Starting phenix.real_space_refine on Wed Jun 18 06:23:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sey_40433/06_2025/8sey_40433.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sey_40433/06_2025/8sey_40433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sey_40433/06_2025/8sey_40433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sey_40433/06_2025/8sey_40433.map" model { file = "/net/cci-nas-00/data/ceres_data/8sey_40433/06_2025/8sey_40433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sey_40433/06_2025/8sey_40433.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.123 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 160 5.16 5 C 13360 2.51 5 N 3280 2.21 5 O 3764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20568 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5122 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "B" Number of atoms: 5122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5122 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "C" Number of atoms: 5122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5122 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "D" Number of atoms: 5122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5122 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {' ZN': 1, 'ADN%rna2p': 1} Classifications: {'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {' ZN': 1, 'ADN%rna2p': 1} Classifications: {'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {' ZN': 1, 'ADN%rna2p': 1} Classifications: {'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {' ZN': 1, 'ADN%rna2p': 1} Classifications: {'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4448 SG CYS A4958 56.002 81.276 88.845 1.00 44.66 S ATOM 4473 SG CYS A4961 58.248 82.388 91.794 1.00 41.54 S ATOM 9570 SG CYS B4958 60.404 56.002 88.845 1.00 44.78 S ATOM 9595 SG CYS B4961 59.292 58.248 91.794 1.00 41.58 S ATOM 14692 SG CYS C4958 85.678 60.404 88.845 1.00 44.43 S ATOM 14717 SG CYS C4961 83.432 59.292 91.794 1.00 41.45 S ATOM 19814 SG CYS D4958 81.277 85.678 88.845 1.00 44.61 S ATOM 19839 SG CYS D4961 82.388 83.432 91.794 1.00 41.80 S Time building chain proxies: 11.17, per 1000 atoms: 0.54 Number of scatterers: 20568 At special positions: 0 Unit cell: (142.968, 142.968, 135.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 160 16.00 O 3764 8.00 N 3280 7.00 C 13360 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: 4.46 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5102 " pdb="ZN ZN A5102 " - pdb=" ND1 HIS A4983 " pdb="ZN ZN A5102 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4958 " pdb=" ZN B5102 " pdb="ZN ZN B5102 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5102 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4958 " pdb=" ZN C5102 " pdb="ZN ZN C5102 " - pdb=" ND1 HIS C4983 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4958 " pdb=" ZN D5102 " pdb="ZN ZN D5102 " - pdb=" ND1 HIS D4983 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4958 " Number of angles added : 8 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4720 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 78.8% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 3950 through 3970 removed outlier: 3.532A pdb=" N VAL A3957 " --> pdb=" O LYS A3953 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A3969 " --> pdb=" O LEU A3965 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3983 removed outlier: 3.603A pdb=" N ALA A3981 " --> pdb=" O GLN A3977 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS A3982 " --> pdb=" O GLN A3978 " (cutoff:3.500A) Processing helix chain 'A' and resid 3984 through 4006 removed outlier: 4.015A pdb=" N HIS A3998 " --> pdb=" O HIS A3994 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A4005 " --> pdb=" O MET A4001 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP A4006 " --> pdb=" O LYS A4002 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4031 removed outlier: 3.951A pdb=" N GLU A4015 " --> pdb=" O GLU A4011 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A4031 " --> pdb=" O LEU A4027 " (cutoff:3.500A) Processing helix chain 'A' and resid 4038 through 4051 removed outlier: 3.504A pdb=" N ARG A4042 " --> pdb=" O GLY A4038 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A4043 " --> pdb=" O MET A4039 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4056 Processing helix chain 'A' and resid 4198 through 4207 Processing helix chain 'A' and resid 4207 through 4224 Processing helix chain 'A' and resid 4229 through 4252 Processing helix chain 'A' and resid 4544 through 4558 Processing helix chain 'A' and resid 4558 through 4578 Processing helix chain 'A' and resid 4638 through 4665 Processing helix chain 'A' and resid 4665 through 4683 Processing helix chain 'A' and resid 4696 through 4703 Processing helix chain 'A' and resid 4704 through 4708 removed outlier: 3.862A pdb=" N ASN A4707 " --> pdb=" O LEU A4704 " (cutoff:3.500A) Processing helix chain 'A' and resid 4719 through 4733 removed outlier: 5.207A pdb=" N ASP A4730 " --> pdb=" O ASP A4726 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE A4731 " --> pdb=" O LYS A4727 " (cutoff:3.500A) Processing helix chain 'A' and resid 4733 through 4742 Processing helix chain 'A' and resid 4744 through 4749 removed outlier: 3.655A pdb=" N SER A4747 " --> pdb=" O ASP A4744 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A4749 " --> pdb=" O ALA A4746 " (cutoff:3.500A) Processing helix chain 'A' and resid 4773 through 4786 Processing helix chain 'A' and resid 4786 through 4805 removed outlier: 3.775A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4813 Processing helix chain 'A' and resid 4814 through 4820 removed outlier: 4.288A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) Processing helix chain 'A' and resid 4820 through 4833 removed outlier: 3.697A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN A4833 " --> pdb=" O SER A4829 " (cutoff:3.500A) Processing helix chain 'A' and resid 4833 through 4859 Processing helix chain 'A' and resid 4860 through 4863 Processing helix chain 'A' and resid 4878 through 4893 removed outlier: 4.562A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG A4892 " --> pdb=" O TYR A4888 " (cutoff:3.500A) Processing helix chain 'A' and resid 4896 through 4900 Processing helix chain 'A' and resid 4909 through 4924 Processing helix chain 'A' and resid 4926 through 4957 removed outlier: 4.025A pdb=" N ILE A4932 " --> pdb=" O LEU A4928 " (cutoff:3.500A) Processing helix chain 'A' and resid 4964 through 4969 removed outlier: 3.984A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) Processing helix chain 'A' and resid 4973 through 4981 Processing helix chain 'A' and resid 4984 through 4998 Processing helix chain 'A' and resid 5004 through 5016 Processing helix chain 'A' and resid 5027 through 5037 removed outlier: 6.525A pdb=" N ASP A5034 " --> pdb=" O LYS A5030 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLN A5035 " --> pdb=" O GLN A5031 " (cutoff:3.500A) Processing helix chain 'B' and resid 3951 through 3970 removed outlier: 3.534A pdb=" N VAL B3957 " --> pdb=" O LYS B3953 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B3969 " --> pdb=" O LEU B3965 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3983 removed outlier: 3.587A pdb=" N ALA B3981 " --> pdb=" O GLN B3977 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS B3982 " --> pdb=" O GLN B3978 " (cutoff:3.500A) Processing helix chain 'B' and resid 3984 through 4006 removed outlier: 4.001A pdb=" N HIS B3998 " --> pdb=" O HIS B3994 