Starting phenix.real_space_refine on Fri Aug 7 10:02:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sf0_40435/08_2026/8sf0_40435.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sf0_40435/08_2026/8sf0_40435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8sf0_40435/08_2026/8sf0_40435.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sf0_40435/08_2026/8sf0_40435.cif" model { file = "/net/cci-nas-00/data/ceres_data/8sf0_40435/08_2026/8sf0_40435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sf0_40435/08_2026/8sf0_40435.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sf0_40435/08_2026/8sf0_40435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sf0_40435/08_2026/8sf0_40435.map" } resolution = 2.9 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= 0.054 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 13432 2.51 5 N 3288 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 67 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20664 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5143 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 15, 'TRANS': 612} Chain breaks: 4 Chain: "B" Number of atoms: 5143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5143 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 15, 'TRANS': 612} Chain breaks: 4 Chain: "C" Number of atoms: 5143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5143 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 15, 'TRANS': 612} Chain breaks: 4 Chain: "D" Number of atoms: 5143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5143 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 15, 'TRANS': 612} Chain breaks: 4 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' ZN': 1} Classifications: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' ZN': 1} Classifications: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' ZN': 1} Classifications: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' ZN': 1} Classifications: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4469 SG CYS A4958 55.702 81.546 88.347 1.00 47.31 S ATOM 4494 SG CYS A4961 58.158 82.398 91.197 1.00 45.93 S ATOM 9612 SG CYS B4958 60.133 55.703 88.347 1.00 47.35 S ATOM 9637 SG CYS B4961 59.282 58.157 91.198 1.00 45.70 S ATOM 14755 SG CYS C4958 85.978 60.133 88.347 1.00 47.42 S ATOM 14780 SG CYS C4961 83.523 59.282 91.197 1.00 45.49 S ATOM 19898 SG CYS D4958 81.547 85.978 88.347 1.00 47.46 S ATOM 19923 SG CYS D4961 82.398 83.522 91.198 1.00 46.04 S Time building chain proxies: 3.50, per 1000 atoms: 0.17 Number of scatterers: 20664 At special positions: 0 Unit cell: (142.968, 142.968, 131.376, 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 3288 7.00 C 13432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.03 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " distance=2.03 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " distance=2.03 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 688.9 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 A4961 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4958 " pdb=" ZN B5102 " pdb="ZN ZN B5102 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5102 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4958 " pdb=" ZN C5102 " pdb="ZN ZN C5102 " - pdb=" ND1 HIS C4983 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4958 " pdb=" ZN D5102 " pdb="ZN ZN D5102 " - pdb=" ND1 HIS D4983 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4958 " Number of angles added : 8 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4728 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 8 sheets defined 79.3% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 3950 through 3970 removed outlier: 3.575A pdb=" N ALA A3958 " --> pdb=" O ALA A3954 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN A3960 " --> pdb=" O SER A3956 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A3969 " --> pdb=" O LEU A3965 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3983 removed outlier: 3.690A pdb=" N HIS A3982 " --> pdb=" O GLN A3978 " (cutoff:3.500A) Processing helix chain 'A' and resid 3984 through 4006 removed outlier: 3.523A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) Processing helix chain 'A' and resid 4010 through 4032 removed outlier: 3.629A pdb=" N ASP A4018 " --> pdb=" O LYS A4014 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A4019 " --> pdb=" O GLU A4015 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN A4020 " --> pdb=" O LEU A4016 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A4021 " --> pdb=" O LEU A4017 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A4025 " --> pdb=" O LYS A4021 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET A4026 " --> pdb=" O ASP A4022 " (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 4226 through 4252 removed outlier: 4.429A pdb=" N MET A4231 " --> pdb=" O GLU A4227 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU A4232 " --> pdb=" O ALA A4228 " (cutoff:3.500A) Processing helix chain 'A' and resid 4541 through 4558 Processing helix chain 'A' and resid 4558 through 4578 Processing helix chain 'A' and resid 4638 through 4665 removed outlier: 3.776A pdb=" N TRP A4644 " --> pdb=" O GLU A4640 " (cutoff:3.500A) 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: 3.863A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) removed outlier: 4.666A 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: 4.723A pdb=" N ASP A4730 " --> pdb=" O ASP A4726 " (cutoff:3.500A) removed outlier: 5.457A 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 4750 removed outlier: 3.659A pdb=" N LEU A4748 " --> pdb=" O ASP A4744 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU A4749 " --> pdb=" O LEU A4745 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A4750 " --> pdb=" O ALA A4746 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4744 through 4750' Processing helix chain 'A' and resid 4773 through 4784 Processing helix chain 'A' and resid 4786 through 4805 removed outlier: 3.852A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4813 Processing helix chain 'A' and resid 4814 through 4820 removed outlier: 3.833A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) Processing helix chain 'A' and resid 4820 through 4833 removed outlier: 3.656A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASN A4833 " --> pdb=" O SER A4829 " (cutoff:3.500A) Processing helix chain 'A' and resid 4833 through 4859 removed outlier: 3.565A pdb=" N ASN A4857 " --> pdb=" O VAL A4853 " (cutoff:3.500A) Processing helix chain 'A' and resid 4860 through 4863 Processing helix chain 'A' and resid 4878 through 4890 Processing helix chain 'A' and resid 4896 through 4901 removed outlier: 4.213A pdb=" N GLU A4900 " --> 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: 3.734A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) Processing helix chain 'A' and resid 4973 through 4982 Processing helix chain 'A' and resid 4984 through 4998 Processing helix chain 'A' and resid 5004 through 5016 Processing helix chain 'A' and resid 5027 through 5032 Processing helix chain 'A' and resid 5032 through 5037 Processing helix chain 'B' and resid 3951 through 3970 removed outlier: 3.575A pdb=" N ALA B3958 " --> pdb=" O ALA B3954 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B3960 " --> pdb=" O SER B3956 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B3969 " --> pdb=" O LEU B3965 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3983 removed outlier: 3.690A pdb=" N HIS B3982 " --> pdb=" O GLN B3978 " (cutoff:3.500A) Processing helix chain 'B' and resid 3984 through 4006 removed outlier: 3.522A pdb=" N MET B4001 " --> pdb=" O ALA B3997 " (cutoff:3.500A) Processing helix chain 'B' and resid 4010 through 4032 removed outlier: 3.629A pdb=" N ASP B4018 " --> pdb=" O LYS B4014 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B4019 " --> pdb=" O GLU B4015 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN B4020 " --> pdb=" O LEU B4016 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B4021 " --> pdb=" O LEU B4017 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B4025 " --> pdb=" O LYS B4021 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET B4026 " --> pdb=" O ASP B4022 " (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 4226 through 4252 removed outlier: 4.430A pdb=" N MET B4231 " --> pdb=" O GLU B4227 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU B4232 " --> pdb=" O ALA B4228 " (cutoff:3.500A) Processing helix chain 'B' and resid 4541 through 4558 Processing helix chain 'B' and resid 4558 through 4578 Processing helix chain 'B' and resid 4638 through 4665 removed outlier: 3.776A pdb=" N TRP B4644 " --> pdb=" O GLU B4640 " (cutoff:3.500A) 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: 3.862A pdb=" N LEU B4706 " --> pdb=" O ASP B4702 " (cutoff:3.500A) removed outlier: 4.665A 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: 4.723A pdb=" N ASP B4730 " --> pdb=" O ASP B4726 " (cutoff:3.500A) removed outlier: 5.457A 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 4750 removed outlier: 3.659A pdb=" N LEU B4748 " --> pdb=" O ASP B4744 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU B4749 " --> pdb=" O LEU B4745 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B4750 " --> pdb=" O ALA B4746 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4744 through 4750' Processing helix chain 'B' and resid 4773 through 4784 Processing helix chain 'B' and resid 4786 through 4805 removed outlier: 3.853A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4806 through 4813 Processing helix chain 'B' and resid 4814 through 4820 removed outlier: 3.833A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) Processing helix chain 'B' and resid 4820 through 4833 removed outlier: 3.656A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASN