0.00049 / 0.02 ( 4) SS BOND : angle 1.09511 / 0.75 ( 8) hydrogen bonds : bond 0.03833 / 2.54 ( 1396) hydrogen bonds : angle 3.99931 / 2.89 ( 4068) metal coordination : bond 0.00138 / 0.08 ( 16) metal coordination : angle 3.78625 / 2.63 ( 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 377 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 285 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4020 GLN cc_start: 0.7066 (tt0) cc_final: 0.6780 (tp40) REVERT: A 4047 MET cc_start: 0.6512 (tmm) cc_final: 0.5836 (tmm) REVERT: A 4188 ARG cc_start: 0.8048 (mmm160) cc_final: 0.7277 (tpt170) REVERT: A 4207 MET cc_start: 0.8441 (mmm) cc_final: 0.8202 (mtp) REVERT: A 4223 ASN cc_start: 0.8338 (t0) cc_final: 0.8027 (t0) REVERT: A 4580 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.6572 (t80) REVERT: A 4639 MET cc_start: 0.8091 (mmm) cc_final: 0.7580 (mtm) REVERT: A 4725 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6398 (tp) REVERT: A 4735 GLU cc_start: 0.6934 (tp30) cc_final: 0.6143 (pm20) REVERT: A 4821 LYS cc_start: 0.8101 (mmmt) cc_final: 0.7865 (mmmm) REVERT: A 4844 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8444 (tp) REVERT: A 5006 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7464 (pt0) REVERT: A 5016 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: A 5030 LYS cc_start: 0.8386 (ttmt) cc_final: 0.7908 (ttmt) REVERT: B 4020 GLN cc_start: 0.7050 (tt0) cc_final: 0.6783 (tp40) REVERT: B 4047 MET cc_start: 0.6507 (tmm) cc_final: 0.5832 (tmm) REVERT: B 4188 ARG cc_start: 0.8042 (mmm160) cc_final: 0.7271 (tpt170) REVERT: B 4207 MET cc_start: 0.8456 (mmm) cc_final: 0.8217 (mtp) REVERT: B 4223 ASN cc_start: 0.8337 (t0) cc_final: 0.8029 (t0) REVERT: B 4580 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.6576 (t80) REVERT: B 4639 MET cc_start: 0.8088 (mmm) cc_final: 0.7577 (mtm) REVERT: B 4725 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6390 (tp) REVERT: B 4735 GLU cc_start: 0.6927 (tp30) cc_final: 0.6136 (pm20) REVERT: B 4821 LYS cc_start: 0.8117 (mmmt) cc_final: 0.7879 (mmmm) REVERT: B 4844 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8451 (tp) REVERT: B 5006 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7456 (pt0) REVERT: B 5016 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8190 (mp0) REVERT: B 5030 LYS cc_start: 0.8386 (ttmt) cc_final: 0.7927 (ttmt) REVERT: C 4020 GLN cc_start: 0.7071 (tt0) cc_final: 0.6772 (tp40) REVERT: C 4047 MET cc_start: 0.6526 (tmm) cc_final: 0.5853 (tmm) REVERT: C 4188 ARG cc_start: 0.8033 (mmm160) cc_final: 0.7263 (tpt170) REVERT: C 4207 MET cc_start: 0.8448 (mmm) cc_final: 0.8208 (mtp) REVERT: C 4223 ASN cc_start: 0.8330 (t0) cc_final: 0.8022 (t0) REVERT: C 4580 TYR cc_start: 0.8672 (OUTLIER) cc_final: 0.6574 (t80) REVERT: C 4639 MET cc_start: 0.8101 (mmm) cc_final: 0.7590 (mtm) REVERT: C 4725 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6385 (tp) REVERT: C 4735 GLU cc_start: 0.6934 (tp30) cc_final: 0.6141 (pm20) REVERT: C 4821 LYS cc_start: 0.8099 (mmmt) cc_final: 0.7867 (mmmm) REVERT: C 4844 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8448 (tp) REVERT: C 5006 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7451 (pt0) REVERT: C 5016 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8177 (mp0) REVERT: C 5030 LYS cc_start: 0.8372 (ttmt) cc_final: 0.7914 (ttmt) REVERT: D 4020 GLN cc_start: 0.7051 (tt0) cc_final: 0.6784 (tp40) REVERT: D 4047 MET cc_start: 0.6518 (tmm) cc_final: 0.5839 (tmm) REVERT: D 4188 ARG cc_start: 0.8038 (mmm160) cc_final: 0.7275 (tpt170) REVERT: D 4207 MET cc_start: 0.8440 (mmm) cc_final: 0.8198 (mtp) REVERT: D 4223 ASN cc_start: 0.8331 (t0) cc_final: 0.8027 (t0) REVERT: D 4580 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.6568 (t80) REVERT: D 4639 MET cc_start: 0.8093 (mmm) cc_final: 0.7583 (mtm) REVERT: D 4725 