Starting phenix.real_space_refine on Wed May 21 04:35:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sez_40434/05_2025/8sez_40434.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sez_40434/05_2025/8sez_40434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sez_40434/05_2025/8sez_40434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sez_40434/05_2025/8sez_40434.map" model { file = "/net/cci-nas-00/data/ceres_data/8sez_40434/05_2025/8sez_40434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sez_40434/05_2025/8sez_40434.cif" } resolution = 3.54 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= -0.002 sd= 0.108 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 13384 2.51 5 N 3288 2.21 5 O 3744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20580 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5134 Classifications: {'peptide': 627} Link IDs: {'PTRANS': 15, 'TRANS': 611} Chain breaks: 4 Chain: "B" Number of atoms: 5134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5134 Classifications: {'peptide': 627} Link IDs: {'PTRANS': 15, 'TRANS': 611} Chain breaks: 4 Chain: "C" Number of atoms: 5134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5134 Classifications: {'peptide': 627} Link IDs: {'PTRANS': 15, 'TRANS': 611} Chain breaks: 4 Chain: "D" Number of atoms: 5134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5134 Classifications: {'peptide': 627} Link IDs: {'PTRANS': 15, 'TRANS': 611} Chain breaks: 4 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'DNA': 1} Modifications used: {'5*END': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'DNA': 1} Modifications used: {'5*END': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'DNA': 1} Modifications used: {'5*END': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'DNA': 1} Modifications used: {'5*END': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4460 SG CYS A4958 55.913 81.190 88.783 1.00 95.73 S ATOM 4485 SG CYS A4961 58.694 82.144 91.244 1.00 93.45 S ATOM 9594 SG CYS B4958 60.490 55.913 88.783 1.00 95.73 S ATOM 9619 SG CYS B4961 59.536 58.694 91.244 1.00 93.45 S ATOM 14728 SG CYS C4958 85.767 60.490 88.783 1.00 95.73 S ATOM 14753 SG CYS C4961 82.986 59.536 91.244 1.00 93.45 S ATOM 19862 SG CYS D4958 81.190 85.767 88.783 1.00 95.73 S ATOM 19887 SG CYS D4961 82.144 82.986 91.244 1.00 93.45 S Time building chain proxies: 12.26, per 1000 atoms: 0.60 Number of scatterers: 20580 At special positions: 0 Unit cell: (142.968, 142.968, 131.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 160 16.00 O 3744 8.00 N 3288 7.00 C 13384 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: 5.60 Conformation dependent library (CDL) restraints added in 2.8 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 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 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: 124 helices and 8 sheets defined 77.4% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 3950 through 3969 removed outlier: 3.531A pdb=" N VAL A3957 " --> pdb=" O LYS A3953 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A3969 " --> pdb=" O LEU A3965 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3983 removed outlier: 3.650A pdb=" N HIS A3982 " --> pdb=" O GLN A3978 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A3983 " --> pdb=" O SER A3979 " (cutoff:3.500A) Processing helix chain 'A' and resid 3984 through 4006 removed outlier: 3.500A pdb=" N GLY A3991 " --> pdb=" O ASP A3987 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET A4000 " --> pdb=" O PHE A3996 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A4002 " --> pdb=" O HIS A3998 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A4006 " --> pdb=" O LYS A4002 " (cutoff:3.500A) Processing helix chain 'A' and resid 4010 through 4031 removed outlier: 3.626A