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET B4001 " --> pdb=" O ALA B3997 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN B4005 " --> pdb=" O MET B4001 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP B4006 " --> pdb=" O LYS B4002 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4031 removed outlier: 3.942A pdb=" N GLU B4015 " --> pdb=" O GLU B4011 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN B4020 " --> pdb=" O LEU B4016 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B4031 " --> pdb=" O LEU B4027 " (cutoff:3.500A) Processing helix chain 'B' and resid 4038 through 4051 Processing helix chain 'B' and resid 4051 through 4056 Processing helix chain 'B' and resid 4198 through 4207 Processing helix chain 'B' and resid 4207 through 4224 Processing helix chain 'B' and resid 4229 through 4252 Processing helix chain 'B' and resid 4544 through 4558 Processing helix chain 'B' and resid 4558 through 4578 Processing helix chain 'B' and resid 4638 through 4665 Processing helix chain 'B' and resid 4665 through 4683 Processing helix chain 'B' and resid 4696 through 4703 Processing helix chain 'B' and resid 4704 through 4708 removed outlier: 3.863A pdb=" N ASN B4707 " --> pdb=" O LEU B4704 " (cutoff:3.500A) Processing helix chain 'B' and resid 4719 through 4733 removed outlier: 5.207A pdb=" N ASP B4730 " --> pdb=" O ASP B4726 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE B4731 " --> pdb=" O LYS B4727 " (cutoff:3.500A) Processing helix chain 'B' and resid 4733 through 4742 Processing helix chain 'B' and resid 4744 through 4749 removed outlier: 3.655A pdb=" N SER B4747 " --> pdb=" O ASP B4744 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU B4749 " --> pdb=" O ALA B4746 " (cutoff:3.500A) Processing helix chain 'B' and resid 4773 through 4786 Processing helix chain 'B' and resid 4786 through 4805 removed outlier: 3.775A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4806 through 4813 Processing helix chain 'B' and resid 4814 through 4820 removed outlier: 4.289A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) Processing helix chain 'B' and resid 4820 through 4833 removed outlier: 3.696A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASN B4833 " --> pdb=" O SER B4829 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4859 Processing helix chain 'B' and resid 4860 through 4863 Processing helix chain 'B' and resid 4878 through 4893 removed outlier: 4.563A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG B4892 " --> pdb=" O TYR B4888 " (cutoff:3.500A) Processing helix chain 'B' and resid 4896 through 4900 Processing helix chain 'B' and resid 4909 through 4924 Processing helix chain 'B' and resid 4926 through 4957 removed outlier: 4.024A pdb=" N ILE B4932 " --> pdb=" O LEU B4928 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4969 removed outlier: 3.984A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4981 Processing helix chain 'B' and resid 4984 through 4998 Processing helix chain 'B' and resid 5004 through 5016 Processing helix chain 'B' and resid 5027 through 5037 removed outlier: 6.524A pdb=" N ASP B5034 " --> pdb=" O LYS B5030 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN B5035 " --> pdb=" O GLN B5031 " (cutoff:3.500A) Processing helix chain 'C' and resid 3951 through 3970 removed outlier: 3.534A pdb=" N VAL C3957 " --> pdb=" O LYS C3953 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C3969 " --> pdb=" O LEU C3965 " (cutoff:3.500A) Processing helix chain 'C' and resid 3973 through 3983 removed outlier: 3.587A pdb=" N ALA C3981 " --> pdb=" O GLN C3977 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS C3982 " --> pdb=" O GLN C3978 " (cutoff:3.500A) Processing helix chain 'C' and resid 3984 through 4006 removed outlier: 4.002A pdb=" N HIS C3998 " --> pdb=" O HIS C3994 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN C4005 " --> pdb=" O MET C4001 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP C4006 " --> pdb=" O LYS C4002 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4031 removed outlier: 3.942A pdb=" N GLU C4015 " --> pdb=" O GLU C4011 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN C4020 " --> pdb=" O LEU C4016 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C4031 " --> pdb=" O LEU C4027 " (cutoff:3.500A) Processing helix chain 'C' and resid 4038 through 4051 Processing helix chain 'C' and resid 4051 through 4056 Processing helix chain 'C' and resid 4198 through 4207 Processing helix chain 'C' and resid 4207 through 4224 Processing helix chain 'C' and resid 4229 through 4252 Processing helix chain 'C' and resid 4544 through 4558 Processing helix chain 'C' and resid 4558 through 4578 Processing helix chain 'C' and resid 4638 through 4665 Processing helix chain 'C' and resid 4665 through 4683 Processing helix chain 'C' and resid 4696 through 4703 Processing helix chain 'C' and resid 4704 through 4708 removed outlier: 3.863A pdb=" N ASN C4707 " --> pdb=" O LEU C4704 " (cutoff:3.500A) Processing helix chain 'C' and resid 4719 through 4733 removed outlier: 5.207A pdb=" N ASP C4730 " --> pdb=" O ASP C4726 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE C4731 " --> pdb=" O LYS C4727 " (cutoff:3.500A) Processing helix chain 'C' and resid 4733 through 4742 Processing helix chain 'C' and resid 4744 through 4749 removed outlier: 3.655A pdb=" N SER C4747 " --> pdb=" O ASP C4744 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU C4749 " --> pdb=" O ALA C4746 " (cutoff:3.500A) Processing helix chain 'C' and resid 4773 through 4786 Processing helix chain 'C' and resid 4786 through 4805 removed outlier: 3.775A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4806 through 4813 Processing helix chain 'C' and resid 4814 through 4820 removed outlier: 4.289A pdb=" N MET C4818 " --> pdb=" O LEU C4814 " (cutoff:3.500A) Processing helix chain 'C' and resid 4820 through 4833 removed outlier: 3.695A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN C4833 " --> pdb=" O SER C4829 " (cutoff:3.500A) Processing helix chain 'C' and resid 4833 through 4859 Processing helix chain 'C' and resid 4860 through 4863 Processing helix chain 'C' and resid 4878 through 4893 removed outlier: 4.562A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG C4892 " --> pdb=" O TYR C4888 " (cutoff:3.500A) Processing helix chain 'C' and resid 4896 through 4900 Processing helix chain 'C' and resid 4909 through 4924 Processing helix chain 'C' and resid 4926 through 4957 removed outlier: 4.023A pdb=" N ILE C4932 " --> pdb=" O LEU C4928 " (cutoff:3.500A) Processing helix chain 'C' and resid 4964 through 4969 removed outlier: 3.984A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) Processing helix chain 'C' and resid 4973 through 4981 Processing helix chain 'C' and resid 4984 through 4998 Processing helix chain 'C' and resid 5004 through 5016 Processing helix chain 'C' and resid 5027 through 5037 removed outlier: 6.524A pdb=" N ASP C5034 " --> pdb=" O LYS C5030 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN C5035 " --> pdb=" O GLN C5031 " (cutoff:3.500A) Processing helix chain 'D' and resid 3951 through 3970 removed outlier: 3.534A pdb=" N VAL D3957 " --> pdb=" O LYS D3953 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D3969 " --> pdb=" O LEU D3965 " (cutoff:3.500A) Processing helix chain 'D' and resid 3973 through 3983 removed outlier: 3.587A pdb=" N ALA D3981 " --> pdb=" O GLN D3977 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS D3982 " --> pdb=" O GLN D3978 " (cutoff:3.500A) Processing helix chain 'D' and resid 3984 through 4006 removed outlier: 