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6391 (tp) REVERT: D 4735 GLU cc_start: 0.6932 (tp30) cc_final: 0.6139 (pm20) REVERT: D 4821 LYS cc_start: 0.8100 (mmmt) cc_final: 0.7865 (mmmm) REVERT: D 4844 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8448 (tp) REVERT: D 5006 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7448 (pt0) REVERT: D 5016 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8181 (mp0) REVERT: D 5030 LYS cc_start: 0.8374 (ttmt) cc_final: 0.7917 (ttmt) outliers start: 92 outliers final: 49 residues processed: 353 average time/residue: 0.5243 time to fit residues: 212.9068 Evaluate side-chains 355 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 286 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3959 LYS Chi-restraints excluded: chain A residue 4030 LEU 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 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 4030 LEU 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 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 4030 LEU 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 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 4030 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 202 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 54 optimal weight: 0.0570 chunk 91 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 246 optimal weight: 0.0870 chunk 174 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.179740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.144480 restraints weight = 23653.679| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.98 r_work: 0.3278 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21068 Z= 0.110 Angle : 0.476 6.484 28432 Z= 0.243 Chirality : 0.035 0.182 3080 Planarity : 0.005 0.106 3592 Dihedral : 7.453 139.444 2748 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.95 % Favored : 97.89 % Rotamer: Outliers : 3.94 % Allowed : 15.95 % 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: 2.54 (0.17), residues: 2464 helix: 2.48 (0.12), residues: 1680 sheet: -1.15 (0.48), residues: 104 loop : 0.16 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B4189 TYR 0.010 0.001 TYR B4554 PHE 0.015 0.001 PHE B4916 TRP 0.007 0.001 TRP D5011 HIS 0.003 0.001 HIS A3998 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (21048) covalent geometry : angle 0.47191 / 0.24 (28416) SS BOND : bond 0.00039 / 0.02 ( 4) SS BOND : angle 1.10020 / 0.75 ( 8) hydrogen bonds : bond 0.03790 / 2.51 ( 1396) hydrogen bonds : angle 3.98683 / 2.88 ( 4068) metal coordination : bond 0.00220 / 0.13 ( 16) metal coordination : angle 3.69983 / 2.58 ( 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 378 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 290 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4020 GLN cc_start: 0.7033 (tt0) cc_final: 0.6755 (tp40) REVERT: A 4047 MET cc_start: 0.6361 (tmm) cc_final: 0.5760 (tmm) REVERT: A 4188 ARG cc_start: 0.8152 (mmm160) cc_final: 0.7316 (tpt170) REVERT: A 4207 MET cc_start: 0.8423 (mmm) cc_final: 0.8153 (mtp) REVERT: A 4223 ASN cc_start: 0.8302 (t0) cc_final: 0.8019 (t0) REVERT: A 4580 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.6665 (t80) REVERT: A 4639 MET cc_start: 0.8147 (mmm) cc_final: 0.7551 (mtm) REVERT: A 4725 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6415 (tp) REVERT: A 4821 LYS cc_start: 0.8168 (mmmt) cc_final: 0.7906 (mmmm) REVERT: A 4844 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8466 (tp) REVERT: A 5006 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7566 (pt0) REVERT: A 5030 LYS cc_start: 0.8434 (ttmt) cc_final: 0.7947 (ttmt) REVERT: B 4020 GLN cc_start: 0.7038 (tt0) cc_final: 0.6766 (tp40) REVERT: B 4047 MET cc_start: 0.6395 (tmm) cc_final: 0.5750 (tmm) REVERT: B 4188 ARG cc_start: 0.8150 (mmm160) cc_final: 0.7314 (tpt170) REVERT: B 