pdb=" N LYS A4014 " --> pdb=" O ILE A4010 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU A4015 " --> pdb=" O GLU A4011 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A4025 " --> pdb=" O LYS A4021 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A4026 " --> pdb=" O ASP A4022 " (cutoff:3.500A) Processing helix chain 'A' and resid 4038 through 4056 removed outlier: 3.572A pdb=" N GLU A4050 " --> pdb=" O ASP A4046 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N SER A4053 " --> pdb=" O VAL A4049 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASN A4054 " --> pdb=" O GLU A4050 " (cutoff:3.500A) Processing helix chain 'A' and resid 4198 through 4206 Processing helix chain 'A' and resid 4207 through 4225 Processing helix chain 'A' and resid 4226 through 4252 removed outlier: 4.608A pdb=" N MET A4231 " --> pdb=" O GLU A4227 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLU A4232 " --> pdb=" O ALA A4228 " (cutoff:3.500A) Processing helix chain 'A' and resid 4541 through 4558 Processing helix chain 'A' and resid 4558 through 4578 Processing helix chain 'A' and resid 4638 through 4665 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: 4.019A pdb=" N ASN A4707 " --> pdb=" O LEU A4704 " (cutoff:3.500A) Processing helix chain 'A' and resid 4719 through 4733 removed outlier: 5.616A pdb=" N ASP A4730 " --> pdb=" O ASP A4726 " (cutoff:3.500A) removed outlier: 5.891A 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 4748 Processing helix chain 'A' and resid 4773 through 4786 Processing helix chain 'A' and resid 4786 through 4805 removed outlier: 3.835A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4814 removed outlier: 3.558A pdb=" N HIS A4812 " --> pdb=" O PHE A4809 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A4813 " --> pdb=" O ALA A4810 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A4814 " --> pdb=" O ALA A4811 " (cutoff:3.500A) Processing helix chain 'A' and resid 4815 through 4820 Processing helix chain 'A' and resid 4820 through 4832 removed outlier: 3.590A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) Processing helix chain 'A' and resid 4833 through 4859 removed outlier: 3.511A pdb=" N PHE A4858 " --> pdb=" O VAL A4854 " (cutoff:3.500A) Processing helix chain 'A' and resid 4878 through 4890 Processing helix chain 'A' and resid 4909 through 4925 Processing helix chain 'A' and resid 4925 through 4957 removed outlier: 5.065A pdb=" N ILE A4932 " --> pdb=" O LEU A4928 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN A4933 " --> pdb=" O LEU A4929 " (cutoff:3.500A) Processing helix chain 'A' and resid 4964 through 4969 removed outlier: 4.112A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) Processing helix chain 'A' and resid 4973 through 4982 Processing helix chain 'A' and resid 4984 through 4998 Processing helix chain 'A' and resid 5004 through 5016 Processing helix chain 'A' and resid 5027 through 5037 removed outlier: 6.116A pdb=" N ASP A5034 " --> pdb=" O LYS A5030 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN A5035 " --> pdb=" O GLN A5031 " (cutoff:3.500A) Processing helix chain 'B' and resid 3951 through 3969 removed outlier: 3.531A pdb=" N VAL B3957 " --> pdb=" O LYS B3953 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE B3969 " --> pdb=" O LEU B3965 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3983 removed outlier: 3.650A pdb=" N HIS B3982 " --> pdb=" O GLN B3978 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER B3983 " --> pdb=" O SER B3979 " (cutoff:3.500A) Processing helix chain 'B' and resid 3984 through 4006 removed outlier: 3.500A pdb=" N GLY B3991 " --> pdb=" O ASP B3987 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET B4000 " --> pdb=" O PHE B3996 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N MET B4001 " --> pdb=" O ALA B3997 