B4833 " --> pdb=" O SER B4829 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4859 removed outlier: 3.563A pdb=" N ASN B4857 " --> pdb=" O VAL B4853 " (cutoff:3.500A) Processing helix chain 'B' and resid 4860 through 4863 Processing helix chain 'B' and resid 4878 through 4890 Processing helix chain 'B' and resid 4896 through 4901 removed outlier: 4.212A pdb=" N GLU B4900 " --> 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: 3.734A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4982 Processing helix chain 'B' and resid 4984 through 4998 Processing helix chain 'B' and resid 5004 through 5016 Processing helix chain 'B' and resid 5027 through 5032 Processing helix chain 'B' and resid 5032 through 5037 Processing helix chain 'C' and resid 3951 through 3970 removed outlier: 3.575A pdb=" N ALA C3958 " --> pdb=" O ALA C3954 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN C3960 " --> pdb=" O SER C3956 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C3969 " --> pdb=" O LEU C3965 " (cutoff:3.500A) Processing helix chain 'C' and resid 3973 through 3983 removed outlier: 3.690A pdb=" N HIS C3982 " --> pdb=" O GLN C3978 " (cutoff:3.500A) Processing helix chain 'C' and resid 3984 through 4006 removed outlier: 3.522A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) Processing helix chain 'C' and resid 4010 through 4032 removed outlier: 3.629A pdb=" N ASP C4018 " --> pdb=" O LYS C4014 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU C4019 " --> pdb=" O GLU C4015 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN C4020 " --> pdb=" O LEU C4016 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C4021 " --> pdb=" O LEU C4017 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL C4025 " --> pdb=" O LYS C4021 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET C4026 " --> pdb=" O ASP C4022 " (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 4226 through 4252 removed outlier: 4.429A pdb=" N MET C4231 " --> pdb=" O GLU C4227 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU C4232 " --> pdb=" O ALA C4228 " (cutoff:3.500A) Processing helix chain 'C' and resid 4541 through 4558 Processing helix chain 'C' and resid 4558 through 4578 Processing helix chain 'C' and resid 4638 through 4665 removed outlier: 3.777A pdb=" N TRP C4644 " --> pdb=" O GLU C4640 " (cutoff:3.500A) 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: 3.862A pdb=" N LEU C4706 " --> pdb=" O ASP C4702 " (cutoff:3.500A) removed outlier: 4.665A 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: 4.723A pdb=" N ASP C4730 " --> pdb=" O ASP C4726 " (cutoff:3.500A) removed outlier: 5.457A 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 4750 removed outlier: 3.659A pdb=" N LEU C4748 " --> pdb=" O ASP C4744 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU C4749 " --> pdb=" O LEU C4745 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE C4750 " --> pdb=" O ALA C4746 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4744 through 4750' Processing helix chain 'C' and resid 4773 through 4784 Processing helix chain 'C' and resid 4786 through 4805 removed outlier: 3.853A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4806 through 4813 Processing helix chain 'C' and resid 4814 through 4820 removed outlier: 3.836A pdb=" N MET C4818 " --> pdb=" O LEU C4814 " (cutoff:3.500A) Processing helix chain 'C' and resid 4820 through 4833 removed outlier: 3.656A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN C4833 " --> pdb=" O SER C4829 " (cutoff:3.500A) Processing helix chain 'C' and resid 4833 through 4859 removed outlier: 3.562A pdb=" N ASN C4857 " --> pdb=" O VAL C4853 " (cutoff:3.500A) Processing helix chain 'C' and resid 4860 through 4863 Processing helix chain 'C' and resid 4878 through 4890 Processing helix chain 'C' and resid 4896 through 4901 removed outlier: 4.212A pdb=" N GLU C4900 " --> 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: 3.734A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) Processing helix chain 'C' and resid 4973 through 4982 Processing helix chain 'C' and resid 4984 through 4998 Processing helix chain 'C' and resid 5004 through 5016 Processing helix chain 'C' and resid 5027 through 5032 Processing helix chain 'C' and resid 5032 through 5037 Processing helix chain 'D' and resid 3951 through 3970 removed outlier: 3.575A pdb=" N ALA D3958 " --> pdb=" O ALA D3954 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN D3960 " --> pdb=" O SER D3956 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE D3969 " --> pdb=" O LEU D3965 " (cutoff:3.500A) Processing helix chain 'D' and resid 3973 through 3983 removed outlier: 3.690A pdb=" N HIS D3982 " --> pdb=" O GLN D3978 " (cutoff:3.500A) Processing helix chain 'D' and resid 3984 through 4006 removed outlier: 3.523A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) Processing helix chain 'D' and resid 4010 through 4032 removed outlier: 3.629A pdb=" N ASP D4018 " --> pdb=" O LYS D4014 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU D4019 " --> pdb=" O GLU D4015 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN D4020 " --> pdb=" O LEU D4016 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS D4021 " --> pdb=" O LEU D4017 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D4025 " --> pdb=" O LYS D4021 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET D4026 " --> pdb=" O ASP D4022 " (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 4226 through 4252 removed outlier: 4.429A pdb=" N MET D4231 " --> pdb=" O GLU D4227 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLU D4232 " --> pdb=" O ALA D4228 " (cutoff:3.500A) Processing helix chain 'D' and resid 4541 through 4558 Processing helix chain 'D' and resid 4558 through 4578 Processing helix chain 'D' and resid 4638 through 4665 removed outlier: 3.779A pdb=" N TRP D4644 " --> pdb=" O GLU D4640 " (cutoff:3.500A) 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: 3.862A pdb=" N LEU D4706 " --> pdb=" O ASP D4702 " (cutoff:3.500A) removed outlier: 4.666A 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: 4.723A pdb=" N ASP D4730 " --> pdb=" O ASP D4726 " (cutoff:3.500A) removed outlier: 5.457A 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 4750 removed outlier: 3.659A pdb=" N LEU D4748 " --> pdb=" O ASP D4744 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU D4749 " --> pdb=" O LEU D4745 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE D4750 " --> pdb=" O ALA D4746 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4744 through 4750' Processing helix chain 'D' and resid 4773 through 4784 Processing helix chain 'D' and resid 4786 through 4805 removed outlier: 3.852A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4806 through 4813 Processing helix chain 'D' and resid 4814 through 4820 removed outlier: 3.834A pdb=" N MET D4818 " --> pdb=" O LEU D4814 " (cutoff:3.500A) Processing helix chain 'D' and resid 4820 through 4833 removed outlier: 3.656A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN D4833 " --> pdb=" O SER D4829 " (cutoff:3.500A) Processing helix chain 'D' and resid 4833 through 4859 removed outlier: 3.561A pdb=" N ASN D4857 " --> pdb=" O VAL D4853 " (cutoff:3.500A) Processing helix chain 'D' and resid 4860 through 4863 Processing helix chain 'D' and resid 4878 through 4890 Processing helix chain 'D' and resid 4896 through 4901 removed outlier: 4.211A pdb=" N GLU D4900 " --> 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: 3.734A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) Processing helix chain 'D' and resid 4973 through 4982 Processing helix chain 'D' and resid 4984 through 4998 Processing helix chain 'D' and resid 5004 through 5016 Processing helix chain 'D' and resid 5027 through 5032 Processing helix chain 'D' and resid 5032 through 5037 Processing sheet with id=AA1, first strand: chain 'A' and resid 4178 through 4184 Processing sheet with id=AA2, first strand: chain 'A' and resid 4580 through 4583 Processing sheet with id=AA3, first strand: chain 'B' and resid 4178 through 4184 Processing sheet with id=AA4, first strand: chain 'B' and resid 4580 through 4583 Processing sheet with id=AA5, first strand: chain 'C' and resid 4178 through 4184 Processing sheet with id=AA6, first strand: chain 'C' and resid 4580 through 4583 Processing sheet with id=AA7, first strand: chain 'D' and resid 4178 through 4184 Processing sheet with id=AA8, first strand: chain 'D' and resid 4580 through 4583 1361 hydrogen bonds defined for protein. 