4.001A pdb=" N HIS D3998 " --> pdb=" O HIS D3994 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN D4005 " --> pdb=" O MET D4001 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP D4006 " --> pdb=" O LYS D4002 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4031 removed outlier: 3.942A pdb=" N GLU D4015 " --> pdb=" O GLU D4011 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN D4020 " --> pdb=" O LEU D4016 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU D4031 " --> pdb=" O LEU D4027 " (cutoff:3.500A) Processing helix chain 'D' and resid 4038 through 4051 Processing helix chain 'D' and resid 4051 through 4056 Processing helix chain 'D' and resid 4198 through 4207 Processing helix chain 'D' and resid 4207 through 4224 Processing helix chain 'D' and resid 4229 through 4252 Processing helix chain 'D' and resid 4544 through 4558 Processing helix chain 'D' and resid 4558 through 4578 Processing helix chain 'D' and resid 4638 through 4665 Processing helix chain 'D' and resid 4665 through 4683 Processing helix chain 'D' and resid 4696 through 4703 Processing helix chain 'D' and resid 4704 through 4708 removed outlier: 3.864A pdb=" N ASN D4707 " --> pdb=" O LEU D4704 " (cutoff:3.500A) Processing helix chain 'D' and resid 4719 through 4733 removed outlier: 5.207A pdb=" N ASP D4730 " --> pdb=" O ASP D4726 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE D4731 " --> pdb=" O LYS D4727 " (cutoff:3.500A) Processing helix chain 'D' and resid 4733 through 4742 Processing helix chain 'D' and resid 4744 through 4749 removed outlier: 3.655A pdb=" N SER D4747 " --> pdb=" O ASP D4744 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU D4749 " --> pdb=" O ALA D4746 " (cutoff:3.500A) Processing helix chain 'D' and resid 4773 through 4786 Processing helix chain 'D' and resid 4786 through 4805 removed outlier: 3.775A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4806 through 4813 Processing helix chain 'D' and resid 4814 through 4820 removed outlier: 4.288A pdb=" N MET D4818 " --> pdb=" O LEU D4814 " (cutoff:3.500A) Processing helix chain 'D' and resid 4820 through 4833 removed outlier: 3.695A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN D4833 " --> pdb=" O SER D4829 " (cutoff:3.500A) Processing helix chain 'D' and resid 4833 through 4859 Processing helix chain 'D' and resid 4860 through 4863 Processing helix chain 'D' and resid 4878 through 4893 removed outlier: 4.563A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG D4892 " --> pdb=" O TYR D4888 " (cutoff:3.500A) Processing helix chain 'D' and resid 4896 through 4900 Processing helix chain 'D' and resid 4909 through 4924 Processing helix chain 'D' and resid 4926 through 4957 removed outlier: 4.023A pdb=" N ILE D4932 " --> pdb=" O LEU D4928 " (cutoff:3.500A) Processing helix chain 'D' and resid 4964 through 4969 removed outlier: 3.984A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) Processing helix chain 'D' and resid 4973 through 4981 Processing helix chain 'D' and resid 4984 through 4998 Processing helix chain 'D' and resid 5004 through 5016 Processing helix chain 'D' and resid 5027 through 5037 removed outlier: 6.524A pdb=" N ASP D5034 " --> pdb=" O LYS D5030 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN D5035 " --> pdb=" O GLN D5031 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4181 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 4181 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 4181 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 4181 through 4184 Processing sheet with id=AA8, first strand: chain 'D' and resid 4580 through 4583 1368 hydrogen bonds defined for protein. 3960 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: 5.89 Time building geometry restraints manager: 5.35 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: 6489 1.34 - 1.46: 4662 1.46 - 1.58: 9621 1.58 - 1.69: 0 1.69 - 1.81: 276 Bond restraints: 21048 Sorted by residual: bond pdb=" C4' ADN B5101 " pdb=" O4' ADN B5101 " ideal model delta sigma weight residual 1.422 1.455 -0.033 2.00e-02 2.50e+03 2.64e+00 bond pdb=" C4' ADN A5101 " pdb=" O4' ADN A5101 " ideal model delta sigma weight residual 1.422 1.454 -0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" C4' ADN C5101 " pdb=" O4' ADN C5101 " ideal model delta sigma weight residual 1.422 1.453 -0.031 2.00e-02 2.50e+03 2.48e+00 bond pdb=" C4' ADN D5101 " pdb=" O4' ADN D5101 " ideal model delta sigma weight residual 1.422 1.453 -0.031 2.00e-02 2.50e+03 2.48e+00 bond pdb=" C3' ADN A5101 " pdb=" O3' ADN A5101 " ideal model delta sigma weight residual 1.399 1.427 -0.028 2.00e-02 2.50e+03 1.97e+00 ... (remaining 21043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 27232 0.96 - 1.92: 890 1.92 - 2.89: 165 2.89 - 3.85: 81 3.85 - 4.81: 44 Bond angle restraints: 28412 Sorted by residual: angle pdb=" C GLU C4900 " pdb=" N ILE C4901 " pdb=" CA ILE C4901 " ideal model delta sigma weight residual 122.48 119.40 3.08 1.13e+00 7.83e-01 7.44e+00 angle pdb=" C GLU A4900 " pdb=" N ILE A4901 " pdb=" CA ILE A4901 " ideal model delta sigma weight residual 122.48 119.40 3.08 1.13e+00 7.83e-01 7.44e+00 angle pdb=" C GLU D4900 " pdb=" N ILE D4901 " pdb=" CA ILE D4901 " ideal model delta sigma weight residual 122.48 119.45 3.03 1.13e+00 7.83e-01 7.20e+00 angle pdb=" C GLU B4900 " pdb=" N ILE B4901 " pdb=" CA ILE B4901 " ideal model delta sigma weight residual 122.48 119.50 2.98 1.13e+00 7.83e-01 6.96e+00 angle pdb=" C ASN B4857 " pdb=" N PHE B4858 " pdb=" CA PHE B4858 " ideal model delta sigma weight residual 122.58 118.33 4.25 2.07e+00 2.33e-01 4.22e+00 ... (remaining 28407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 11290 16.69 - 33.37: 946 33.37 - 50.06: 113 50.06 - 66.75: 72 66.75 - 83.44: 39 Dihedral angle restraints: 12460 sinusoidal: 5140 harmonic: 7320 Sorted by residual: dihedral pdb=" CA GLY D3971 " pdb=" C GLY D3971 " pdb=" N PRO D3972 " pdb=" CA PRO D3972 " ideal model delta harmonic sigma weight residual -180.00 -150.34 -29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLY A3971 " pdb=" C GLY A3971 " pdb=" N PRO A3972 " pdb=" CA PRO A3972 " ideal model delta harmonic sigma weight residual -180.00 -150.34 -29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLY C3971 " pdb=" C GLY C3971 " pdb=" N PRO C3972 " pdb=" CA PRO C3972 " ideal model delta harmonic sigma weight residual -180.00 -150.38 -29.62 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 12457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2537 0.047 - 0.095: 487 0.095 - 0.142: 52 0.142 - 0.190: 8 0.190 - 0.237: 4 Chirality restraints: 3088 Sorted by residual: chirality pdb=" C2' ADN D5101 " pdb=" C1' ADN D5101 " pdb=" C3' ADN D5101 " pdb=" O2' ADN D5101 " both_signs ideal model delta sigma weight residual False -2.75 -2.51 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C2' ADN C5101 " pdb=" C1' ADN C5101 " pdb=" C3' ADN C5101 " pdb=" O2' ADN C5101 " both_signs ideal model delta sigma weight residual False -2.75 -2.52 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C2' ADN A5101 " pdb=" C1' ADN A5101 " pdb=" C3' ADN A5101 " pdb=" O2' ADN A5101 " both_signs ideal model delta sigma weight residual False -2.75 -2.52 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 3085 not shown) Planarity restraints: 3592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B4666 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO B4667 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B4667 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B4667 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C4666 