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS B4002 " --> pdb=" O HIS B3998 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP B4006 " --> pdb=" O LYS B4002 " (cutoff:3.500A) Processing helix chain 'B' and resid 4010 through 4031 removed outlier: 3.626A pdb=" N LYS B4014 " --> pdb=" O ILE B4010 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU B4015 " --> pdb=" O GLU B4011 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B4025 " --> pdb=" O LYS B4021 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET B4026 " --> pdb=" O ASP B4022 " (cutoff:3.500A) Processing helix chain 'B' and resid 4038 through 4056 removed outlier: 3.572A pdb=" N GLU B4050 " --> pdb=" O ASP B4046 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N SER B4053 " --> pdb=" O VAL B4049 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASN B4054 " --> pdb=" O GLU B4050 " (cutoff:3.500A) Processing helix chain 'B' and resid 4198 through 4206 Processing helix chain 'B' and resid 4207 through 4225 Processing helix chain 'B' and resid 4226 through 4252 removed outlier: 4.608A pdb=" N MET B4231 " --> pdb=" O GLU B4227 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLU B4232 " --> pdb=" O ALA B4228 " (cutoff:3.500A) Processing helix chain 'B' and resid 4541 through 4558 Processing helix chain 'B' and resid 4558 through 4578 Processing helix chain 'B' and resid 4638 through 4665 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: 4.019A pdb=" N ASN B4707 " --> pdb=" O LEU B4704 " (cutoff:3.500A) Processing helix chain 'B' and resid 4719 through 4733 removed outlier: 5.616A pdb=" N ASP B4730 " --> pdb=" O ASP B4726 " (cutoff:3.500A) removed outlier: 5.891A 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 4748 Processing helix chain 'B' and resid 4773 through 4786 Processing helix chain 'B' and resid 4786 through 4805 removed outlier: 3.835A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4806 through 4814 removed outlier: 3.558A pdb=" N HIS B4812 " --> pdb=" O PHE B4809 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B4813 " --> pdb=" O ALA B4810 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B4814 " --> pdb=" O ALA B4811 " (cutoff:3.500A) Processing helix chain 'B' and resid 4815 through 4820 Processing helix chain 'B' and resid 4820 through 4832 removed outlier: 3.590A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4859 removed outlier: 3.511A pdb=" N PHE B4858 " --> pdb=" O VAL B4854 " (cutoff:3.500A) Processing helix chain 'B' and resid 4878 through 4890 Processing helix chain 'B' and resid 4909 through 4925 Processing helix chain 'B' and resid 4925 through 4957 removed outlier: 5.065A pdb=" N ILE B4932 " --> pdb=" O LEU B4928 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN B4933 " --> pdb=" O LEU B4929 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4969 removed outlier: 4.112A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4982 Processing helix chain 'B' and resid 4984 through 4998 Processing helix chain 'B' and resid 5004 through 5016 Processing helix chain 'B' and resid 5027 through 5037 removed outlier: 6.116A pdb=" N ASP B5034 " --> pdb=" O LYS B5030 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN B5035 " --> pdb=" O GLN B5031 " (cutoff:3.500A) Processing helix chain 'C' and resid 3951 through 3969 removed outlier: 3.531A pdb=" N VAL C3957 " --> pdb=" O LYS C3953 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE C3969 " --> pdb=" O LEU C3965 " (cutoff:3.500A) Processing helix chain 'C' and resid 3973 through 3983 removed outlier: 3.650A pdb=" N HIS C3982 " --> pdb=" O GLN C3978 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER C3983 " --> pdb=" O SER C3979 " (cutoff:3.500A) Processing helix chain 'C' and resid 3984 through 4006 removed outlier: 3.500A pdb=" N GLY C3991 " --> pdb=" O ASP C3987 