3999 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: 3.29 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6479 1.34 - 1.46: 4267 1.46 - 1.58: 10130 1.58 - 1.69: 8 1.69 - 1.81: 276 Bond restraints: 21160 Sorted by residual: bond pdb=" C4' CMP A5101 " pdb=" C5' CMP A5101 " ideal model delta sigma weight residual 1.524 1.499 0.025 2.00e-02 2.50e+03 1.54e+00 bond pdb=" C4' CMP C5101 " pdb=" C5' CMP C5101 " ideal model delta sigma weight residual 1.524 1.499 0.025 2.00e-02 2.50e+03 1.54e+00 bond pdb=" C4' CMP D5101 " pdb=" C5' CMP D5101 " ideal model delta sigma weight residual 1.524 1.500 0.024 2.00e-02 2.50e+03 1.47e+00 bond pdb=" C4' CMP B5101 " pdb=" C5' CMP B5101 " ideal model delta sigma weight residual 1.524 1.500 0.024 2.00e-02 2.50e+03 1.47e+00 bond pdb=" C4 CMP D5101 " pdb=" C5 CMP D5101 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.21e+00 ... (remaining 21155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 28232 1.98 - 3.96: 275 3.96 - 5.95: 49 5.95 - 7.93: 8 7.93 - 9.91: 12 Bond angle restraints: 28576 Sorted by residual: angle pdb=" N GLU B4676 " pdb=" CA GLU B4676 " pdb=" CB GLU B4676 " ideal model delta sigma weight residual 110.16 115.18 -5.02 1.48e+00 4.57e-01 1.15e+01 angle pdb=" N GLU D4676 " pdb=" CA GLU D4676 " pdb=" CB GLU D4676 " ideal model delta sigma weight residual 110.16 115.12 -4.96 1.48e+00 4.57e-01 1.12e+01 angle pdb=" N GLU C4676 " pdb=" CA GLU C4676 " pdb=" CB GLU C4676 " ideal model delta sigma weight residual 110.16 115.12 -4.96 1.48e+00 4.57e-01 1.12e+01 angle pdb=" N GLU A4676 " pdb=" CA GLU A4676 " pdb=" CB GLU A4676 " ideal model delta sigma weight residual 110.16 115.11 -4.95 1.48e+00 4.57e-01 1.12e+01 angle pdb=" C1' CMP B5101 " pdb=" C2' CMP B5101 " pdb=" C3' CMP B5101 " ideal model delta sigma weight residual 111.00 101.09 9.91 3.00e+00 1.11e-01 1.09e+01 ... (remaining 28571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.94: 12145 31.94 - 63.87: 247 63.87 - 95.81: 36 95.81 - 127.74: 4 127.74 - 159.68: 8 Dihedral angle restraints: 12440 sinusoidal: 5104 harmonic: 7336 Sorted by residual: dihedral pdb=" C3' CMP B5101 " pdb=" O3' CMP B5101 " pdb=" P CMP B5101 " pdb=" O1P CMP B5101 " ideal model delta sinusoidal sigma weight residual -60.00 99.68 -159.68 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C3' CMP A5101 " pdb=" O3' CMP A5101 " pdb=" P CMP A5101 " pdb=" O1P CMP A5101 " ideal model delta sinusoidal sigma weight residual -60.00 99.66 -159.66 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C3' CMP C5101 " pdb=" O3' CMP C5101 " pdb=" P CMP C5101 " pdb=" O1P CMP C5101 " ideal model delta sinusoidal sigma weight residual -60.00 99.66 -159.66 1 2.00e+01 2.50e-03 4.65e+01 ... (remaining 12437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2630 0.053 - 0.105: 427 0.105 - 0.158: 27 0.158 - 0.210: 4 0.210 - 0.263: 4 Chirality restraints: 3092 Sorted by residual: chirality pdb=" C2' CMP D5101 " pdb=" C1' CMP D5101 " pdb=" C3' CMP D5101 " pdb=" O2' CMP D5101 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C2' CMP C5101 " pdb=" C1' CMP C5101 " pdb=" C3' CMP C5101 " pdb=" O2' CMP C5101 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C2' CMP A5101 " pdb=" C1' CMP A5101 " pdb=" C3' CMP A5101 " pdb=" O2' CMP A5101 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 3089 not shown) Planarity restraints: 3604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D3971 " -0.054 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO D3972 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO D3972 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO D3972 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A3971 " -0.054 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO A3972 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A3972 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A3972 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B3971 " 0.054 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO B3972 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B3972 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B3972 " 0.045 5.00e-02 4.00e+02 ... (remaining 3601 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 387 2.71 - 3.26: 21313 3.26 - 3.80: 34046 3.80 - 4.35: 42769 4.35 - 4.90: 71782 Nonbonded interactions: 170297 Sorted by model distance: nonbonded pdb=" OH TYR B4967 " pdb=" OE2 GLU B5033 " model vdw 2.161 3.040 nonbonded pdb=" OH TYR D4967 " pdb=" OE2 GLU D5033 " model vdw 2.161 3.040 nonbonded pdb=" OH TYR C4967 " pdb=" OE2 GLU C5033 " model vdw 2.162 3.040 nonbonded pdb=" OH TYR A4967 " pdb=" OE2 GLU A5033 " model vdw 2.162 3.040 nonbonded pdb=" OE1 GLU A4232 " pdb=" NE1 TRP A5019 " model vdw 2.272 3.120 ... (remaining 170292 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.210 Find NCS groups from input model: 0.120 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:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.003 0.029 21180 Z= 0.134 Angle : 0.561 9.911 28592 Z= 0.282 Chirality : 0.038 0.263 3092 Planarity : 0.004 0.082 3604 Dihedral : 14.764 159.680 7700 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 1.75 (0.17), residues: 2472 helix: 1.87 (0.12), residues: 1724 sheet: 0.55 (0.52), residues: 104 loop : -0.66 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D4202 TYR 0.012 0.001 TYR B5032 PHE 0.017 0.001 PHE A4683 TRP 0.011 0.001 TRP D4644 HIS 0.004 0.001 HIS D4803 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (21160) covalent geometry : angle 0.55439 / 0.28 (28576) SS BOND : bond 0.00034 / 0.02 ( 4) SS BOND : angle 0.68023 / 0.46 ( 8) hydrogen bonds : bond 0.15430 / 10.65 ( 1361) hydrogen bonds : angle 4.98847 / 3.54 ( 3999) metal coordination : bond 0.00438 / 0.27 ( 16) metal coordination : angle 5.27049 / 3.44 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.613 Fit side-chains REVERT: A 4043 GLN cc_start: 0.8272 (mm110) cc_final: 0.7683 (mm110) REVERT: A 4633 GLU cc_start: 0.6843 (tp30) cc_final: 0.6570 (pp20) REVERT: A 4851 TYR cc_start: 0.8835 (m-80) cc_final: 0.8625 (m-80) REVERT: A 4980 LEU cc_start: 0.8247 (mt) cc_final: 0.7849 (tp) REVERT: B 4043 GLN cc_start: 0.8272 (mm110) cc_final: 0.7686 (mm110) REVERT: B 4633 GLU cc_start: 0.6826 (tp30) cc_final: 0.6607 (pp20) REVERT: B 4851 TYR cc_start: 0.8726 (m-80) cc_final: 0.8517 (m-80) REVERT: B 4980 LEU cc_start: 0.8237 (mt) cc_final: 0.7841 (tp) REVERT: C 4043 GLN cc_start: 0.8268 (mm110) cc_final: 0.7684 (mm110) REVERT: C 4633 GLU cc_start: 0.6814 (tp30) cc_final: 0.6600 (pp20) REVERT: C 4980 LEU cc_start: 0.8249 (mt) cc_final: 0.7852 (tp) REVERT: D 4043 GLN cc_start: 0.8270 (mm110) cc_final: 0.7678 (mm110) REVERT: D 4633 GLU cc_start: 0.6830 (tp30) cc_final: 0.6593 (pp20) REVERT: D 4980 LEU cc_start: 0.8245 (mt) cc_final: 0.7850 (tp) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.6787 time to fit residues: 278.8704 Evaluate side-chains 301 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3982 HIS A3998 HIS A4223 ASN ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4662 ASN B3982 HIS B3998 HIS B4223 ASN ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4662 ASN C3982 HIS C3998 HIS C4223 ASN ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4662 ASN D3982 HIS D3998 HIS D4223 ASN ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4662 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.187166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.128386 restraints weight = 23169.083| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.58 r_work: 0.3225 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 21180 Z= 0.212 Angle : 0.627 7.498 28592 Z= 0.320 Chirality : 0.039 0.129 3092 Planarity : 0.005 0.065 3604 Dihedral : 11.679 179.018 2748 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.50 % Allowed : 7.68 % Favored : 89.82 % 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: 1.35 (0.17), residues: 2472 helix: 1.52 (0.12), residues: 1732 sheet: 0.13 (0.51), residues: 104 loop : -0.60 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D4736 TYR 0.015 0.002 TYR C4994 PHE 0.016 0.002 PHE D4916 TRP 0.009 0.001 TRP C4716 HIS 0.003 0.001 HIS C4650 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (21160) covalent geometry : angle 0.62521 / 0.32 (28576) SS BOND : bond 0.00207 / 0.10 ( 4) SS BOND : angle 1.34991 / 0.89 ( 8) hydrogen bonds : bond 0.05648 / 3.81 ( 1361) hydrogen bonds : angle 4.64930 / 3.37 ( 3999) metal coordination : bond 0.00996 / 0.59 ( 16) metal coordination : angle 2.73406 / 1.97 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 307 time to evaluate : 0.587 Fit side-chains REVERT: A 4000 MET cc_start: 0.6375 (mtt) cc_final: 0.6115 (mtm) REVERT: A 4043 GLN cc_start: 0.8121 (mm110) cc_final: 0.7571 (mm-40) REVERT: A 4057 MET cc_start: 0.6861 (tpt) cc_final: 0.6370 (tpt) REVERT: A 4633 GLU cc_start: 0.7756 (tp30) cc_final: 0.6540 (pp20) REVERT: A 4911 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7619 (mm) REVERT: A 4933 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7667 (mm110) REVERT: A 4980 LEU cc_start: 0.8241 (mt) cc_final: 0.7626 (tp) REVERT: A 5027 CYS cc_start: 0.8324 (p) cc_final: 0.7870 (p) REVERT: B 4000 MET cc_start: 0.6379 (mtt) cc_final: 0.6113 (mtm) REVERT: B 4043 GLN cc_start: 0.8127 (mm110) cc_final: 0.7577 (mm-40) REVERT: B 4057 MET cc_start: 0.6854 (tpt) cc_final: 0.6364 (tpt) REVERT: B 4633 GLU cc_start: 0.7752 (tp30) cc_final: 0.6538 (pp20) REVERT: B 4911 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7612 (mm) REVERT: B 4933 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7669 (mm110) REVERT: B 4980 LEU cc_start: 0.8243 (mt) cc_final: 0.7625 (tp) REVERT: B 5027 CYS cc_start: 0.8311 (p) cc_final: 0.7939 (p) REVERT: C 4000 MET cc_start: 0.6382 (mtt) cc_final: 0.6104 (mtm) REVERT: C 4043 GLN cc_start: 0.8127 (mm110) cc_final: 0.7581 (mm-40) REVERT: C 4633 GLU cc_start: 0.7747 (tp30) cc_final: 0.6542 (pp20) REVERT: C 4911 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7614 (mm) REVERT: C 4980 LEU cc_start: 0.8250 (mt) cc_final: 0.7644 (tp) REVERT: C 5027 CYS cc_start: 0.8317 (p) cc_final: 0.7863 (p) REVERT: D 4000 MET cc_start: 0.6381 (mtt) cc_final: 0.6116 (mtm) REVERT: D 4043 GLN cc_start: 0.8125 (mm110) cc_final: 0.7575 (mm-40) REVERT: D 4057 MET cc_start: 0.6866 (tpt) cc_final: 0.6371 (tpt) REVERT: D 4633 GLU cc_start: 0.7761 (tp30) cc_final: 0.6548 (pp20) REVERT: D 4911 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7613 (mm) REVERT: D 4980 LEU cc_start: 0.8248 (mt) cc_final: 0.7633 (tp) REVERT: D 5027 CYS cc_start: 0.8323 (p) cc_final: 0.7869 (p) outliers start: 56 outliers final: 12 residues processed: 323 average time/residue: 0.6392 time to fit residues: 230.5385 Evaluate side-chains 316 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 298 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4215 ARG Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain A residue 4976 GLU Chi-restraints excluded: chain B residue 4215 ARG Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain B residue 4976 GLU Chi-restraints excluded: chain C residue 4215 ARG Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain C residue 4976 GLU Chi-restraints excluded: chain D residue 4215 