4207 MET cc_start: 0.8444 (mmm) cc_final: 0.8178 (mtp) REVERT: B 4223 ASN cc_start: 0.8303 (t0) cc_final: 0.8019 (t0) REVERT: B 4580 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.6670 (t80) REVERT: B 4639 MET cc_start: 0.8157 (mmm) cc_final: 0.7557 (mtm) REVERT: B 4725 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6404 (tp) REVERT: B 4821 LYS cc_start: 0.8174 (mmmt) cc_final: 0.7911 (mmmm) REVERT: B 4844 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8469 (tp) REVERT: B 5006 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7557 (pt0) REVERT: B 5030 LYS cc_start: 0.8443 (ttmt) cc_final: 0.7976 (ttmt) REVERT: C 4020 GLN cc_start: 0.7048 (tt0) cc_final: 0.6769 (tp40) REVERT: C 4047 MET cc_start: 0.6382 (tmm) cc_final: 0.5770 (tmm) REVERT: C 4188 ARG cc_start: 0.8151 (mmm160) cc_final: 0.7315 (tpt170) REVERT: C 4207 MET cc_start: 0.8426 (mmm) cc_final: 0.8156 (mtp) REVERT: C 4223 ASN cc_start: 0.8293 (t0) cc_final: 0.8007 (t0) REVERT: C 4580 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.6669 (t80) REVERT: C 4639 MET cc_start: 0.8166 (mmm) cc_final: 0.7570 (mtm) REVERT: C 4725 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6401 (tp) REVERT: C 4821 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7905 (mmmm) REVERT: C 4844 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8467 (tp) REVERT: C 5006 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7560 (pt0) REVERT: C 5030 LYS cc_start: 0.8435 (ttmt) cc_final: 0.7982 (ttmt) REVERT: D 4020 GLN cc_start: 0.7040 (tt0) cc_final: 0.6771 (tp40) REVERT: D 4047 MET cc_start: 0.6410 (tmm) cc_final: 0.5761 (tmm) REVERT: D 4188 ARG cc_start: 0.8150 (mmm160) cc_final: 0.7317 (tpt170) REVERT: D 4207 MET cc_start: 0.8446 (mmm) cc_final: 0.8179 (mtp) REVERT: D 4223 ASN cc_start: 0.8280 (t0) cc_final: 0.7998 (t0) REVERT: D 4580 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.6666 (t80) REVERT: D 4639 MET cc_start: 0.8162 (mmm) cc_final: 0.7566 (mtm) REVERT: D 4725 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6403 (tp) REVERT: D 4821 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7908 (mmmm) REVERT: D 4844 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8465 (tp) REVERT: D 5006 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7559 (pt0) REVERT: D 5030 LYS cc_start: 0.8426 (ttmt) cc_final: 0.7964 (ttmt) outliers start: 88 outliers final: 48 residues processed: 358 average time/residue: 0.5522 time to fit residues: 226.9945 Evaluate side-chains 353 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 289 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 96 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 162 optimal weight: 0.6980 chunk 205 optimal weight: 4.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.177442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.139710 restraints weight = 23499.405| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.01 r_work: 0.3199 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21068 Z= 0.164 Angle : 0.517 6.524 28432 Z= 0.265 Chirality : 0.038 0.181 3080 Planarity : 0.005 0.105 3592 Dihedral : 7.609 141.130 2748 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.70 % Favored : 98.13 % Rotamer: Outliers : 3.23 % Allowed : 17.16 % Favored : 79.61 % 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: 2.18 (0.17), residues: 2464 helix: 2.19 (0.12), residues: 1680 sheet: -1.22 (0.48), residues: 104 loop : 0.08 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B4189 TYR 0.013 0.001 TYR D4994 PHE 0.017 0.002 PHE B4916 TRP 0.010 0.002 TRP A5011 HIS 0.004 0.001 HIS C4650 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (21048) covalent geometry : angle 0.51225 / 0.26 (28416) SS BOND : bond 0.00061 / 0.03 ( 4) SS BOND : angle 1.53509 / 1.05 ( 8) hydrogen bonds : bond 0.04228 / 2.80 ( 1396) hydrogen