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET C4000 " --> pdb=" O PHE C3996 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS C4002 " --> pdb=" O HIS C3998 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP C4006 " --> pdb=" O LYS C4002 " (cutoff:3.500A) Processing helix chain 'C' and resid 4010 through 4031 removed outlier: 3.626A pdb=" N LYS C4014 " --> pdb=" O ILE C4010 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU C4015 " --> pdb=" O GLU C4011 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL C4025 " --> pdb=" O LYS C4021 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET C4026 " --> pdb=" O ASP C4022 " (cutoff:3.500A) Processing helix chain 'C' and resid 4038 through 4056 removed outlier: 3.572A pdb=" N GLU C4050 " --> pdb=" O ASP C4046 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N SER C4053 " --> pdb=" O VAL C4049 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASN C4054 " --> pdb=" O GLU C4050 " (cutoff:3.500A) Processing helix chain 'C' and resid 4198 through 4206 Processing helix chain 'C' and resid 4207 through 4225 Processing helix chain 'C' and resid 4226 through 4252 removed outlier: 4.608A pdb=" N MET C4231 " --> pdb=" O GLU C4227 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLU C4232 " --> pdb=" O ALA C4228 " (cutoff:3.500A) Processing helix chain 'C' and resid 4541 through 4558 Processing helix chain 'C' and resid 4558 through 4578 Processing helix chain 'C' and resid 4638 through 4665 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: 4.019A pdb=" N ASN C4707 " --> pdb=" O LEU C4704 " (cutoff:3.500A) Processing helix chain 'C' and resid 4719 through 4733 removed outlier: 5.616A pdb=" N ASP C4730 " --> pdb=" O ASP C4726 " (cutoff:3.500A) removed outlier: 5.891A 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 4748 Processing helix chain 'C' and resid 4773 through 4786 Processing helix chain 'C' and resid 4786 through 4805 removed outlier: 3.835A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4806 through 4814 removed outlier: 3.558A pdb=" N HIS C4812 " --> pdb=" O PHE C4809 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU C4813 " --> pdb=" O ALA C4810 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU C4814 " --> pdb=" O ALA C4811 " (cutoff:3.500A) Processing helix chain 'C' and resid 4815 through 4820 Processing helix chain 'C' and resid 4820 through 4832 removed outlier: 3.590A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) Processing helix chain 'C' and resid 4833 through 4859 removed outlier: 3.511A pdb=" N PHE C4858 " --> pdb=" O VAL C4854 " (cutoff:3.500A) Processing helix chain 'C' and resid 4878 through 4890 Processing helix chain 'C' and resid 4909 through 4925 Processing helix chain 'C' and resid 4925 through 4957 removed outlier: 5.065A pdb=" N ILE C4932 " --> pdb=" O LEU C4928 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN C4933 " --> pdb=" O LEU C4929 " (cutoff:3.500A) Processing helix chain 'C' and resid 4964 through 4969 removed outlier: 4.112A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) Processing helix chain 'C' and resid 4973 through 4982 Processing helix chain 'C' and resid 4984 through 4998 Processing helix chain 'C' and resid 5004 through 5016 Processing helix chain 'C' and resid 5027 through 5037 removed outlier: 6.116A pdb=" N ASP C5034 " --> pdb=" O LYS C5030 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN C5035 " --> pdb=" O GLN C5031 " (cutoff:3.500A) Processing helix chain 'D' and resid 3951 through 3969 removed outlier: 3.531A pdb=" N VAL D3957 " --> pdb=" O LYS D3953 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE D3969 " --> pdb=" O LEU D3965 " (cutoff:3.500A) Processing helix chain 'D' and resid 3973 through 3983 removed outlier: 3.650A pdb=" N HIS D3982 " --> pdb=" O GLN D3978 