ARG Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain D residue 4976 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 208 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 209 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 241 optimal weight: 0.4980 chunk 240 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 230 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4223 ASN ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4223 ASN ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4933 GLN ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4933 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.189082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.130247 restraints weight = 23271.957| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.60 r_work: 0.3238 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21180 Z= 0.132 Angle : 0.528 8.615 28592 Z= 0.269 Chirality : 0.035 0.135 3092 Planarity : 0.004 0.052 3604 Dihedral : 11.530 176.164 2748 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.07 % Allowed : 9.64 % Favored : 89.29 % 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: 1.64 (0.17), residues: 2472 helix: 1.76 (0.12), residues: 1732 sheet: 0.23 (0.50), residues: 104 loop : -0.56 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C4189 TYR 0.012 0.001 TYR A4994 PHE 0.012 0.001 PHE A4916 TRP 0.007 0.001 TRP C4644 HIS 0.003 0.001 HIS A3998 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (21160) covalent geometry : angle 0.52562 / 0.27 (28576) SS BOND : bond 0.00048 / 0.02 ( 4) SS BOND : angle 0.91576 / 0.61 ( 8) hydrogen bonds : bond 0.04669 / 3.15 ( 1361) hydrogen bonds : angle 4.39831 / 3.19 ( 3999) metal coordination : bond 0.00436 / 0.26 ( 16) metal coordination : angle 2.80281 / 1.99 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 331 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4043 GLN cc_start: 0.8151 (mm110) cc_final: 0.7517 (mm-40) REVERT: A 4224 GLU cc_start: 0.6785 (pm20) cc_final: 0.6355 (pm20) REVERT: A 4633 GLU cc_start: 0.7685 (tp30) cc_final: 0.6435 (pp20) REVERT: A 4684 ASP cc_start: 0.8431 (m-30) cc_final: 0.8068 (m-30) REVERT: A 4911 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7531 (mm) REVERT: A 4933 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7338 (mm110) REVERT: A 4980 LEU cc_start: 0.8258 (mt) cc_final: 0.7656 (tp) REVERT: A 5027 CYS cc_start: 0.8301 (p) cc_final: 0.7915 (p) REVERT: B 4043 GLN cc_start: 0.8152 (mm110) cc_final: 0.7521 (mm-40) REVERT: B 4224 GLU cc_start: 0.6791 (pm20) cc_final: 0.6362 (pm20) REVERT: B 4633 GLU cc_start: 0.7674 (tp30) cc_final: 0.6426 (pp20) REVERT: B 4684 ASP cc_start: 0.8422 (m-30) cc_final: 0.8059 (m-30) REVERT: B 4911 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7526 (mm) REVERT: B 4933 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7320 (mm110) REVERT: B 4980 LEU cc_start: 0.8258 (mt) cc_final: 0.7652 (tp) REVERT: B 5027 CYS cc_start: 0.8304 (p) cc_final: 0.7813 (p) REVERT: C 4043 GLN cc_start: 0.8151 (mm110) cc_final: 0.7522 (mm-40) REVERT: C 4057 MET cc_start: 0.6671 (tpt) cc_final: 0.6148 (tpp) REVERT: C 4224 GLU cc_start: 0.6789 (pm20) cc_final: 0.6360 (pm20) REVERT: C 4633 GLU cc_start: 0.7670 (tp30) cc_final: 0.6436 (pp20) REVERT: C 4684 ASP cc_start: 0.8423 (m-30) cc_final: 0.8061 (m-30) REVERT: C 4911 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7527 (mm) REVERT: C 4980 LEU cc_start: 0.8271 (mt) cc_final: 0.7670 (tp) REVERT: C 5027 CYS cc_start: 0.8297 (p) cc_final: 0.7911 (p) REVERT: D 4043 GLN cc_start: 0.8149 (mm110) cc_final: 0.7521 (mm-40) REVERT: D 4224 GLU cc_start: 0.6790 (pm20) cc_final: 0.6358 (pm20) REVERT: D 4633 GLU cc_start: 0.7676 (tp30) cc_final: 0.6435 (pp20) REVERT: D 4684 ASP cc_start: 0.8432 (m-30) cc_final: 0.8065 (m-30) REVERT: D 4911 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7524 (mm) REVERT: D 4980 LEU cc_start: 0.8268 (mt) cc_final: 0.7672 (tp) REVERT: D 5027 CYS cc_start: 0.8297 (p) cc_final: 0.7912 (p) outliers start: 24 outliers final: 2 residues processed: 347 average time/residue: 0.6435 time to fit residues: 249.7729 Evaluate side-chains 315 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 307 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4669 VAL Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain C residue 4669 VAL Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain D residue 4911 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 82 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 chunk 2 optimal weight: 0.0970 chunk 74 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 23 optimal weight: 0.0770 chunk 3 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.190147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.134641 restraints weight = 23339.152| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.88 r_work: 0.3237 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21180 Z= 0.111 Angle : 0.513 8.057 28592 Z= 0.257 Chirality : 0.034 0.130 3092 Planarity : 0.003 0.042 3604 Dihedral : 11.428 174.689 2748 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.61 % Allowed : 10.85 % Favored : 87.54 % 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: 1.84 (0.17), residues: 2472 helix: 1.89 (0.12), residues: 1740 sheet: 0.23 (0.50), residues: 104 loop : -0.45 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B4189 TYR 0.011 0.001 TYR A4994 PHE 0.012 0.001 PHE B4219 TRP 0.008 0.001 TRP D4644 HIS 0.003 0.001 HIS A3998 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (21160) covalent geometry : angle 0.51069 / 0.26 (28576) SS BOND : bond 0.00032 / 0.02 ( 4) SS BOND : angle 0.76489 / 0.51 ( 8) hydrogen bonds : bond 0.04094 / 2.75 ( 1361) hydrogen bonds : angle 4.27191 / 3.10 ( 3999) metal coordination : bond 0.00295 / 0.17 ( 16) metal coordination : angle 2.69299 / 1.93 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 327 time to evaluate : 0.782 Fit side-chains REVERT: A 3967 GLU cc_start: 0.5976 (tm-30) cc_final: 0.5569 (tp30) REVERT: A 4001 MET cc_start: 0.7251 (mtt) cc_final: 0.6295 (ptt) REVERT: A 4204 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6667 (mt0) REVERT: A 4633 GLU cc_start: 0.7775 (tp30) cc_final: 0.6686 (pp20) REVERT: A 4662 ASN cc_start: 0.8510 (t0) cc_final: 0.8310 (t0) REVERT: A 4684 ASP cc_start: 0.8453 (m-30) cc_final: 0.8087 (m-30) REVERT: A 4851 TYR cc_start: 0.8943 (m-80) cc_final: 0.8741 (m-80) REVERT: A 4911 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7810 (mm) REVERT: A 4933 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7594 (mm110) REVERT: A 4980 LEU cc_start: 0.8444 (mt) cc_final: 0.7897 (tp) REVERT: A 5027 CYS cc_start: 0.8563 (p) cc_final: 0.8221 (p) REVERT: B 3967 GLU cc_start: 0.5887 (tm-30) cc_final: 0.5468 (tp30) REVERT: B 4001 MET cc_start: 0.7249 (mtt) cc_final: 0.6291 (ptt) REVERT: B 4204 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6659 (mt0) REVERT: B 4633 GLU cc_start: 0.7767 (tp30) cc_final: 0.6675 (pp20) REVERT: B 4684 ASP cc_start: 0.8440 (m-30) cc_final: 0.8072 (m-30) REVERT: B 4911 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7810 (mm) REVERT: B 4933 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7553 (mm110) REVERT: B 4980 LEU cc_start: 0.8444 (mt) cc_final: 0.7893 (tp) REVERT: B 5027 CYS cc_start: 0.8511 (p) cc_final: 0.8169 (p) REVERT: C 3967 GLU cc_start: 0.5877 (tm-30) cc_final: 0.5464 (tp30) REVERT: C 4001 MET cc_start: 0.7028 (mtt) cc_final: 0.6012 (ptt) REVERT: C 4204 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6654 (mt0) REVERT: C 4633 GLU cc_start: 0.7764 (tp30) cc_final: 0.6676 (pp20) REVERT: C 4662 ASN cc_start: 0.8503 (t0) cc_final: 0.8294 (t0) REVERT: C 4684 ASP cc_start: 0.8443 (m-30) cc_final: 0.8074 (m-30) REVERT: C 4911 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7804 (mm) REVERT: C 4980 LEU cc_start: 0.8457 (mt) cc_final: 0.7912 (tp) REVERT: C 5027 CYS cc_start: 0.8560 (p) cc_final: 0.8211 (p) REVERT: D 3967 GLU cc_start: 0.5872 (tm-30) cc_final: 0.5456 (tp30) REVERT: D 4001 MET cc_start: 0.7253 (mtt) cc_final: 0.6297 (ptt) REVERT: D 4204 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6662 (mt0) REVERT: D 4633 GLU cc_start: 0.7756 (tp30) cc_final: 0.6674 (pp20) REVERT: D 4684 ASP cc_start: 0.8438 (m-30) cc_final: 0.8067 (m-30) REVERT: D 4911 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7803 (mm) REVERT: D 4980 LEU cc_start: 0.8452 (mt) cc_final: 0.7910 (tp) REVERT: D 5027 CYS cc_start: 0.8563 (p) cc_final: 0.8219 (p) outliers start: 36 outliers final: 16 residues processed: 349 average time/residue: 0.6778 time to fit residues: 263.6157 Evaluate side-chains 335 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 309 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3987 ASP Chi-restraints excluded: chain A residue 4026 MET Chi-restraints excluded: chain A residue 4204 GLN Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain B residue 3987 ASP Chi-restraints excluded: chain B residue 4026 MET Chi-restraints excluded: chain B residue 4204 GLN Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain C residue 3987 ASP Chi-restraints excluded: chain C residue 4026 MET Chi-restraints excluded: chain C residue 4204 GLN Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain D residue 3987 ASP Chi-restraints excluded: chain D residue 4026 MET Chi-restraints excluded: chain D residue 4204 GLN Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4971 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 32 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 224 optimal weight: 0.6980 chunk 128 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3978 GLN ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4223 ASN ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4662 ASN C3978 GLN ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4933 GLN ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4933 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.189407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.134052 restraints weight = 23242.210| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.81 r_work: 0.3209 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21180 Z= 0.130 Angle : 0.529 10.468 28592 Z= 0.266 Chirality : 0.035 0.119 3092 Planarity : 0.004 0.038 3604 Dihedral : 11.400 174.489 2748 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.23 % Allowed : 10.76 % Favored : 87.01 % 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: 1.81 (0.17), residues: 2472 helix: 1.89 (0.12), residues: 1752 sheet: 0.16 (0.50), residues: 104 loop : -0.56 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D4189 TYR 0.012 0.001 TYR D4994 PHE 0.011 0.001 PHE B4916 TRP 0.007 0.001 TRP A4716 HIS 0.004 0.001 HIS C3998 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (21160) covalent geometry : angle 0.52758 / 0.27 (28576) SS BOND : bond 0.00104 / 0.05 ( 4) SS BOND : angle 0.96419 / 0.64 ( 8) hydrogen bonds : bond 0.04165 / 2.81 ( 1361) hydrogen bonds : angle 4.34354 / 3.16 ( 3999) metal coordination : bond 0.00502 / 0.30 ( 16) metal coordination : angle 2.42067 / 1.73 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 319 time to evaluate : 0.650 Fit side-chains REVERT: A 3967 GLU cc_start: 0.5621 (tm-30) cc_final: 0.5165 (tp30) REVERT: A 4039 MET cc_start: 0.6746 (tmt) cc_final: 0.5701 (tmm) REVERT: A 4043 GLN cc_start: 0.8377 (mm110) cc_final: 0.7788 (mm110) REVERT: A 4633 GLU cc_start: 0.7831 (tp30) cc_final: 0.6738 (pp20) REVERT: A 4684 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8096 (m-30) REVERT: A 4796 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8329 (tmm) REVERT: A 4911 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7832 (mm) REVERT: A 4933 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7713 (mm110) REVERT: A 4980 LEU cc_start: 0.8436 (mt) cc_final: 0.7936 (tp) REVERT: A 5027 CYS cc_start: 0.8577 (p) cc_final: 0.8241 (p) REVERT: B 3967 GLU cc_start: 0.5531 (tm-30) cc_final: 0.5271 (tp30) REVERT: B 4039 MET cc_start: 0.6758 (tmt) cc_final: 0.5713 (tmm) REVERT: B 4043 GLN cc_start: 0.8380 (mm110) cc_final: 0.7783 (mm110) REVERT: B 4204 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6700 (mt0) REVERT: B 4633 GLU cc_start: 0.7832 (tp30) cc_final: 0.6727 (pp20) REVERT: B 4684 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8091 (m-30) REVERT: B 4796 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8266 (tmm) REVERT: B 4911 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7822 (mm) REVERT: B 4933 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7629 (mm110) REVERT: B 4980 LEU cc_start: 0.8441 (mt) cc_final: 0.7941 (tp) REVERT: B 5027 CYS cc_start: 0.8577 (p) cc_final: 0.8240 (p) REVERT: C 3967 GLU cc_start: 0.5523 (tm-30) cc_final: 0.5265 (tp30) REVERT: C 4039 MET cc_start: 0.6770 (tmt) cc_final: 0.5728 (tmm) REVERT: C 4043 GLN cc_start: 0.8384 (mm110) cc_final: 0.7790 (mm110) REVERT: C 4633 GLU cc_start: 0.7828 (tp30) cc_final: 0.6740 (pp20) REVERT: C 4684 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8084 (m-30) REVERT: C 4796 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8273 (tmm) REVERT: C 4911 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7822 (mm) REVERT: C 4980 LEU cc_start: 0.8449 (mt) cc_final: 0.7952 (tp) REVERT: C 5027 CYS cc_start: 0.8562 (p) cc_final: 0.8220 (p) REVERT: D 3967 GLU cc_start: 0.5525 (tm-30) cc_final: 0.5269 (tp30) REVERT: D 4039 MET cc_start: 0.6756 (tmt) cc_final: 0.5712 (tmm) REVERT: D 4043 GLN cc_start: 0.8376 (mm110) cc_final: 0.7782 (mm110) REVERT: D 4633 GLU cc_start: 0.7818 (tp30) cc_final: 0.6740 (pp20) REVERT: D 4684 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8072 (m-30) REVERT: D 4796 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8284 (tmm) REVERT: D 4911 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7821 (mm) REVERT: D 4980 LEU cc_start: 0.8446 (mt) cc_final: 0.7951 (tp) REVERT: D 5027 CYS cc_start: 0.8564 (p) cc_final: 0.8226 (p) outliers start: 50 outliers final: 12 residues processed: 343 average time/residue: 0.6408 time to fit residues: 245.3193 Evaluate side-chains 338 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 311 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4026 MET Chi-restraints excluded: chain A residue 4684 ASP Chi-restraints excluded: chain A residue 4796 MET Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain B residue 4026 MET Chi-restraints excluded: chain B residue 4204 GLN Chi-restraints excluded: chain B residue 4684 ASP Chi-restraints excluded: chain B residue 4796 MET Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain C residue 4026 MET Chi-restraints excluded: chain C residue 4684 ASP Chi-restraints excluded: chain C residue 4796 MET Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain D residue 4026 MET Chi-restraints excluded: chain D residue 4684 ASP Chi-restraints excluded: chain D residue 4796 MET Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4971 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 244 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 172 optimal weight: 0.0870 chunk 4 optimal weight: 9.9990 chunk 163 optimal weight: 0.5980 chunk 188 optimal weight: 0.2980 chunk 149 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.190270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.135309 restraints weight = 23177.432| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.86 r_work: 0.3282 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21180 Z= 0.116 Angle : 0.528 10.475 28592 Z= 0.265 Chirality : 0.034 0.130 3092 Planarity : 0.004 0.044 3604 Dihedral : 11.318 172.715 2748 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.19 % Allowed : 12.81 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.17), residues: 2472 helix: 1.93 (0.12), residues: 1736 sheet: 0.23 (0.50), residues: 104 loop : -0.49 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D4189 TYR 0.014 0.001 TYR A4177 PHE 0.014 0.001 PHE A4219 TRP 0.007 0.001 TRP D4644 HIS 0.003 0.001 HIS C4803 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (21160) covalent geometry : angle 0.52639 / 0.26 (28576) SS BOND : bond 0.00045 / 0.02 ( 4) SS BOND : angle 0.83374 / 0.56 ( 8) hydrogen bonds : bond 0.03929 / 2.63 ( 1361) hydrogen bonds : angle 4.29622 / 3.12 ( 3999) metal coordination : bond 0.00306 / 0.18 ( 16) metal coordination : angle 2.36146 / 1.69 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 319 time to evaluate : 0.795 Fit side-chains REVERT: A 3967 GLU cc_start: 0.5456 (tm-30) cc_final: 0.5197 (tp30) REVERT: A 4001 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6681 (pmt) REVERT: A 4039 MET cc_start: 0.6676 (tmt) cc_final: 0.5645 (tmm) REVERT: A 4043 GLN cc_start: 0.8377 (mm110) cc_final: 0.7767 (mm-40) REVERT: A 4057 MET cc_start: 0.6788 (tpt) cc_final: 0.6501 (ttp) REVERT: A 4633 GLU cc_start: 0.7758 (tp30) cc_final: 0.6689 (pp20) REVERT: A 4684 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8080 (m-30) REVERT: A 4796 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8256 (tmm) REVERT: A 4851 TYR cc_start: 0.8948 (m-80) cc_final: 0.8708 (m-80) REVERT: A 4911 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7798 (mm) REVERT: A 4933 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7693 (mm110) REVERT: A 4980 LEU cc_start: 0.8419 (mt) cc_final: 0.7925 (tp) REVERT: A 5027 CYS cc_start: 0.8550 (p) cc_final: 0.8205 (p) REVERT: B 3967 GLU cc_start: 0.5609 (tm-30) cc_final: 0.5230 (tp30) REVERT: B 4001 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6688 (pmt) REVERT: B 4039 MET cc_start: 0.6682 (tmt) cc_final: 0.5658 (tmm) REVERT: B 4043 GLN cc_start: 0.8381 (mm110) cc_final: 0.7771 (mm-40) REVERT: B 4057 MET cc_start: 0.6786 (tpt) cc_final: 0.6496 (ttp) REVERT: B 4633 GLU cc_start: 0.7760 (tp30) cc_final: 0.6687 (pp20) REVERT: B 4684 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8058 (m-30) REVERT: B 4796 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8244 (tmm) REVERT: B 4911 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7789 (mm) REVERT: B 4933 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7668 (mm110) REVERT: B 4980 LEU cc_start: 0.8421 (mt) cc_final: 0.7920 (tp) REVERT: B 5027 CYS cc_start: 0.8510 (p) cc_final: 0.8167 (p) REVERT: C 3967 GLU cc_start: 0.5601 (tm-30) cc_final: 0.5229 (tp30) REVERT: C 4001 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6063 (pmm) REVERT: C 4039 MET cc_start: 0.6692 (tmt) cc_final: 0.5663 (tmm) REVERT: C 4043 GLN cc_start: 0.8377 (mm110) cc_final: 0.7771 (mm-40) REVERT: C 4633 GLU cc_start: 0.7768 (tp30) cc_final: 0.6702 (pp20) REVERT: C 4684 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8072 (m-30) REVERT: C 4796 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8246 (tmm) REVERT: C 4911 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7793 (mm) REVERT: C 4980 LEU cc_start: 0.8431 (mt) cc_final: 0.7930 (tp) REVERT: C 5027 CYS cc_start: 0.8538 (p) cc_final: 0.8186 (p) REVERT: D 3967 GLU cc_start: 0.5595 (tm-30) cc_final: 0.5225 (tp30) REVERT: D 4001 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.6680 (pmt) REVERT: D 4039 MET cc_start: 0.6680 (tmt) cc_final: 0.5651 (tmm) REVERT: D 4043 GLN cc_start: 0.8369 (mm110) cc_final: 0.7766 (mm-40) REVERT: D 4057 MET cc_start: 0.6798 (tpt) cc_final: 0.6504 (ttp) REVERT: D 4633 GLU cc_start: 0.7752 (tp30) cc_final: 0.6698 (pp20) REVERT: D 4684 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8055 (m-30) REVERT: D 4796 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8251 (tmm) REVERT: D 4911 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7798 (mm) REVERT: D 4933 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7700 (mm110) REVERT: D 4980 LEU cc_start: 0.8432 (mt) cc_final: 0.7943 (tp) REVERT: D 5027 CYS cc_start: 0.8542 (p) cc_final: 0.8197 (p) outliers start: 49 outliers final: 16 residues processed: 334 average time/residue: 0.6605 time to fit residues: 246.8890 Evaluate side-chains 348 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 313 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4001 MET Chi-restraints excluded: chain A residue 4026 MET Chi-restraints excluded: chain A residue 4215 ARG Chi-restraints excluded: chain A residue 4684 ASP Chi-restraints excluded: chain A residue 4796 MET Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain B residue 4001 MET Chi-restraints excluded: chain B residue 4026 MET Chi-restraints excluded: chain B residue 4215 ARG Chi-restraints excluded: chain B residue 4684 ASP Chi-restraints excluded: chain B residue 4796 MET Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain C residue 4001 MET Chi-restraints excluded: chain C residue 4026 MET Chi-restraints excluded: chain C residue 4215 ARG Chi-restraints excluded: chain C residue 4684 ASP Chi-restraints excluded: chain C residue 4796 MET Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain D residue 4001 MET Chi-restraints excluded: chain D residue 4026 MET Chi-restraints excluded: chain D residue 4215 ARG Chi-restraints excluded: chain D residue 4684 ASP Chi-restraints excluded: chain D residue 4796 MET Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4971 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 115 optimal weight: 3.9990 chunk 241 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 171 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4662 ASN ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4662 ASN C4933 GLN D3963 ASN ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4662 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.189713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.134076 restraints weight = 23355.860| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.60 r_work: 0.3271 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21180 Z= 0.129 Angle : 0.529 9.434 28592 Z= 0.269 Chirality : 0.035 0.119 3092 Planarity : 0.004 0.050 3604 Dihedral : 11.253 171.315 2748 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.37 % Allowed : 13.48 % Favored : 84.15 % 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: 1.86 (0.17), residues: 2472 helix: 1.93 (0.12), residues: 1752 sheet: 0.15 (0.49), residues: 104 loop : -0.55 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B4189 TYR 0.011 0.001 TYR A4994 PHE 0.011 0.001 PHE D4916 TRP 0.006 0.001 TRP B4644 HIS 0.004 0.001 HIS C3998 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (21160) covalent geometry : angle 0.52756 / 0.27 (28576) SS BOND : bond 0.00086 / 0.04 ( 4) SS BOND : angle 0.94373 / 0.63 ( 8) hydrogen bonds : bond 0.04014 / 2.69 ( 1361) hydrogen bonds : angle 4.33379 / 3.15 ( 3999) metal coordination : bond 0.00487 / 0.29 ( 16) metal coordination : angle 2.21083 / 1.58 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 326 time to evaluate : 0.755 Fit side-chains REVERT: A 4000 MET cc_start: 0.7058 (mmt) cc_final: 0.6787 (mmm) REVERT: A 4001 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6079 (pmt) REVERT: A 4184 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7286 (tmm) REVERT: A 4189 ARG cc_start: 0.7989 (ptm160) cc_final: 0.7697 (ptm160) REVERT: A 4633 GLU cc_start: 0.7756 (tp30) cc_final: 0.6631 (pp20) REVERT: A 4680 LYS cc_start: 0.7931 (mtmm) cc_final: 0.7586 (mtpm) REVERT: A 4684 ASP cc_start: 0.8362 (m-30) cc_final: 0.8014 (m-30) REVERT: A 4796 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8284 (tmm) REVERT: A 4911 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7799 (mm) REVERT: A 4933 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7596 (mm-40) REVERT: A 4980 LEU cc_start: 0.8423 (mt) cc_final: 0.7930 (tp) REVERT: A 5027 CYS cc_start: 0.8530 (p) cc_final: 0.8186 (p) REVERT: B 3967 GLU cc_start: 0.5473 (tm-30) cc_final: 0.5174 (tp30) REVERT: B 4000 MET cc_start: 0.7067 (mmt) cc_final: 0.6790 (mmm) REVERT: B 4001 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6093 (pmt) REVERT: B 4184 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7276 (tmm) REVERT: B 4189 ARG cc_start: 0.7997 (ptm160) cc_final: 0.7708 (ptm160) REVERT: B 4633 GLU cc_start: 0.7766 (tp30) cc_final: 0.6571 (pp20) REVERT: B 4680 LYS cc_start: 0.7934 (mtmm) cc_final: 0.7585 (mtpm) REVERT: B 4684 ASP cc_start: 0.8349 (m-30) cc_final: 0.8002 (m-30) REVERT: B 4796 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8268 (tmm) REVERT: B 4911 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7793 (mm) REVERT: B 4933 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7616 (mm-40) REVERT: B 4980 LEU cc_start: 0.8432 (mt) cc_final: 0.7934 (tp) REVERT: B 5027 CYS cc_start: 0.8484 (p) cc_final: 0.8138 (p) REVERT: C 3967 GLU cc_start: 0.5462 (tm-30) cc_final: 0.5171 (tp30) REVERT: C 4000 MET cc_start: 0.6873 (mmt) cc_final: 0.6578 (mmm) REVERT: C 4001 MET cc_start: 0.7649 (mpp) cc_final: 0.6457 (pmm) REVERT: C 4184 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7249 (tmm) REVERT: C 4189 ARG cc_start: 0.8003 (ptm160) cc_final: 0.7712 (ptm160) REVERT: C 4633 GLU cc_start: 0.7757 (tp30) cc_final: 0.6627 (pp20) REVERT: C 4680 LYS cc_start: 0.7934 (mtmm) cc_final: 0.7590 (mtpm) REVERT: C 4684 ASP cc_start: 0.8388 (m-30) cc_final: 0.8044 (m-30) REVERT: C 4796 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8274 (tmm) REVERT: C 4911 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7789 (mm) REVERT: C 4980 LEU cc_start: 0.8434 (mt) cc_final: 0.7942 (tp) REVERT: C 5027 CYS cc_start: 0.8518 (p) cc_final: 0.8166 (p) REVERT: D 3967 GLU cc_start: 0.5471 (tm-30) cc_final: 0.5166 (tp30) REVERT: D 4000 MET cc_start: 0.7069 (mmt) cc_final: 0.6799 (mmm) REVERT: D 4001 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6081 (pmt) REVERT: D 4184 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7267 (tmm) REVERT: D 4189 ARG cc_start: 0.7997 (ptm160) cc_final: 0.7713 (ptm160) REVERT: D 4633 GLU cc_start: 0.7747 (tp30) cc_final: 0.6626 (pp20) REVERT: D 4680 LYS cc_start: 0.7944 (mtmm) cc_final: 0.7591 (mtpm) REVERT: D 4684 ASP cc_start: 0.8393 (m-30) cc_final: 0.8050 (m-30) REVERT: D 4796 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8269 (tmm) REVERT: D 4911 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7798 (mm) REVERT: D 4933 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7703 (mm110) REVERT: D 4980 LEU cc_start: 0.8440 (mt) cc_final: 0.7953 (tp) REVERT: D 5027 CYS cc_start: 0.8524 (p) cc_final: 0.8179 (p) outliers start: 53 outliers final: 18 residues processed: 350 average time/residue: 0.6027 time to fit residues: 236.5985 Evaluate side-chains 353 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 317 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4001 MET Chi-restraints excluded: chain A residue 4026 MET Chi-restraints excluded: chain A residue 4184 MET Chi-restraints excluded: chain A residue 4215 ARG Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4796 MET Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain B residue 4001 MET Chi-restraints excluded: chain B residue 4026 MET Chi-restraints excluded: chain B residue 4184 MET Chi-restraints excluded: chain B residue 4215 ARG Chi-restraints excluded: chain B residue 4796 MET Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain C residue 4026 MET Chi-restraints excluded: chain C residue 4184 MET Chi-restraints excluded: chain C residue 4215 ARG Chi-restraints excluded: chain C residue 4796 MET Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain D residue 4001 MET Chi-restraints excluded: chain D residue 4026 MET Chi-restraints excluded: chain D residue 4184 MET Chi-restraints excluded: chain D residue 4215 ARG Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4796 MET Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4971 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 185 optimal weight: 0.0170 chunk 162 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 228 optimal weight: 1.9990 chunk 226 optimal weight: 0.7980 chunk 245 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4043 GLN A4223 ASN ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4043 GLN B4223 ASN ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3963 ASN C4043 GLN ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3963 ASN D4043 GLN ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.189983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.131538 restraints weight = 23209.530| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.56 r_work: 0.3296 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21180 Z= 0.122 Angle : 0.535 10.278 28592 Z= 0.271 Chirality : 0.035 0.126 3092 Planarity : 0.004 0.043 3604 Dihedral : 11.196 169.892 2748 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.74 % Allowed : 15.22 % Favored : 83.04 % 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: 1.88 (0.17), residues: 2472 helix: 1.94 (0.12), residues: 1752 sheet: 0.21 (0.50), residues: 104 loop : -0.53 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B4189 TYR 0.014 0.001 TYR D4177 PHE 0.017 0.001 PHE C4219 TRP 0.006 0.001 TRP B4644 HIS 0.003 0.001 HIS B3998 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (21160) covalent geometry : angle 0.53369 / 0.27 (28576) SS BOND : bond 0.00067 / 0.03 ( 4) SS BOND : angle 0.89148 / 0.60 ( 8) hydrogen bonds : bond 0.03943 / 2.65 ( 1361) hydrogen bonds : angle 4.32424 / 3.14 ( 3999) metal coordination : bond 0.00377 / 0.22 ( 16) metal coordination : angle 2.23434 / 1.60 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 331 time to evaluate : 0.696 Fit side-chains REVERT: A 3967 GLU cc_start: 0.5679 (tp30) cc_final: 0.5386 (tp30) REVERT: A 4000 MET cc_start: 0.7077 (mmt) cc_final: 