bonds : angle 4.13791 / 2.99 ( 4068) metal coordination : bond 0.00729 / 0.43 ( 16) metal coordination : angle 4.14553 / 2.94 ( 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 361 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 289 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4000 MET cc_start: 0.4651 (tpt) cc_final: 0.3979 (mmm) REVERT: A 4020 GLN cc_start: 0.7010 (tt0) cc_final: 0.6750 (tp40) REVERT: A 4047 MET cc_start: 0.6428 (tmm) cc_final: 0.5811 (tmm) REVERT: A 4207 MET cc_start: 0.8447 (mmm) cc_final: 0.8177 (mtp) REVERT: A 4223 ASN cc_start: 0.8328 (t0) cc_final: 0.8032 (t0) REVERT: A 4580 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.6597 (t80) REVERT: A 4725 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6633 (tp) REVERT: A 4821 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7868 (mmmm) REVERT: A 4844 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8476 (tp) REVERT: A 5006 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7460 (pt0) REVERT: A 5016 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: A 5030 LYS cc_start: 0.8402 (ttmt) cc_final: 0.7509 (ttpt) REVERT: B 4000 MET cc_start: 0.4651 (tpt) cc_final: 0.3985 (mmm) REVERT: B 4020 GLN cc_start: 0.7060 (tt0) cc_final: 0.6819 (tp40) REVERT: B 4047 MET cc_start: 0.6413 (tmm) cc_final: 0.5802 (tmm) REVERT: B 4207 MET cc_start: 0.8473 (mmm) cc_final: 0.8204 (mtp) REVERT: B 4223 ASN cc_start: 0.8332 (t0) cc_final: 0.8037 (t0) REVERT: B 4580 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.6604 (t80) REVERT: B 4725 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6622 (tp) REVERT: B 4821 LYS cc_start: 0.8112 (mmmt) cc_final: 0.7870 (mmmm) REVERT: B 4844 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8476 (tp) REVERT: B 5006 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7454 (pt0) REVERT: B 5016 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8198 (mp0) REVERT: B 5030 LYS cc_start: 0.8403 (ttmt) cc_final: 0.7508 (ttpt) REVERT: C 4000 MET cc_start: 0.4655 (tpt) cc_final: 0.3988 (mmm) REVERT: C 4020 GLN cc_start: 0.7051 (tt0) cc_final: 0.6817 (tp40) REVERT: C 4047 MET cc_start: 0.6434 (tmm) cc_final: 0.5818 (tmm) REVERT: C 4207 MET cc_start: 0.8454 (mmm) cc_final: 0.8183 (mtp) REVERT: C 4223 ASN cc_start: 0.8326 (t0) cc_final: 0.8032 (t0) REVERT: C 4580 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.6600 (t80) REVERT: C 4725 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6620 (tp) REVERT: C 4821 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7863 (mmmm) REVERT: C 4844 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8479 (tp) REVERT: C 5006 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7451 (pt0) REVERT: C 5016 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8205 (mp0) REVERT: C 5030 LYS cc_start: 0.8395 (ttmt) cc_final: 0.7510 (ttpt) REVERT: D 4000 MET cc_start: 0.4656 (tpt) cc_final: 0.3988 (mmm) REVERT: D 4020 GLN cc_start: 0.7065 (tt0) cc_final: 0.6823 (tp40) REVERT: D 4047 MET cc_start: 0.6427 (tmm) cc_final: 0.5811 (tmm) REVERT: D 4207 MET cc_start: 0.8447 (mmm) cc_final: 0.8177 (mtp) REVERT: D 4223 ASN cc_start: 0.8326 (t0) cc_final: 0.8032 (t0) REVERT: D 4580 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.6599 (t80) REVERT: D 4725 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6628 (tp) REVERT: D 4821 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7874 (mmmm) REVERT: D 4844 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8476 (tp) REVERT: D 5006 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7456 (pt0) REVERT: D 5016 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8192 (mp0) REVERT: D 5030 LYS cc_start: 0.8408 (ttmt) cc_final: 0.7512 (ttpt) outliers start: 72 outliers final: 40 residues processed: 348 average time/residue: 0.5536 time to fit residues: 220.9890 