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER D3983 " --> pdb=" O SER D3979 " (cutoff:3.500A) Processing helix chain 'D' and resid 3984 through 4006 removed outlier: 3.500A pdb=" N GLY D3991 " --> pdb=" O ASP D3987 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET D4000 " --> pdb=" O PHE D3996 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS D4002 " --> pdb=" O HIS D3998 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP D4006 " --> pdb=" O LYS D4002 " (cutoff:3.500A) Processing helix chain 'D' and resid 4010 through 4031 removed outlier: 3.626A pdb=" N LYS D4014 " --> pdb=" O ILE D4010 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU D4015 " --> pdb=" O GLU D4011 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL D4025 " --> pdb=" O LYS D4021 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET D4026 " --> pdb=" O ASP D4022 " (cutoff:3.500A) Processing helix chain 'D' and resid 4038 through 4056 removed outlier: 3.572A pdb=" N GLU D4050 " --> pdb=" O ASP D4046 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N SER D4053 " --> pdb=" O VAL D4049 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASN D4054 " --> pdb=" O GLU D4050 " (cutoff:3.500A) Processing helix chain 'D' and resid 4198 through 4206 Processing helix chain 'D' and resid 4207 through 4225 Processing helix chain 'D' and resid 4226 through 4252 removed outlier: 4.608A pdb=" N MET D4231 " --> pdb=" O GLU D4227 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLU D4232 " --> pdb=" O ALA D4228 " (cutoff:3.500A) Processing helix chain 'D' and resid 4541 through 4558 Processing helix chain 'D' and resid 4558 through 4578 Processing helix chain 'D' and resid 4638 through 4665 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: 4.019A pdb=" N ASN D4707 " --> pdb=" O LEU D4704 " (cutoff:3.500A) Processing helix chain 'D' and resid 4719 through 4733 removed outlier: 5.616A pdb=" N ASP D4730 " --> pdb=" O ASP D4726 " (cutoff:3.500A) removed outlier: 5.891A 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 4748 Processing helix chain 'D' and resid 4773 through 4786 Processing helix chain 'D' and resid 4786 through 4805 removed outlier: 3.835A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4806 through 4814 removed outlier: 3.558A pdb=" N HIS D4812 " --> pdb=" O PHE D4809 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU D4813 " --> pdb=" O ALA D4810 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU D4814 " --> pdb=" O ALA D4811 " (cutoff:3.500A) Processing helix chain 'D' and resid 4815 through 4820 Processing helix chain 'D' and resid 4820 through 4832 removed outlier: 3.590A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) Processing helix chain 'D' and resid 4833 through 4859 removed outlier: 3.511A pdb=" N PHE D4858 " --> pdb=" O VAL D4854 " (cutoff:3.500A) Processing helix chain 'D' and resid 4878 through 4890 Processing helix chain 'D' and resid 4909 through 4925 Processing helix chain 'D' and resid 4925 through 4957 removed outlier: 5.065A pdb=" N ILE D4932 " --> pdb=" O LEU D4928 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN D4933 " --> pdb=" O LEU D4929 " (cutoff:3.500A) Processing helix chain 'D' and resid 4964 through 4969 removed outlier: 4.112A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) Processing helix chain 'D' and resid 4973 through 4982 Processing helix chain 'D' and resid 4984 through 4998 Processing helix chain 'D' and resid 5004 through 5016 Processing helix chain 'D' and resid 5027 through 5037 removed outlier: 6.116A pdb=" N ASP D5034 " --> pdb=" O LYS D5030 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN D5035 " --> pdb=" O GLN D5031 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4178 through 4184 removed outlier: 3.521A pdb=" N PHE A4195 " --> pdb=" O GLY A4179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4580 