0.6861 (mmm) REVERT: A 4039 MET cc_start: 0.6779 (tmt) cc_final: 0.5708 (tmm) REVERT: A 4043 GLN cc_start: 0.8285 (mm-40) cc_final: 0.7780 (mm110) REVERT: A 4057 MET cc_start: 0.6676 (tpt) cc_final: 0.6264 (ttp) REVERT: A 4184 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.6833 (tmm) REVERT: A 4189 ARG cc_start: 0.7632 (ptm160) cc_final: 0.7372 (ptm160) REVERT: A 4633 GLU cc_start: 0.7691 (tp30) cc_final: 0.6359 (pp20) REVERT: A 4680 LYS cc_start: 0.7625 (mtmm) cc_final: 0.7332 (mtpm) REVERT: A 4684 ASP cc_start: 0.8321 (m-30) cc_final: 0.7958 (m-30) REVERT: A 4796 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8193 (tmm) REVERT: A 4851 TYR cc_start: 0.8872 (m-80) cc_final: 0.8634 (m-80) REVERT: A 4911 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7585 (mm) REVERT: A 4933 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7448 (mm-40) REVERT: A 4980 LEU cc_start: 0.8228 (mt) cc_final: 0.7663 (tp) REVERT: A 5027 CYS cc_start: 0.8285 (p) cc_final: 0.7891 (p) REVERT: B 3967 GLU cc_start: 0.5305 (tm-30) cc_final: 0.5052 (tp30) REVERT: B 4000 MET cc_start: 0.7086 (mmt) cc_final: 0.6863 (mmm) REVERT: B 4039 MET cc_start: 0.6782 (tmt) cc_final: 0.5710 (tmm) REVERT: B 4043 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7780 (mm110) REVERT: B 4057 MET cc_start: 0.6669 (tpt) cc_final: 0.6259 (ttp) REVERT: B 4184 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.6817 (tmm) REVERT: B 4189 ARG cc_start: 0.7641 (ptm160) cc_final: 0.7380 (ptm160) REVERT: B 4633 GLU cc_start: 0.7689 (tp30) cc_final: 0.6348 (pp20) REVERT: B 4680 LYS cc_start: 0.7629 (mtmm) cc_final: 0.7334 (mtpm) REVERT: B 4684 ASP cc_start: 0.8306 (m-30) cc_final: 0.7940 (m-30) REVERT: B 4796 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8194 (tmm) REVERT: B 4911 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7579 (mm) REVERT: B 4933 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7537 (mm110) REVERT: B 4980 LEU cc_start: 0.8225 (mt) cc_final: 0.7659 (tp) REVERT: B 5027 CYS cc_start: 0.8243 (p) cc_final: 0.7851 (p) REVERT: C 3967 GLU cc_start: 0.5295 (tm-30) cc_final: 0.5046 (tp30) REVERT: C 4000 MET cc_start: 0.6911 (mmt) cc_final: 0.6692 (mmm) REVERT: C 4001 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.6521 (pmm) REVERT: C 4039 MET cc_start: 0.6793 (tmt) cc_final: 0.5720 (tmm) REVERT: C 4043 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7780 (mm110) REVERT: C 4184 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.6849 (tmm) REVERT: C 4189 ARG cc_start: 0.7652 (ptm160) cc_final: 0.7388 (ptm160) REVERT: C 4633 GLU cc_start: 0.7685 (tp30) cc_final: 0.6354 (pp20) REVERT: C 4680 LYS cc_start: 0.7630 (mtmm) cc_final: 0.7338 (mtpm) REVERT: C 4684 ASP cc_start: 0.8310 (m-30) cc_final: 0.7942 (m-30) REVERT: C 4796 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8202 (tmm) REVERT: C 4911 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7582 (mm) REVERT: C 4980 LEU cc_start: 0.8246 (mt) cc_final: 0.7681 (tp) REVERT: C 5027 CYS cc_start: 0.8267 (p) cc_final: 0.7873 (p) REVERT: D 3967 GLU cc_start: 0.5294 (tm-30) cc_final: 0.5046 (tp30) REVERT: D 4000 MET cc_start: 0.7087 (mmt) cc_final: 0.6866 (mmm) REVERT: D 4039 MET cc_start: 0.6786 (tmt) cc_final: 0.5715 (tmm) REVERT: D 4043 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7772 (mm110) REVERT: D 4057 MET cc_start: 0.6678 (tpt) cc_final: 0.6262 (ttp) REVERT: D 4184 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.6859 (tmm) REVERT: D 4189 ARG cc_start: 0.7694 (ptm160) cc_final: 0.7419 (ptm160) REVERT: D 4633 GLU cc_start: 0.7687 (tp30) cc_final: 0.6367 (pp20) REVERT: D 4680 LYS cc_start: 0.7624 (mtmm) cc_final: 0.7330 (mtpm) REVERT: D 4684 ASP cc_start: 0.8307 (m-30) cc_final: 0.7940 (m-30) REVERT: D 4796 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8197 (tmm) REVERT: D 4911 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7589 (mm) REVERT: D 4980 LEU cc_start: 0.8237 (mt) cc_final: 0.7672 (tp) REVERT: D 5027 CYS cc_start: 0.8266 (p) cc_final: 0.7872 (p) outliers start: 39 outliers final: 18 residues processed: 344 average time/residue: 0.6284 time to fit residues: 240.7184 Evaluate side-chains 356 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 323 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4026 MET Chi-restraints excluded: chain A residue 4184 MET Chi-restraints excluded: chain A residue 4215 ARG Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4796 MET Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain B residue 4026 MET Chi-restraints excluded: chain B residue 4184 MET Chi-restraints excluded: chain B residue 4215 ARG Chi-restraints excluded: chain B residue 4796 MET Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain C residue 4001 MET Chi-restraints excluded: chain C residue 4026 MET Chi-restraints excluded: chain C residue 4184 MET Chi-restraints excluded: chain C residue 4215 ARG Chi-restraints excluded: chain C residue 4796 MET Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain D residue 4026 MET Chi-restraints excluded: chain D residue 4184 MET Chi-restraints excluded: chain D residue 4215 ARG Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4796 MET Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4971 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 74 optimal weight: 5.9990 chunk 234 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3963 ASN A4223 ASN ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3963 ASN B4223 ASN ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3963 ASN ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4933 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.188663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.132126 restraints weight = 23239.573| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.71 r_work: 0.3204 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21180 Z= 0.163 Angle : 0.578 11.407 28592 Z= 0.295 Chirality : 0.037 0.131 3092 Planarity : 0.004 0.040 3604 Dihedral : 11.261 170.687 2748 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.74 % Allowed : 15.71 % Favored : 82.54 % 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: 1.69 (0.17), residues: 2472 helix: 1.80 (0.12), residues: 1748 sheet: 0.07 (0.49), residues: 104 loop : -0.58 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D4189 TYR 0.016 0.002 TYR B4177 PHE 0.019 0.001 PHE A4219 TRP 0.005 0.001 TRP A4716 HIS 0.004 0.001 HIS C3998 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (21160) covalent geometry : angle 0.57724 / 0.29 (28576) SS BOND : bond 0.00184 / 0.09 ( 4) SS BOND : angle 1.13528 / 0.76 ( 8) hydrogen bonds : bond 0.04274 / 2.86 ( 1361) hydrogen bonds : angle 4.43480 / 3.22 ( 3999) metal coordination : bond 0.00842 / 0.50 ( 16) metal coordination : angle 1.92485 / 1.37 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 323 time to evaluate : 0.694 Fit side-chains REVERT: A 3967 GLU cc_start: 0.5873 (tp30) cc_final: 0.5440 (tp30) REVERT: A 4039 MET cc_start: 0.6703 (tmt) cc_final: 0.5722 (tmm) REVERT: A 4043 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7728 (mm-40) REVERT: A 4184 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7165 (tmm) REVERT: A 4189 ARG cc_start: 0.7995 (ptm160) cc_final: 0.7767 (ptm160) REVERT: A 4633 GLU cc_start: 0.7935 (tp30) cc_final: 0.6659 (pp20) REVERT: A 4680 LYS cc_start: 0.7923 (mtmm) cc_final: 0.7592 (mtpm) REVERT: A 4684 ASP cc_start: 0.8387 (m-30) cc_final: 0.8040 (m-30) REVERT: A 4911 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7850 (mm) REVERT: A 4933 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7738 (mm-40) REVERT: A 4980 LEU cc_start: 0.8444 (mt) cc_final: 0.7950 (tp) REVERT: A 5027 CYS cc_start: 0.8558 (p) cc_final: 0.8122 (p) REVERT: B 3967 GLU cc_start: 0.5500 (tm-30) cc_final: 0.5274 (tp30) REVERT: B 4001 MET cc_start: 0.7560 (pmt) cc_final: 0.7356 (pmm) REVERT: B 4039 MET cc_start: 0.6676 (tmt) cc_final: 0.5684 (tmm) REVERT: B 4043 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7734 (mm-40) REVERT: B 4184 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7133 (tmm) REVERT: B 4189 ARG cc_start: 0.7996 (ptm160) cc_final: 0.7769 (ptm160) REVERT: B 4633 GLU cc_start: 0.7924 (tp30) cc_final: 0.6718 (pp20) REVERT: B 4680 LYS cc_start: 0.7913 (mtmm) cc_final: 0.7580 (mtpm) REVERT: B 4684 ASP cc_start: 0.8350 (m-30) cc_final: 0.8002 (m-30) REVERT: B 4911 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7841 (mm) REVERT: B 4933 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7757 (mm-40) REVERT: B 4980 LEU cc_start: 0.8440 (mt) cc_final: 0.7941 (tp) REVERT: B 5027 CYS cc_start: 0.8536 (p) cc_final: 0.8196 (p) REVERT: C 3967 GLU cc_start: 0.5486 (tm-30) cc_final: 0.5263 (tp30) REVERT: C 4000 MET cc_start: 0.6909 (mmt) cc_final: 0.6691 (mmm) REVERT: C 4001 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7354 (pmm) REVERT: C 4039 MET cc_start: 0.6692 (tmt) cc_final: 0.5695 (tmm) REVERT: C 4043 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7731 (mm-40) REVERT: C 4057 MET cc_start: 0.6256 (tpt) cc_final: 0.6045 (ttt) REVERT: C 4184 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7118 (tmm) REVERT: C 4189 ARG cc_start: 0.8015 (ptm160) cc_final: 0.7784 (ptm160) REVERT: C 4633 GLU cc_start: 0.7929 (tp30) cc_final: 0.6661 (pp20) REVERT: C 4680 LYS cc_start: 0.7867 (mtmm) cc_final: 0.7548 (mtpm) REVERT: C 4684 ASP cc_start: 0.8370 (m-30) cc_final: 0.8019 (m-30) REVERT: C 4911 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7840 (mm) REVERT: C 4980 LEU cc_start: 0.8450 (mt) cc_final: 0.7958 (tp) REVERT: C 5027 CYS cc_start: 0.8554 (p) cc_final: 0.8115 (p) REVERT: D 3967 GLU cc_start: 0.5493 (tm-30) cc_final: 0.5269 (tp30) REVERT: D 4001 MET cc_start: 0.7562 (pmt) cc_final: 0.7358 (pmm) REVERT: D 4039 MET cc_start: 0.6683 (tmt) cc_final: 0.5682 (tmm) REVERT: D 4043 