Evaluate side-chains 340 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 280 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 194 optimal weight: 0.2980 chunk 241 optimal weight: 0.7980 chunk 229 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 chunk 80 optimal weight: 0.0470 chunk 4 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.179549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.143530 restraints weight = 23542.913| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.85 r_work: 0.3301 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2340 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= 0.111 Angle : 0.504 6.679 28432 Z= 0.257 Chirality : 0.036 0.182 3080 Planarity : 0.005 0.101 3592 Dihedral : 7.498 139.814 2748 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.11 % Favored : 97.73 % Rotamer: Outliers : 2.55 % Allowed : 18.19 % Favored : 79.26 % 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: 2.41 (0.17), residues: 2464 helix: 2.38 (0.12), residues: 1680 sheet: -1.26 (0.48), residues: 104 loop : 0.13 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D4188 TYR 0.010 0.001 TYR C4554 PHE 0.014 0.001 PHE A4916 TRP 0.007 0.001 TRP A4716 HIS 0.003 0.001 HIS C3998 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (21048) covalent geometry : angle 0.50015 / 0.26 (28416) SS BOND : bond 0.00042 / 0.02 ( 4) SS BOND : angle 1.06258 / 0.73 ( 8) hydrogen bonds : bond 0.03762 / 2.49 ( 1396) hydrogen bonds : angle 4.00320 / 2.89 ( 4068) metal coordination : bond 0.00154 / 0.09 ( 16) metal coordination : angle 3.73271 / 2.59 ( 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 358 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 301 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3967 GLU cc_start: 0.7990 (mm-30) cc_final: 0.6989 (tm-30) REVERT: A 4020 GLN cc_start: 0.6907 (tt0) cc_final: 0.6646 (tp40) REVERT: A 4047 MET cc_start: 0.6385 (tmm) cc_final: 0.5791 (tmm) REVERT: A 4188 ARG cc_start: 0.8104 (mmm160) cc_final: 0.7198 (tpt170) REVERT: A 4207 MET cc_start: 0.8361 (mmm) cc_final: 0.8076 (mtp) REVERT: A 4580 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.6601 (t80) REVERT: A 4725 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6538 (tp) REVERT: A 4821 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7844 (mmmm) REVERT: A 4844 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8436 (tp) REVERT: A 5006 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7500 (pt0) REVERT: A 5016 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8216 (mp0) REVERT: A 5030 LYS cc_start: 0.8360 (ttmt) cc_final: 0.7410 (ttpt) REVERT: B 3967 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7002 (tm-30) REVERT: B 4000 MET cc_start: 0.4667 (tpt) cc_final: 0.4004 (mmm) REVERT: B 4020 GLN cc_start: 0.7042 (tt0) cc_final: 0.6810 (tp40) REVERT: B 4047 MET cc_start: 0.6378 (tmm) cc_final: 0.5783 (tmm) REVERT: B 4188 ARG cc_start: 0.8088 (mmm160) cc_final: 0.7185 (tpt170) REVERT: B 4207 MET cc_start: 0.8375 (mmm) cc_final: 0.8091 (mtp) REVERT: B 4580 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.6612 (t80) REVERT: B 4725 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6534 (tp) REVERT: B 4821 LYS cc_start: 0.8121 (mmmt) cc_final: 0.7850 (mmmm) REVERT: B 4844 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8438 (tp) REVERT: B 5006 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7490 (pt0) REVERT: B 5016 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8237 (mp0) REVERT: B 5030 LYS cc_start: 0.8366 (ttmt) cc_final: 0.7421 (ttpt) REVERT: C 3967 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7080 (tm-30) REVERT: C 4000 MET cc_start: 0.4666 (tpt) cc_final: 0.3999 (mmm) REVERT: C 4020 GLN cc_start: 0.7027 (tt0) cc_final: 0.6801 (tp40) REVERT: C 4047 MET cc_start: 0.6397 (tmm) cc_final: 