through 4581 removed outlier: 3.575A pdb=" N LYS A4581 " --> pdb=" O PHE A4631 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE A4631 " --> pdb=" O LYS A4581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 4178 through 4184 removed outlier: 3.521A pdb=" N PHE B4195 " --> pdb=" O GLY B4179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4580 through 4581 removed outlier: 3.575A pdb=" N LYS B4581 " --> pdb=" O PHE B4631 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE B4631 " --> pdb=" O LYS B4581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 4178 through 4184 removed outlier: 3.521A pdb=" N PHE C4195 " --> pdb=" O GLY C4179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 4580 through 4581 removed outlier: 3.575A pdb=" N LYS C4581 " --> pdb=" O PHE C4631 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE C4631 " --> pdb=" O LYS C4581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 4178 through 4184 removed outlier: 3.521A pdb=" N PHE D4195 " --> pdb=" O GLY D4179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 4580 through 4581 removed outlier: 3.575A pdb=" N LYS D4581 " --> pdb=" O PHE D4631 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE D4631 " --> pdb=" O LYS D4581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 1345 hydrogen bonds defined for protein. 3963 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.30 Time building geometry restraints manager: 6.33 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: 6496 1.34 - 1.46: 5238 1.46 - 1.58: 9054 1.58 - 1.70: 4 1.70 - 1.81: 276 Bond restraints: 21068 Sorted by residual: bond pdb=" CA SER D4213 " pdb=" CB SER D4213 " ideal model delta sigma weight residual 1.528 1.495 0.034 1.56e-02 4.11e+03 4.69e+00 bond pdb=" N GLU A4212 " pdb=" CA GLU A4212 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.59e+00 bond pdb=" N GLU C4212 " pdb=" CA GLU C4212 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.36e+00 bond pdb=" N GLU D4212 " pdb=" CA GLU D4212 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.34e+00 bond pdb=" N GLU B4212 " pdb=" CA GLU B4212 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.33e+00 ... (remaining 21063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 27872 1.64 - 3.29: 436 3.29 - 4.93: 80 4.93 - 6.58: 32 6.58 - 8.22: 12 Bond angle restraints: 28432 Sorted by residual: angle pdb=" N SER D4213 " pdb=" CA SER D4213 " pdb=" C SER D4213 " ideal model delta sigma weight residual 111.28 107.54 3.74 1.09e+00 8.42e-01 1.18e+01 angle pdb=" N LYS D4211 " pdb=" CA LYS D4211 " pdb=" C LYS D4211 " ideal model delta sigma weight residual 111.28 108.00 3.28 1.09e+00 8.42e-01 9.06e+00 angle pdb=" N GLU A4212 " pdb=" CA GLU A4212 " pdb=" C GLU A4212 " ideal model delta sigma weight residual 111.36 108.09 3.27 1.09e+00 8.42e-01 9.03e+00 angle pdb=" N GLU C4212 " pdb=" CA GLU C4212 " pdb=" C GLU C4212 " ideal model delta sigma weight residual 111.36 108.13 3.23 1.09e+00 8.42e-01 8.76e+00 angle pdb=" N GLU B4212 " pdb=" CA GLU B4212 " pdb=" C GLU B4212 " ideal model delta sigma weight residual 111.36 108.15 3.21 1.09e+00 8.42e-01 8.67e+00 ... (remaining 28427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 11220 16.96 - 33.91: 975 33.91 - 50.87: 132 50.87 - 67.83: 21 67.83 - 84.79: 24 Dihedral angle restraints: 12372 sinusoidal: 5048 harmonic: 7324 Sorted by residual: dihedral pdb=" CA LEU A4928 " pdb=" C LEU A4928 " pdb=" N LEU A4929 " pdb=" CA LEU A4929 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA LEU B4928 " pdb=" C LEU B4928 " pdb=" N LEU B4929 " pdb=" CA LEU B4929 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA LEU C4928 " pdb=" C LEU C4928 " pdb=" N LEU C4929 " pdb=" CA LEU C4929 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 12369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2171 