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO C4667 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO C4667 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C4667 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A4666 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.66e+00 pdb=" N PRO A4667 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A4667 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A4667 " 0.018 5.00e-02 4.00e+02 ... (remaining 3589 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3640 2.76 - 3.29: 19983 3.29 - 3.83: 34719 3.83 - 4.36: 40004 4.36 - 4.90: 69643 Nonbonded interactions: 167989 Sorted by model distance: nonbonded pdb=" OD2 ASP A4917 " pdb=" OH TYR D4888 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR C4888 " pdb=" OD2 ASP D4917 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR B4888 " pdb=" OD2 ASP C4917 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR A4888 " pdb=" OD2 ASP B4917 " model vdw 2.224 3.040 nonbonded pdb=" O THR A4825 " pdb=" OG SER A4828 " model vdw 2.235 3.040 ... (remaining 167984 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.030 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: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 44.840 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.002 0.033 21068 Z= 0.116 Angle : 0.489 10.395 28428 Z= 0.262 Chirality : 0.037 0.237 3088 Planarity : 0.003 0.041 3592 Dihedral : 13.784 83.436 7728 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.17), residues: 2464 helix: 2.01 (0.13), residues: 1652 sheet: -1.32 (0.52), residues: 112 loop : -0.49 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B5011 HIS 0.004 0.001 HIS D5003 PHE 0.011 0.001 PHE A4916 TYR 0.008 0.001 TYR A4994 ARG 0.002 0.000 ARG C4913 Details of bonding type rmsd hydrogen bonds : bond 0.13793 ( 1368) hydrogen bonds : angle 4.56950 ( 3960) metal coordination : bond 0.00320 ( 16) metal coordination : angle 7.45404 ( 8) SS BOND : bond 0.00232 ( 4) SS BOND : angle 0.68530 ( 8) covalent geometry : bond 0.00234 (21048) covalent geometry : angle 0.47295 (28412) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 2.218 Fit side-chains REVERT: A 4026 MET cc_start: 0.7916 (ttp) cc_final: 0.7621 (ttm) REVERT: A 4949 GLN cc_start: 0.7719 (tt0) cc_final: 0.7432 (tt0) REVERT: A 4953 ASP cc_start: 0.7014 (m-30) cc_final: 0.6771 (m-30) REVERT: B 4026 MET cc_start: 0.7890 (ttp) cc_final: 0.7601 (ttm) REVERT: B 4196 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6604 (mm-30) REVERT: B 4949 GLN cc_start: 0.7716 (tt0) cc_final: 0.7429 (tt0) REVERT: B 4953 ASP cc_start: 0.7011 (m-30) cc_final: 0.6768 (m-30) REVERT: C 4026 MET cc_start: 0.7889 (ttp) cc_final: 0.7602 (ttm) REVERT: C 4196 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6600 (mm-30) REVERT: C 4949 GLN cc_start: 0.7724 (tt0) cc_final: 0.7436 (tt0) REVERT: C 4953 ASP cc_start: 0.7014 (m-30) cc_final: 0.6772 (m-30) REVERT: D 4026 MET cc_start: 0.7889 (ttp) cc_final: 0.7603 (ttm) REVERT: D 4949 GLN cc_start: 0.7725 (tt0) cc_final: 0.7434 (tt0) REVERT: D 4953 ASP cc_start: 0.7011 (m-30) cc_final: 0.6769 (m-30) outliers start: 0 outliers final: 4 residues processed: 349 average time/residue: 1.4695 time to fit residues: 573.7756 Evaluate side-chains 254 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 250 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4777 ILE Chi-restraints excluded: chain B residue 4777 ILE Chi-restraints excluded: chain C residue 4777 ILE Chi-restraints excluded: chain D residue 4777 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.0570 chunk 187 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 225 optimal weight: 0.8980 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3950 ASN A4020 GLN B3950 ASN B4020 GLN C3950 ASN C4020 GLN D3950 ASN D4020 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.143380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.112538 restraints weight = 26332.824| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.22 r_work: 0.3054 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21068 Z= 0.154 Angle : 0.501 9.338 28428 Z= 0.267 Chirality : 0.037 0.130 3088 Planarity : 0.004 0.058 3592 Dihedral : 7.329 43.060 2792 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.19 % Allowed : 7.96 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.17), residues: 2464 helix: 2.08 (0.12), residues: 1680 sheet: -1.71 (0.49), residues: 112 loop : -0.24 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A4701 HIS 0.004 0.001 HIS D4812 PHE 0.015 0.001 PHE B4916 TYR 0.009 0.001 TYR A5009 ARG 0.006 0.001 ARG D4913 Details of bonding type rmsd hydrogen bonds : bond 0.05067 ( 1368) hydrogen bonds : angle 3.98553 ( 3960) metal coordination : bond 0.00781 ( 16) metal coordination : angle 2.22199 ( 8) SS BOND : bond 0.00040 ( 4) SS BOND : angle 0.99364 ( 8) covalent geometry : bond 0.00348 (21048) covalent geometry : angle 0.49961 (28412) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 275 time to evaluate : 2.238 Fit side-chains REVERT: A 4735 GLU cc_start: 0.8463 (tp30) cc_final: 0.8185 (tp30) REVERT: A 4949 GLN cc_start: 0.8160 (tt0) cc_final: 0.7844 (tt0) REVERT: A 4953 ASP cc_start: 0.7647 (m-30) cc_final: 0.7429 (m-30) REVERT: A 5034 ASP cc_start: 0.6557 (OUTLIER) cc_final: 0.6224 (p0) REVERT: B 4735 GLU cc_start: 0.8453 (tp30) cc_final: 0.8219 (tp30) REVERT: B 4949 GLN cc_start: 0.8168 (tt0) cc_final: 0.7853 (tt0) REVERT: B 4953 ASP cc_start: 0.7646 (m-30) cc_final: 0.7428 (m-30) REVERT: B 5034 ASP cc_start: 0.6569 (OUTLIER) cc_final: 0.6232 (p0) REVERT: C 4735 GLU cc_start: 0.8457 (tp30) cc_final: 0.8225 (tp30) REVERT: C 4949 GLN cc_start: 0.8168 (tt0) cc_final: 0.7856 (tt0) REVERT: C 4953 ASP cc_start: 0.7651 (m-30) cc_final: 0.7434 (m-30) REVERT: C 5034 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.6222 (p0) REVERT: D 4735 GLU cc_start: 0.8460 (tp30) cc_final: 0.8183 (tp30) REVERT: D 4949 GLN cc_start: 0.8155 (tt0) cc_final: 0.7843 (tt0) REVERT: D 4953 ASP cc_start: 0.7654 (m-30) cc_final: 0.7438 (m-30) REVERT: D 5034 ASP cc_start: 0.6554 (OUTLIER) cc_final: 0.6221 (p0) outliers start: 49 outliers final: 19 residues processed: 311 average time/residue: 1.5615 time to fit residues: 540.3817 Evaluate side-chains 271 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 248 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain A residue 5034 ASP Chi-restraints excluded: chain B residue 3951 PHE Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain B residue 5034 ASP Chi-restraints excluded: chain C residue 3951 PHE Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain C residue 5034 ASP Chi-restraints excluded: chain D residue 3951 PHE Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5001 THR Chi-restraints excluded: chain D residue 5034 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 58 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 134 optimal weight: 0.3980 chunk 57 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3950 ASN A4020 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4020 GLN ** B4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4020 GLN ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4020 GLN ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.142799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.111751 restraints weight = 26139.631| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.15 r_work: 0.3050 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21068 Z= 0.151 Angle : 0.486 5.974 28428 Z= 0.259 Chirality : 0.037 0.129 3088 