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7728 (mm-40) REVERT: D 4184 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7123 (tmm) REVERT: D 4189 ARG cc_start: 0.7992 (ptm160) cc_final: 0.7760 (ptm160) REVERT: D 4633 GLU cc_start: 0.7925 (tp30) cc_final: 0.6660 (pp20) REVERT: D 4680 LYS cc_start: 0.7910 (mtmm) cc_final: 0.7581 (mtpm) REVERT: D 4684 ASP cc_start: 0.8367 (m-30) cc_final: 0.8015 (m-30) REVERT: D 4911 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7845 (mm) REVERT: D 4980 LEU cc_start: 0.8445 (mt) cc_final: 0.7954 (tp) REVERT: D 5027 CYS cc_start: 0.8550 (p) cc_final: 0.8112 (p) outliers start: 39 outliers final: 17 residues processed: 339 average time/residue: 0.6231 time to fit residues: 234.4764 Evaluate side-chains 343 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 315 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4026 MET Chi-restraints excluded: chain A residue 4184 MET Chi-restraints excluded: chain A residue 4215 ARG Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain B residue 4026 MET Chi-restraints excluded: chain B residue 4184 MET Chi-restraints excluded: chain B residue 4215 ARG Chi-restraints excluded: chain B residue 4221 VAL Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain C residue 4001 MET Chi-restraints excluded: chain C residue 4026 MET Chi-restraints excluded: chain C residue 4184 MET Chi-restraints excluded: chain C residue 4215 ARG Chi-restraints excluded: chain C residue 4221 VAL Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain D residue 4026 MET Chi-restraints excluded: chain D residue 4184 MET Chi-restraints excluded: chain D residue 4215 ARG Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4971 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 5 optimal weight: 8.9990 chunk 231 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 230 optimal weight: 0.5980 chunk 129 optimal weight: 0.4980 chunk 167 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4223 ASN ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4223 ASN ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4933 GLN ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4933 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.189684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.132357 restraints weight = 23288.157| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.80 r_work: 0.3233 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21180 Z= 0.127 Angle : 0.580 13.430 28592 Z= 0.291 Chirality : 0.035 0.126 3092 Planarity : 0.004 0.044 3604 Dihedral : 11.195 168.951 2748 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.43 % Allowed : 16.21 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.79 (0.17), residues: 2472 helix: 1.87 (0.12), residues: 1732 sheet: 0.25 (0.50), residues: 104 loop : -0.49 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B4736 TYR 0.024 0.001 TYR C4715 PHE 0.011 0.001 PHE B4916 TRP 0.007 0.001 TRP C4716 HIS 0.003 0.001 HIS C3998 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (21160) covalent geometry : angle 0.57851 / 0.29 (28576) SS BOND : bond 0.00042 / 0.02 ( 4) SS BOND : angle 0.89605 / 0.60 ( 8) hydrogen bonds : bond 0.04015 / 2.67 ( 1361) hydrogen bonds : angle 4.38747 / 3.19 ( 3999) metal coordination : bond 0.00392 / 0.24 ( 16) metal coordination : angle 2.07252 / 1.48 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 321 time to evaluate : 0.489 Fit side-chains REVERT: A 3967 GLU cc_start: 0.5472 (tp30) cc_final: 0.5016 (tp30) REVERT: A 4039 MET cc_start: 0.6734 (tmt) cc_final: 0.5672 (tmm) REVERT: A 4043 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7743 (mm110) REVERT: A 4057 MET cc_start: 0.6700 (tpt) cc_final: 0.6318 (mtm) REVERT: A 4184 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7130 (tmm) REVERT: A 4189 ARG cc_start: 0.7887 (ptm160) cc_final: 0.7660 (ptm160) REVERT: A 4633 GLU cc_start: 0.7916 (tp30) cc_final: 0.6705 (pp20) REVERT: A 4680 LYS cc_start: 0.7917 (mtmm) cc_final: 0.7594 (mtpm) REVERT: A 4684 ASP cc_start: 0.8373 (m-30) cc_final: 0.8019 (m-30) REVERT: A 4911 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7796 (mm) REVERT: A 4933 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7636 (mm-40) REVERT: A 4980 LEU cc_start: 0.8414 (mt) cc_final: 0.7907 (tp) REVERT: A 5027 CYS cc_start: 0.8467 (p) cc_final: 0.8119 (p) REVERT: B 3967 GLU cc_start: 0.5444 (tm-30) cc_final: 0.5104 (tp30) REVERT: B 4001 MET cc_start: 0.7384 (pmt) cc_final: 0.7164 (pmm) REVERT: B 4039 MET cc_start: 0.6627 (tmt) cc_final: 0.5523 (tmm) REVERT: B 4043 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7744 (mm110) REVERT: B 4057 MET cc_start: 0.6593 (tpt) cc_final: 0.6252 (mtm) REVERT: B 4184 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7097 (tmm) REVERT: B 4189 ARG cc_start: 0.7913 (ptm160) cc_final: 0.7686 (ptm160) REVERT: B 4633 GLU cc_start: 0.7811 (tp30) cc_final: 0.6572 (pp20) REVERT: B 4680 LYS cc_start: 0.7916 (mtmm) cc_final: 0.7597 (mtpm) REVERT: B 4684 ASP cc_start: 0.8349 (m-30) cc_final: 0.7995 (m-30) REVERT: B 4911 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7784 (mm) REVERT: B 4933 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7647 (mm-40) REVERT: B 4980 LEU cc_start: 0.8417 (mt) cc_final: 0.7909 (tp) REVERT: B 5027 CYS cc_start: 0.8498 (p) cc_final: 0.8055 (p) REVERT: C 3967 GLU cc_start: 0.5436 (tm-30) cc_final: 0.5096 (tp30) REVERT: C 4001 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7356 (pmm) REVERT: C 4039 MET cc_start: 0.6644 (tmt) cc_final: 0.5545 (tmm) REVERT: C 4043 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7680 (mm110) REVERT: C 4057 MET cc_start: 0.6343 (tpt) cc_final: 0.6076 (ttt) REVERT: C 4184 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7088 (tmm) REVERT: C 4633 GLU cc_start: 0.7903 (tp30) cc_final: 0.6693 (pp20) REVERT: C 4680 LYS cc_start: 0.7810 (mtmm) cc_final: 0.7576 (mtpm) REVERT: C 4684 ASP cc_start: 0.8352 (m-30) cc_final: 0.7995 (m-30) REVERT: C 4911 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7790 (mm) REVERT: C 4980 LEU cc_start: 0.8431 (mt) cc_final: 0.7926 (tp) REVERT: C 5027 CYS cc_start: 0.8455 (p) cc_final: 0.8108 (p) REVERT: D 3967 GLU cc_start: 0.5433 (tm-30) cc_final: 0.5087 (tp30) REVERT: D 4001 MET cc_start: 0.7391 (pmt) cc_final: 0.7170 (pmm) REVERT: D 4039 MET cc_start: 0.6638 (tmt) cc_final: 0.5534 (tmm) REVERT: D 4043 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7670 (mm110) REVERT: D 4057 MET cc_start: 0.6625 (tpt) cc_final: 0.6257 (mtm) REVERT: D 4184 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7086 (tmm) REVERT: D 4189 ARG cc_start: 0.7887 (ptm160) cc_final: 0.7659 (ptm160) REVERT: D 4633 GLU cc_start: 0.7910 (tp30) cc_final: 0.6708 (pp20) REVERT: D 4680 LYS cc_start: 0.7913 (mtmm) cc_final: 0.7589 (mtpm) REVERT: D 4684 ASP cc_start: 0.8353 (m-30) cc_final: 0.7978 (m-30) REVERT: D 4911 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7791 (mm) REVERT: D 4980 LEU cc_start: 0.8426 (mt) cc_final: 0.7922 (tp) REVERT: D 5027 CYS cc_start: 0.8458 (p) cc_final: 0.8110 (p) outliers start: 32 outliers final: 18 residues processed: 334 average time/residue: 0.6414 time to fit residues: 237.4383 Evaluate side-chains 339 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 310 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4026 MET Chi-restraints excluded: chain A residue 4184 MET Chi-restraints excluded: chain A residue 4215 ARG Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain B residue 4026 MET Chi-restraints excluded: chain B residue 4184 MET Chi-restraints excluded: chain B residue 4215 ARG Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain C residue 4001 MET Chi-restraints excluded: chain C residue 4026 MET Chi-restraints excluded: chain C residue 4184 MET Chi-restraints excluded: chain C residue 4215 ARG Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain D residue 4026 MET Chi-restraints excluded: chain D residue 4184 MET Chi-restraints excluded: chain D residue 4215 ARG Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4971 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 71 optimal weight: 7.9990 chunk 243 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 227 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 228 optimal weight: 0.3980 chunk 32 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4223 ASN ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4223 ASN ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4933 GLN ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4933 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.189540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.130535 restraints weight = 23364.536| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.61 r_work: 0.3259 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21180 Z= 0.139 Angle : 0.577 11.968 28592 Z= 0.293 Chirality : 0.036 0.117 3092 Planarity : 0.003 0.037 3604 Dihedral : 11.164 168.286 2748 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.52 % Allowed : 15.62 % Favored : 82.86 % 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: 1.79 (0.17), residues: 2472 helix: 1.87 (0.12), residues: 1736 sheet: 0.29 (0.50), residues: 104 loop : -0.53 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B4189 TYR 0.016 0.001 TYR B4177 PHE 0.020 0.001 PHE A4219 TRP 0.006 0.001 TRP B4716 HIS 0.004 0.001 HIS D3998 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (21160) covalent geometry : angle 0.57587 / 0.29 (28576) SS BOND : bond 0.00108 / 0.05 ( 4) SS BOND : angle 0.98185 / 0.66 ( 8) hydrogen bonds : bond 0.04080 / 2.72 ( 1361) hydrogen bonds : angle 4.40084 / 3.20 ( 3999) metal coordination : bond 0.00606 / 0.36 ( 16) metal coordination : angle 1.99669 / 1.42 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8019.54 seconds wall clock time: 136 minutes 46.99 seconds (8206.99 seconds total)