0.037 - 0.075: 753 0.075 - 0.112: 125 0.112 - 0.150: 8 0.150 - 0.187: 11 Chirality restraints: 3068 Sorted by residual: chirality pdb=" CA GLU A4212 " pdb=" N GLU A4212 " pdb=" C GLU A4212 " pdb=" CB GLU A4212 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CA GLU C4212 " pdb=" N GLU C4212 " pdb=" C GLU C4212 " pdb=" CB GLU C4212 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CA GLU B4212 " pdb=" N GLU B4212 " pdb=" C GLU B4212 " pdb=" CB GLU B4212 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.41e-01 ... (remaining 3065 not shown) Planarity restraints: 3600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C3971 " -0.085 5.00e-02 4.00e+02 1.28e-01 2.63e+01 pdb=" N PRO C3972 " 0.222 5.00e-02 4.00e+02 pdb=" CA PRO C3972 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO C3972 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D3971 " -0.085 5.00e-02 4.00e+02 1.28e-01 2.63e+01 pdb=" N PRO D3972 " 0.222 5.00e-02 4.00e+02 pdb=" CA PRO D3972 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO D3972 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B3971 " 0.085 5.00e-02 4.00e+02 1.28e-01 2.63e+01 pdb=" N PRO B3972 " -0.222 5.00e-02 4.00e+02 pdb=" CA PRO B3972 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO B3972 " 0.067 5.00e-02 4.00e+02 ... (remaining 3597 not shown) Histogram of nonbonded interaction distances: 0.57 - 1.44: 72 1.44 - 2.30: 168 2.30 - 3.17: 18079 3.17 - 4.03: 52305 4.03 - 4.90: 94381 Warning: very small nonbonded interaction distances. Nonbonded interactions: 165005 Sorted by model distance: nonbonded pdb=" CE2 TYR B4580 " pdb=" CZ PHE C4856 " model vdw 0.570 3.640 nonbonded pdb=" CE2 TYR C4580 " pdb=" CZ PHE D4856 " model vdw 0.570 3.640 nonbonded pdb=" CE2 TYR A4580 " pdb=" CZ PHE B4856 " model vdw 0.570 3.640 nonbonded pdb=" CZ PHE A4856 " pdb=" CE2 TYR D4580 " model vdw 0.570 3.640 nonbonded pdb=" CG PHE A4921 " pdb=" CZ ARG D4892 " model vdw 0.595 3.490 ... (remaining 165000 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 49.560 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 21088 Z= 0.129 Angle : 0.571 8.220 28448 Z= 0.305 Chirality : 0.037 0.187 3068 Planarity : 0.005 0.128 3600 Dihedral : 12.881 84.786 7640 Min Nonbonded Distance : 0.570 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.92 % Favored : 96.92 % Rotamer: Outliers : 0.27 % Allowed : 0.00 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.17), residues: 2468 helix: 2.09 (0.13), residues: 1668 sheet: 0.43 (0.73), residues: 64 loop : -0.49 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B4541 HIS 0.002 0.000 HIS A4650 PHE 0.013 0.001 PHE B4922 TYR 0.014 0.001 TYR C4715 ARG 0.004 0.000 ARG B4913 Details of bonding type rmsd hydrogen bonds : bond 0.14004 ( 1345) hydrogen bonds : angle 5.14535 ( 3963) metal coordination : bond 0.00317 ( 16) metal coordination : angle 3.19718 ( 8) SS BOND : bond 0.00254 ( 4) SS BOND : angle 0.70894 ( 8) covalent geometry : bond 0.00288 (21068) covalent geometry : angle 0.56816 (28432) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 504 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3965 LEU cc_start: 0.8779 (mp) cc_final: 0.8536 (mp) REVERT: A 3968 TYR cc_start: 0.8620 (m-80) cc_final: 0.8303 (m-80) REVERT: A 4000 MET cc_start: 0.7054 (ptt) cc_final: 0.6648 (ptm) REVERT: A 4026 MET cc_start: 0.9095 (tmm) cc_final: 0.8635 (tmm) REVERT: A 4638 TYR cc_start: 0.5376 (p90) cc_final: 0.4255 (p90) REVERT: A 4717 ASP cc_start: 0.7878 (t70) cc_final: 0.7560 (t0) REVERT: A 4798 MET cc_start: 0.7531 (mmt) cc_final: 0.7244 (mmt) REVERT: B 3965 LEU cc_start: 0.8778 (mp) cc_final: 0.8534 (mp) REVERT: B 3968 TYR cc_start: 0.8619 (m-80) cc_final: 0.8304 (m-80) REVERT: B 4000 MET cc_start: 0.7056 (ptt) cc_final: 0.6651 (ptm) REVERT: B 4026 MET cc_start: 0.9096 (tmm) cc_final: 