Planarity : 0.003 0.060 3592 Dihedral : 5.973 39.615 2784 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.97 % Allowed : 9.70 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.17), residues: 2464 helix: 2.27 (0.12), residues: 1648 sheet: -1.93 (0.48), residues: 112 loop : -0.33 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D4701 HIS 0.004 0.001 HIS D4812 PHE 0.015 0.001 PHE C3996 TYR 0.009 0.001 TYR A5009 ARG 0.003 0.000 ARG C4913 Details of bonding type rmsd hydrogen bonds : bond 0.04696 ( 1368) hydrogen bonds : angle 3.98267 ( 3960) metal coordination : bond 0.00846 ( 16) metal coordination : angle 2.13464 ( 8) SS BOND : bond 0.00051 ( 4) SS BOND : angle 1.02333 ( 8) covalent geometry : bond 0.00351 (21048) covalent geometry : angle 0.48437 (28412) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 262 time to evaluate : 2.332 Fit side-chains REVERT: A 3959 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8434 (ttpp) REVERT: A 4026 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8233 (ttm) REVERT: A 4949 GLN cc_start: 0.8229 (tt0) cc_final: 0.7910 (tt0) REVERT: A 4953 ASP cc_start: 0.7682 (m-30) cc_final: 0.7462 (m-30) REVERT: A 5034 ASP cc_start: 0.6610 (OUTLIER) cc_final: 0.6282 (p0) REVERT: B 4026 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8217 (ttm) REVERT: B 4949 GLN cc_start: 0.8234 (tt0) cc_final: 0.7915 (tt0) REVERT: B 4953 ASP cc_start: 0.7678 (m-30) cc_final: 0.7460 (m-30) REVERT: B 5034 ASP cc_start: 0.6608 (OUTLIER) cc_final: 0.6280 (p0) REVERT: C 4026 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8211 (ttm) REVERT: C 4949 GLN cc_start: 0.8228 (tt0) cc_final: 0.7915 (tt0) REVERT: C 4953 ASP cc_start: 0.7690 (m-30) cc_final: 0.7472 (m-30) REVERT: C 5034 ASP cc_start: 0.6605 (OUTLIER) cc_final: 0.6274 (p0) REVERT: D 4026 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8216 (ttm) REVERT: D 4949 GLN cc_start: 0.8230 (tt0) cc_final: 0.7913 (tt0) REVERT: D 4953 ASP cc_start: 0.7678 (m-30) cc_final: 0.7465 (m-30) REVERT: D 5034 ASP cc_start: 0.6597 (OUTLIER) cc_final: 0.6269 (p0) outliers start: 44 outliers final: 19 residues processed: 283 average time/residue: 1.4689 time to fit residues: 465.3250 Evaluate side-chains 288 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 260 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3959 LYS Chi-restraints excluded: chain A residue 4026 MET Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain A residue 5034 ASP Chi-restraints excluded: chain B residue 4026 MET Chi-restraints excluded: chain B residue 4048 LEU Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain B residue 5034 ASP Chi-restraints excluded: chain C residue 4026 MET Chi-restraints excluded: chain C residue 4048 LEU Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain C residue 5034 ASP Chi-restraints excluded: chain D residue 4026 MET Chi-restraints excluded: chain D residue 4048 LEU Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5001 THR Chi-restraints excluded: chain D residue 5034 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 212 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 224 optimal weight: 0.6980 chunk 57 optimal weight: 0.4980 chunk 213 optimal weight: 0.6980 chunk 231 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4201 ASN ** B4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4201 ASN C4020 GLN ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4201 ASN D4020 GLN ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4201 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.144780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.113434 restraints weight = 26441.510| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.33 r_work: 0.3055 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21068 Z= 0.110 Angle : 0.443 6.227 28428 Z= 0.236 Chirality : 0.035 0.132 3088 Planarity : 0.003 0.056 3592 Dihedral : 5.329 38.767 2784 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.97 % Allowed : 11.85 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.17), residues: 2464 helix: 2.33 (0.12), residues: 1668 sheet: -2.02 (0.48), residues: 112 loop : -0.34 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B4701 HIS 0.004 0.001 HIS D4812 PHE 0.015 0.001 PHE D3996 TYR 0.009 0.001 TYR B5009 ARG 0.002 0.000 ARG A4913 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 1368) hydrogen bonds : angle 3.87060 ( 3960) metal coordination : bond 0.00426 ( 16) metal coordination : angle 2.03569 ( 8) SS BOND : bond 0.00030 ( 4) SS BOND : angle 0.73748 ( 8) covalent geometry : bond 0.00237 (21048) covalent geometry : angle 0.44203 (28412) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 268 time to evaluate : 2.607 Fit side-chains REVERT: A 3999 MET cc_start: 0.8372 (mmp) cc_final: 0.8056 (mmm) REVERT: A 4011 GLU cc_start: 0.6607 (pm20) cc_final: 0.6374 (pm20) REVERT: A 4196 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7478 (mm-30) REVERT: A 4735 GLU cc_start: 0.8480 (tp30) cc_final: 0.8184 (tp30) REVERT: A 4949 GLN cc_start: 0.8243 (tt0) cc_final: 0.7943 (tt0) REVERT: A 4953 ASP cc_start: 0.7710 (m-30) cc_final: 0.7494 (m-30) REVERT: A 4980 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8339 (tp) REVERT: B 3999 MET cc_start: 0.8515 (mmp) cc_final: 0.8185 (mmm) REVERT: B 4039 MET cc_start: 0.7875 (tmm) cc_final: 0.7513 (ttt) REVERT: B 4735 GLU cc_start: 0.8495 (tp30) cc_final: 0.8200 (tp30) REVERT: B 4949 GLN cc_start: 0.8253 (tt0) cc_final: 0.7955 (tt0) REVERT: B 4953 ASP cc_start: 0.7713 (m-30) cc_final: 0.7501 (m-30) REVERT: B 4980 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8332 (tp) REVERT: C 3999 MET cc_start: 0.8526 (mmp) cc_final: 0.8196 (mmm) REVERT: C 4039 MET cc_start: 0.7890 (tmm) cc_final: 0.7526 (ttt) REVERT: C 4735 GLU cc_start: 0.8484 (tp30) cc_final: 0.8189 (tp30) REVERT: C 4949 GLN cc_start: 0.8245 (tt0) cc_final: 0.7951 (tt0) REVERT: C 4953 ASP cc_start: 0.7719 (m-30) cc_final: 0.7513 (m-30) REVERT: C 4980 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8331 (tp) REVERT: D 3999 MET cc_start: 0.8528 (mmp) cc_final: 0.8198 (mmm) REVERT: D 4039 MET cc_start: 0.7896 (tmm) cc_final: 0.7531 (ttt) REVERT: D 4735 GLU cc_start: 0.8478 (tp30) cc_final: 0.8183 (tp30) REVERT: D 4949 GLN cc_start: 0.8235 (tt0) cc_final: 0.7938 (tt0) REVERT: D 4953 ASP cc_start: 0.7715 (m-30) cc_final: 0.7503 (m-30) REVERT: D 4980 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8315 (tp) outliers start: 44 outliers final: 9 residues processed: 292 average time/residue: 1.5133 time to fit residues: 493.6774 Evaluate side-chains 266 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 253 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3951 PHE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5001 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 205 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4020 GLN B4054 ASN C4020 GLN C4054 ASN D4020 GLN D4054 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113800 restraints weight = 26495.515| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.52 r_work: 0.3056 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21068 Z= 0.118 Angle : 0.458 8.372 28428 Z= 0.243 Chirality : 0.035 0.145 3088 Planarity : 0.003 0.057 3592 Dihedral : 4.934 37.198 2784 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.33 % Allowed : 12.48 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.17), residues: 2464 helix: 2.33 (0.12), residues: 1680 sheet: -1.98 (0.49), residues: 112 loop : -0.34 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D4701 HIS 0.003 