0.5796 (tmm) REVERT: C 4188 ARG cc_start: 0.8096 (mmm160) cc_final: 0.7194 (tpt170) REVERT: C 4207 MET cc_start: 0.8360 (mmm) cc_final: 0.8075 (mtp) REVERT: C 4580 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.6594 (t80) REVERT: C 4725 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6531 (tp) REVERT: C 4821 LYS cc_start: 0.8115 (mmmt) cc_final: 0.7847 (mmmm) REVERT: C 4844 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8478 (tp) REVERT: C 5006 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7491 (pt0) REVERT: C 5016 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8224 (mp0) REVERT: C 5030 LYS cc_start: 0.8366 (ttmt) cc_final: 0.7428 (ttpt) REVERT: D 3967 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7053 (tm-30) REVERT: D 4000 MET cc_start: 0.4668 (tpt) cc_final: 0.3997 (mmm) REVERT: D 4020 GLN cc_start: 0.7040 (tt0) cc_final: 0.6808 (tp40) REVERT: D 4047 MET cc_start: 0.6392 (tmm) cc_final: 0.5794 (tmm) REVERT: D 4188 ARG cc_start: 0.8101 (mmm160) cc_final: 0.7196 (tpt170) REVERT: D 4207 MET cc_start: 0.8367 (mmm) cc_final: 0.8084 (mtp) REVERT: D 4580 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.6588 (t80) REVERT: D 4725 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6520 (tp) REVERT: D 4821 LYS cc_start: 0.8128 (mmmt) cc_final: 0.7862 (mmmm) REVERT: D 4844 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8436 (tp) REVERT: D 5006 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7494 (pt0) REVERT: D 5016 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8222 (mp0) REVERT: D 5030 LYS cc_start: 0.8365 (ttmt) cc_final: 0.7415 (ttpt) outliers start: 57 outliers final: 27 residues processed: 353 average time/residue: 0.5147 time to fit residues: 208.5678 Evaluate side-chains 338 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 291 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 4666 VAL 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 5006 GLN Chi-restraints excluded: chain A residue 5016 GLU 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 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 4221 VAL 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 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 4221 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 2 optimal weight: 0.0870 chunk 94 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 134 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 146 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.179496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.142836 restraints weight = 23559.851| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.58 r_work: 0.3283 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2415 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= 0.116 Angle : 0.497 5.925 28432 Z= 0.254 Chirality : 0.036 0.194 3080 Planarity : 0.005 0.098 3592 Dihedral : 7.452 139.180 2748 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.58 % Favored : 98.25 % Rotamer: Outliers : 2.42 % Allowed : 18.55 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.17), residues: 2464 helix: 2.36 (0.12), residues: 1680 sheet: -1.25 (0.49), residues: 104 loop : 0.15 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C4188 TYR 0.011 0.001 TYR A4687 PHE 0.016 0.001 PHE A4916 TRP 0.008 0.001 TRP A5011 HIS 0.003 0.001 HIS B3998 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (21048) covalent geometry : angle 0.49330 / 0.25 (28416) SS BOND : bond 0.00060 / 0.03 ( 4) SS BOND : angle 1.11524 / 0.76 ( 8) hydrogen bonds : bond 0.03785 / 2.51 ( 1396) hydrogen bonds : angle 4.01213 / 2.90 ( 4068) metal coordination : bond 0.00245 / 0.15 ( 16) metal coordination : angle 3.68304 / 2.56 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7750.01 seconds wall clock time: 132 minutes 57.76 seconds (7977.76 seconds total)