0.001 HIS D4812 PHE 0.013 0.001 PHE C4916 TYR 0.015 0.001 TYR A5009 ARG 0.002 0.000 ARG D4913 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 1368) hydrogen bonds : angle 3.85992 ( 3960) metal coordination : bond 0.00520 ( 16) metal coordination : angle 1.89144 ( 8) SS BOND : bond 0.00056 ( 4) SS BOND : angle 0.75006 ( 8) covalent geometry : bond 0.00260 (21048) covalent geometry : angle 0.45693 (28412) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 266 time to evaluate : 2.301 Fit side-chains REVERT: A 3999 MET cc_start: 0.8469 (mmp) cc_final: 0.8146 (mmm) REVERT: A 4224 GLU cc_start: 0.7783 (pm20) cc_final: 0.7553 (pm20) REVERT: A 4735 GLU cc_start: 0.8475 (tp30) cc_final: 0.8138 (tp30) REVERT: A 4949 GLN cc_start: 0.8178 (tt0) cc_final: 0.7870 (tt0) REVERT: A 4953 ASP cc_start: 0.7670 (m-30) cc_final: 0.7445 (m-30) REVERT: A 4980 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8250 (tp) REVERT: B 3999 MET cc_start: 0.8490 (mmp) cc_final: 0.8164 (mmm) REVERT: B 4039 MET cc_start: 0.7745 (tmm) cc_final: 0.7384 (tmm) REVERT: B 4224 GLU cc_start: 0.7781 (pm20) cc_final: 0.7550 (pm20) REVERT: B 4735 GLU cc_start: 0.8479 (tp30) cc_final: 0.8143 (tp30) REVERT: B 4949 GLN cc_start: 0.8189 (tt0) cc_final: 0.7881 (tt0) REVERT: B 4953 ASP cc_start: 0.7669 (m-30) cc_final: 0.7443 (m-30) REVERT: B 4980 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8241 (tp) REVERT: C 3999 MET cc_start: 0.8501 (mmp) cc_final: 0.8174 (mmm) REVERT: C 4039 MET cc_start: 0.7744 (tmm) cc_final: 0.7381 (tmm) REVERT: C 4224 GLU cc_start: 0.7789 (pm20) cc_final: 0.7555 (pm20) REVERT: C 4735 GLU cc_start: 0.8469 (tp30) cc_final: 0.8136 (tp30) REVERT: C 4949 GLN cc_start: 0.8180 (tt0) cc_final: 0.7872 (tt0) REVERT: C 4953 ASP cc_start: 0.7678 (m-30) cc_final: 0.7450 (m-30) REVERT: C 4980 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8247 (tp) REVERT: D 3999 MET cc_start: 0.8499 (mmp) cc_final: 0.8170 (mmm) REVERT: D 4039 MET cc_start: 0.7730 (tmm) cc_final: 0.7378 (tmm) REVERT: D 4224 GLU cc_start: 0.7786 (pm20) cc_final: 0.7551 (pm20) REVERT: D 4735 GLU cc_start: 0.8478 (tp30) cc_final: 0.8145 (tp30) REVERT: D 4949 GLN cc_start: 0.8181 (tt0) cc_final: 0.7873 (tt0) REVERT: D 4953 ASP cc_start: 0.7679 (m-30) cc_final: 0.7450 (m-30) REVERT: D 4980 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8255 (tp) outliers start: 52 outliers final: 16 residues processed: 297 average time/residue: 1.3995 time to fit residues: 467.3084 Evaluate side-chains 276 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 256 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3951 PHE Chi-restraints excluded: chain A residue 4247 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain B residue 4048 LEU Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain C residue 4048 LEU Chi-restraints excluded: chain C residue 4247 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain D residue 4048 LEU Chi-restraints excluded: chain D residue 4247 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5001 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 36 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 239 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4020 GLN ** B4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4020 GLN ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4020 GLN ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.141680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.110976 restraints weight = 26304.039| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.48 r_work: 0.3012 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21068 Z= 0.185 Angle : 0.511 8.021 28428 Z= 0.269 Chirality : 0.038 0.131 3088 Planarity : 0.004 0.068 3592 Dihedral : 4.956 36.953 2784 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.09 % Allowed : 11.76 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.17), residues: 2464 helix: 2.23 (0.12), residues: 1640 sheet: -2.20 (0.48), residues: 112 loop : -0.31 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C4778 HIS 0.005 0.001 HIS D4803 PHE 0.018 0.002 PHE B4916 TYR 0.016 0.002 TYR C4804 ARG 0.003 0.000 ARG D5017 Details of bonding type rmsd hydrogen bonds : bond 0.04779 ( 1368) hydrogen bonds : angle 4.02693 ( 3960) metal coordination : bond 0.01264 ( 16) metal coordination : angle 1.77021 ( 8) SS BOND : bond 0.00162 ( 4) SS BOND : angle 1.32271 ( 8) covalent geometry : bond 0.00442 (21048) covalent geometry : angle 0.50980 (28412) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 275 time to evaluate : 2.351 Fit side-chains REVERT: A 3992 PHE cc_start: 0.8715 (m-80) cc_final: 0.8450 (m-80) REVERT: A 3999 MET cc_start: 0.8520 (mmp) cc_final: 0.8142 (mmm) REVERT: A 4011 GLU cc_start: 0.6581 (pm20) cc_final: 0.6378 (pm20) REVERT: A 4735 GLU cc_start: 0.8518 (tp30) cc_final: 0.8239 (tp30) REVERT: A 4980 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8333 (tp) REVERT: A 5034 ASP cc_start: 0.6512 (OUTLIER) cc_final: 0.6201 (p0) REVERT: B 3999 MET cc_start: 0.8475 (mmp) cc_final: 0.8151 (mmm) REVERT: B 4735 GLU cc_start: 0.8526 (tp30) cc_final: 0.8247 (tp30) REVERT: C 3999 MET cc_start: 0.8491 (mmp) cc_final: 0.8171 (mmm) REVERT: C 4735 GLU cc_start: 0.8514 (tp30) cc_final: 0.8237 (tp30) REVERT: D 3999 MET cc_start: 0.8481 (mmp) cc_final: 0.8161 (mmm) REVERT: D 4735 GLU cc_start: 0.8520 (tp30) cc_final: 0.8243 (tp30) REVERT: D 4980 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8333 (tp) outliers start: 69 outliers final: 25 residues processed: 320 average time/residue: 1.4436 time to fit residues: 516.7723 Evaluate side-chains 291 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 263 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3951 PHE Chi-restraints excluded: chain A residue 4247 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 4981 GLU Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain A residue 5013 MET Chi-restraints excluded: chain A residue 5034 ASP Chi-restraints excluded: chain B residue 3951 PHE Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain C residue 3951 PHE Chi-restraints excluded: chain C residue 4247 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain D residue 3951 PHE Chi-restraints excluded: chain D residue 4247 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5001 THR Chi-restraints excluded: chain D residue 5013 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 40 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 163 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4020 GLN C4020 GLN D4020 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.143295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.112359 restraints weight = 26270.103| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.68 r_work: 0.3028 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21068 Z= 0.153 Angle : 0.510 8.529 28428 Z= 0.265 Chirality : 0.037 0.165 3088 Planarity : 0.003 0.064 3592 Dihedral : 4.798 34.774 2784 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.46 % Allowed : 14.00 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.17), residues: 2464 helix: 2.26 (0.12), residues: 1644 sheet: -2.18 (0.48), residues: 112 loop : -0.31 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C4701 HIS 0.003 0.001 HIS D4803 PHE 0.014 0.001 PHE C4916 TYR 0.016 0.001 TYR A4804 ARG 0.002 0.000 ARG B4913 Details of bonding type rmsd hydrogen bonds : bond 0.04511 ( 1368) hydrogen bonds : angle 3.97643 ( 3960) metal coordination : bond 0.00819 ( 16) metal coordination : angle 1.72233 ( 8) SS BOND : bond 0.00122 ( 4) SS BOND : angle 1.01126 ( 8) covalent geometry : bond 0.00359 (21048) covalent geometry : angle 0.50890 (28412) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 267 time to evaluate : 2.183 Fit side-chains REVERT: A 3999 MET cc_start: 0.8515 (mmp) cc_final: 0.8241 (mmm) REVERT: A 4026 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8182 (ttm) REVERT: A 4735 GLU cc_start: 0.8395 (tp30) cc_final: 0.8116 (tp30) REVERT: A 4953 ASP cc_start: 0.7902 (m-30) cc_final: 0.7540 (m-30) REVERT: B 3999 MET cc_start: 0.8481 (mmp) cc_final: 0.8167 (mmm) REVERT: B 4735 GLU cc_start: 0.8397 (tp30) cc_final: 0.8120 (tp30) REVERT: B 4953 ASP cc_start: 0.7915 (m-30) cc_final: 0.7556 (m-30) REVERT: C 3999 MET cc_start: 0.8491 (mmp) cc_final: 0.8178 (mmm) REVERT: C 4735 GLU cc_start: 0.8387 (tp30) cc_final: 0.8113 (tp30) REVERT: C 4953 ASP cc_start: 0.7921 (m-30) cc_final: 0.7562 (m-30) REVERT: D 3999 MET cc_start: 0.8491 (mmp) cc_final: 0.8179 (mmm) REVERT: D 4735 GLU cc_start: 0.8392 (tp30) cc_final: 0.8118 (tp30) REVERT: D 4953 ASP cc_start: 0.7913 (m-30) cc_final: 0.7555 (m-30) outliers start: 55 outliers final: 25 residues processed: 302 average time/residue: 1.3656 time to fit residues: 463.8079 Evaluate side-chains 286 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 260 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3951 PHE Chi-restraints excluded: chain A residue 4026 MET Chi-restraints excluded: chain A residue 4247 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain B residue 3951 PHE Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain B residue 5013 MET Chi-restraints excluded: chain C residue 3951 PHE Chi-restraints excluded: chain C residue 4247 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain D residue 3951 PHE Chi-restraints excluded: chain D residue 4247 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5001 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 223 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 191 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 168 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 151 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4020 GLN B4054 ASN C4020 GLN C4054 ASN D4020 GLN D4054 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.144962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.114704 restraints weight = 26468.497| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.69 r_work: 0.3058 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21068 Z= 0.110 Angle : 0.470 8.393 28428 Z= 0.246 Chirality : 0.035 0.142 3088 Planarity : 0.003 0.057 3592 Dihedral : 4.574 31.570 2784 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.10 % Allowed : 14.40 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.17), residues: 2464 helix: 2.36 (0.12), residues: 1656 sheet: -2.08 (0.49), residues: 112 loop : -0.23 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C5011 HIS 0.003 0.000 HIS D4812 PHE 0.012 0.001 PHE C4916 TYR 0.016 0.001 TYR C4804 ARG 0.002 0.000 ARG A4913 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 1368) hydrogen bonds : angle 3.88121 ( 3960) metal coordination : bond 0.00388 ( 16) metal coordination : angle 1.82413 ( 8) SS BOND : bond 0.00019 ( 4) SS BOND : angle 0.70922 ( 8) covalent geometry : bond 0.00239 (21048) covalent geometry : angle 0.46946 (28412) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 269 time to evaluate : 2.720 Fit side-chains REVERT: A 3999 MET cc_start: 0.8481 (mmp) cc_final: 0.8104 (mmm) REVERT: A 4026 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8072 (ttm) REVERT: A 4224 GLU cc_start: 0.7708 (pm20) cc_final: 0.7469 (pm20) REVERT: A 4571 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7532 (t80) REVERT: A 4707 ASN cc_start: 0.8362 (t0) cc_final: 0.8161 (t0) REVERT: A 4735 GLU cc_start: 0.8362 (tp30) cc_final: 0.8085 (tp30) REVERT: B 3999 MET cc_start: 0.8425 (mmp) cc_final: 0.8159 (mmm) REVERT: B 4224 GLU cc_start: 0.7704 (pm20) cc_final: 0.7465 (pm20) REVERT: B 4571 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7542 (t80) REVERT: B 4735 GLU cc_start: 0.8377 (tp30) cc_final: 0.8101 (tp30) REVERT: C 3999 MET cc_start: 0.8436 (mmp) cc_final: 0.8170 (mmm) REVERT: C 4224 GLU cc_start: 0.7711 (pm20) cc_final: 0.7468 (pm20) REVERT: C 4571 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7541 (t80) REVERT: C 4735 GLU cc_start: 0.8366 (tp30) cc_final: 0.8094 (tp30) REVERT: D 3999 MET cc_start: 0.8429 (mmp) cc_final: 0.8167 (mmm) REVERT: D 4224 GLU cc_start: 0.7711 (pm20) cc_final: 0.7468 (pm20) REVERT: D 4571 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7546 (t80) REVERT: D 4735 GLU cc_start: 0.8363 (tp30) cc_final: 0.8089 (tp30) outliers start: 47 outliers final: 29 residues processed: 300 average time/residue: 1.4558 time to fit residues: 489.5697 Evaluate side-chains 290 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 256 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3951 PHE Chi-restraints excluded: chain A residue 4026 MET Chi-restraints excluded: chain A residue 4247 ILE Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4571 PHE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain B residue 3951 PHE Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4571 PHE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain B residue 5013 MET Chi-restraints excluded: chain C residue 3951 PHE Chi-restraints excluded: chain C residue 4247 ILE Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4571 PHE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain D residue 3951 PHE Chi-restraints excluded: chain D residue 4247 ILE Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4571 PHE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5001 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 106 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 205 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 220 optimal weight: 9.9990 chunk 232 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN B4020 GLN C4020 GLN D4020 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.143895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113141 restraints weight = 26293.242| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.50 r_work: 0.3046 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21068 Z= 0.129 Angle : 0.494 9.715 28428 Z= 0.258 Chirality : 0.036 0.142 3088 Planarity : 0.003 0.059 3592 Dihedral : 4.536 30.679 2784 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.15 % Allowed : 15.03 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.17), residues: 2464 helix: 2.36 (0.12), residues: 1656 sheet: -2.07 (0.49), residues: 112 loop : -0.24 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D4701 HIS 0.003 0.001 HIS C4812 PHE 0.013 0.001 PHE B4916 TYR 0.017 0.001 TYR A4804 ARG 0.002 0.000 ARG B4913 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 1368) hydrogen bonds : angle 3.90734 ( 3960) metal coordination : bond 0.00752 ( 16) metal coordination : angle 1.60511 ( 8) SS BOND : bond 0.00069 ( 4) SS BOND : angle 0.83194 ( 8) covalent geometry : bond 0.00294 (21048) covalent geometry : angle 0.49303 (28412) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 268 time to evaluate : 2.137 Fit side-chains REVERT: A 3999 MET cc_start: 0.8512 (mmp) cc_final: 0.8166 (mmm) REVERT: A 4571 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7548 (t80) REVERT: A 4707 ASN cc_start: 0.8399 (t0) cc_final: 0.8194 (t0) REVERT: A 4735 GLU cc_start: 0.8345 (tp30) cc_final: 0.8070 (tp30) REVERT: A 4953 ASP cc_start: 0.7781 (t0) cc_final: 0.7252 (m-30) REVERT: B 3998 HIS cc_start: 0.7837 (m-70) cc_final: 0.7486 (m-70) REVERT: B 3999 MET cc_start: 0.8432 (mmp) cc_final: 0.8090 (mmm) REVERT: B 4571 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7551 (t80) REVERT: B 4735 GLU cc_start: 0.8362 (tp30) cc_final: 0.8083 (tp30) REVERT: B 4953 ASP cc_start: 0.7777 (t0) cc_final: 0.7245 (m-30) REVERT: C 3998 HIS cc_start: 0.7834 (m-70) cc_final: 0.7483 (m-70) REVERT: C 3999 MET cc_start: 0.8446 (mmp) cc_final: 0.8100 (mmm) REVERT: C 4571 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.7559 (t80) REVERT: C 4735 GLU cc_start: 0.8349 (tp30) cc_final: 0.8076 (tp30) REVERT: C 4953 ASP cc_start: 0.7768 (t0) cc_final: 0.7244 (m-30) REVERT: D 3998 HIS cc_start: 0.7843 (m-70) cc_final: 0.7488 (m-70) REVERT: D 3999 MET cc_start: 0.8446 (mmp) cc_final: 0.8100 (mmm) REVERT: D 4571 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7557 (t80) REVERT: D 4735 GLU cc_start: 0.8344 (tp30) cc_final: 0.8069 (tp30) REVERT: D 4953 ASP cc_start: 0.7775 (t0) cc_final: 0.7247 (m-30) outliers start: 48 outliers final: 32 residues processed: 297 average time/residue: 1.4611 time to fit residues: 484.9699 Evaluate side-chains 300 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 264 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3951 PHE Chi-restraints excluded: chain A residue 4247 ILE Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4571 PHE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain B residue 3951 PHE Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4571 PHE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain B residue 5013 MET Chi-restraints excluded: chain C residue 3951 PHE Chi-restraints excluded: chain C residue 4247 ILE Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4571 PHE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain D residue 3951 PHE Chi-restraints excluded: chain D residue 4247 ILE Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4571 PHE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5001 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 124 optimal weight: 10.0000 chunk 121 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 156 optimal weight: 0.0040 chunk 18 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 146 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN A4054 ASN B4020 GLN B4054 ASN C4020 GLN C4054 ASN D4020 GLN D4054 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.144805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.114264 restraints weight = 26180.725| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.54 r_work: 0.3067 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21068 Z= 0.113 Angle : 0.498 11.624 28428 Z= 0.258 Chirality : 0.036 0.152 3088 Planarity : 0.003 0.057 3592 Dihedral : 4.462 29.943 2784 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.37 % Allowed : 15.43 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.17), residues: 2464 helix: 2.39 (0.12), residues: 1652 sheet: -2.02 (0.49), residues: 112 loop : -0.19 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C5011 HIS 0.003 0.000 HIS D4812 PHE 0.012 0.001 PHE C4916 TYR 0.016 0.001 TYR C5009 ARG 0.002 0.000 ARG B4913 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 1368) hydrogen bonds : angle 3.87347 ( 3960) metal coordination : bond 0.00458 ( 16) metal coordination : angle 1.70037 ( 8) SS BOND : bond 0.00037 ( 4) SS BOND : angle 0.67465 ( 8) covalent geometry : bond 0.00249 (21048) covalent geometry : angle 0.49712 (28412) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 279 time to evaluate : 2.398 Fit side-chains REVERT: A 3998 HIS cc_start: 0.8111 (m-70) cc_final: 0.7834 (m-70) REVERT: A 3999 MET cc_start: 0.8536 (mmp) cc_final: 0.8199 (mmm) REVERT: A 4042 ARG cc_start: 0.7751 (mtm110) cc_final: 0.7541 (ttm-80) REVERT: A 4571 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7579 (t80) REVERT: A 4707 ASN cc_start: 0.8394 (t0) cc_final: 0.8181 (t0) REVERT: A 4735 GLU cc_start: 0.8391 (tp30) cc_final: 0.8127 (tp30) REVERT: A 4953 ASP cc_start: 0.7824 (t0) cc_final: 0.7303 (m-30) REVERT: B 3998 HIS cc_start: 0.7874 (m-70) cc_final: 0.7516 (m-70) REVERT: B 3999 MET cc_start: 0.8458 (mmp) cc_final: 0.8180 (mmm) REVERT: B 4571 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7579 (t80) REVERT: B 4735 GLU cc_start: 0.8406 (tp30) cc_final: 0.8139 (tp30) REVERT: B 4953 ASP cc_start: 0.7800 (t0) cc_final: 0.7282 (m-30) REVERT: C 3998 HIS cc_start: 0.7868 (m-70) cc_final: 0.7514 (m-70) REVERT: C 3999 MET cc_start: 0.8462 (mmp) cc_final: 0.8182 (mmm) REVERT: C 4571 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7581 (t80) REVERT: C 4735 GLU cc_start: 0.8391 (tp30) cc_final: 0.8130 (tp30) REVERT: C 4953 ASP cc_start: 0.7802 (t0) cc_final: 0.7289 (m-30) REVERT: D 3998 HIS cc_start: 0.7876 (m-70) cc_final: 0.7514 (m-70) REVERT: D 3999 MET cc_start: 0.8461 (mmp) cc_final: 0.8184 (mmm) REVERT: D 4196 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7573 (mm-30) REVERT: D 4571 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7585 (t80) REVERT: D 4735 GLU cc_start: 0.8392 (tp30) cc_final: 0.8129 (tp30) REVERT: D 4953 ASP cc_start: 0.7819 (t0) cc_final: 0.7301 (m-30) outliers start: 53 outliers final: 31 residues processed: 318 average time/residue: 1.4874 time to fit residues: 530.7392 Evaluate side-chains 298 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 263 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3951 PHE Chi-restraints excluded: chain A residue 4247 ILE Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4571 PHE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain B residue 3951 PHE Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4571 PHE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain B residue 5013 MET Chi-restraints excluded: chain C residue 3951 PHE Chi-restraints excluded: chain C residue 4247 ILE Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4571 PHE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain D residue 3951 PHE Chi-restraints excluded: chain D residue 4247 ILE Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4571 PHE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5001 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 165 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN B4020 GLN C4020 GLN D4020 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.144214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.113886 restraints weight = 26430.360| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.51 r_work: 0.3056 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21068 Z= 0.132 Angle : 0.530 12.822 28428 Z= 0.274 Chirality : 0.037 0.171 3088 Planarity : 0.003 0.058 3592 Dihedral : 4.465 29.623 2784 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.01 % Allowed : 15.65 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.17), residues: 2464 helix: 2.35 (0.12), residues: 1652 sheet: -2.03 (0.49), residues: 112 loop : -0.18 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D4701 HIS 0.003 0.001 HIS D4812 PHE 0.013 0.001 PHE C4916 TYR 0.018 0.001 TYR C4804 ARG 0.002 0.000 ARG A4913 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 1368) hydrogen bonds : angle 3.90565 ( 3960) metal coordination : bond 0.00737 ( 16) metal coordination : angle 1.56694 ( 8) SS BOND : bond 0.00068 ( 4) SS BOND : angle 0.82982 ( 8) covalent geometry : bond 0.00305 (21048) covalent geometry : angle 0.52966 (28412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15693.47 seconds wall clock time: 267 minutes 35.60 seconds (16055.60 seconds total)