0.8636 (tmm) REVERT: B 4638 TYR cc_start: 0.5373 (p90) cc_final: 0.4251 (p90) REVERT: B 4717 ASP cc_start: 0.7876 (t70) cc_final: 0.7559 (t0) REVERT: B 4798 MET cc_start: 0.7532 (mmt) cc_final: 0.7242 (mmt) REVERT: C 3965 LEU cc_start: 0.8775 (mp) cc_final: 0.8531 (mp) REVERT: C 3968 TYR cc_start: 0.8619 (m-80) cc_final: 0.8304 (m-80) REVERT: C 4000 MET cc_start: 0.7057 (ptt) cc_final: 0.6649 (ptm) REVERT: C 4026 MET cc_start: 0.9097 (tmm) cc_final: 0.8637 (tmm) REVERT: C 4638 TYR cc_start: 0.5373 (p90) cc_final: 0.4253 (p90) REVERT: C 4717 ASP cc_start: 0.7876 (t70) cc_final: 0.7558 (t0) REVERT: C 4798 MET cc_start: 0.7530 (mmt) cc_final: 0.7245 (mmt) REVERT: D 3965 LEU cc_start: 0.8778 (mp) cc_final: 0.8534 (mp) REVERT: D 3968 TYR cc_start: 0.8620 (m-80) cc_final: 0.8304 (m-80) REVERT: D 4000 MET cc_start: 0.7057 (ptt) cc_final: 0.6652 (ptm) REVERT: D 4026 MET cc_start: 0.9096 (tmm) cc_final: 0.8635 (tmm) REVERT: D 4638 TYR cc_start: 0.5376 (p90) cc_final: 0.4255 (p90) REVERT: D 4717 ASP cc_start: 0.7878 (t70) cc_final: 0.7561 (t0) REVERT: D 4798 MET cc_start: 0.7534 (mmt) cc_final: 0.7245 (mmt) outliers start: 6 outliers final: 0 residues processed: 510 average time/residue: 0.2995 time to fit residues: 236.5012 Evaluate side-chains 384 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 194 optimal weight: 0.0770 chunk 75 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 144 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4037 ASN A4223 ASN ** A4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4037 ASN B4223 ASN ** B4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4037 ASN C4223 ASN ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4037 ASN D4223 ASN ** D4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.146005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122283 restraints weight = 35040.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.125402 restraints weight = 19227.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.127384 restraints weight = 13226.176| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 21088 Z= 0.187 Angle : 0.611 11.480 28448 Z= 0.316 Chirality : 0.041 0.255 3068 Planarity : 0.006 0.129 3600 Dihedral : 4.220 19.535 2700 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.43 % Favored : 97.41 % Rotamer: Outliers : 0.81 % Allowed : 9.70 % Favored : 89.49 % 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: 1.81 (0.17), residues: 2468 helix: 1.95 (0.12), residues: 1688 sheet: 0.35 (0.73), residues: 64 loop : -0.53 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B4794 HIS 0.004 0.001 HIS D4650 PHE 0.018 0.001 PHE B4922 TYR 0.034 0.002 TYR B4630 ARG 0.007 0.001 ARG C4892 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 1345) hydrogen bonds : angle 4.53933 ( 3963) metal coordination : bond 0.01178 ( 16) metal coordination : angle 3.07213 ( 8) SS BOND : bond 0.00082 ( 4) SS BOND : angle 0.48809 ( 8) covalent geometry : bond 0.00449 (21068) covalent geometry : angle 0.60924 (28432) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 420 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3968 TYR cc_start: 0.8517 (m-80) cc_final: 0.8263 (m-80) REVERT: A 3992 PHE cc_start: 0.8635 (m-80) cc_final: 0.8005 (m-80) REVERT: A 4026 MET cc_start: 0.9291 (tmm) cc_final: 0.9006 (tmm) REVERT: A 4638 TYR cc_start: 0.5155 (p90) cc_final: 0.4363 (p90) REVERT: A 4798 MET cc_start: 0.8148 (mmt) cc_final: 0.7856 (mmt) REVERT: B 3968 TYR cc_start: 0.8496 (m-80) cc_final: 0.8241 (m-80) REVERT: B 3992 PHE cc_start: 0.8637 (m-80) cc_final: 0.8008 (m-80) REVERT: B 4026 MET cc_start: 0.9288 (tmm) cc_final: 0.9004 (tmm) REVERT: B 4638 TYR cc_start: 0.5153 (p90) cc_final: 0.4360 (p90) REVERT: B 4798 MET cc_start: 0.8147 (mmt) cc_final: 0.7850 (mmt) REVERT: C 3968 TYR cc_start: 0.8497 (m-80) cc_final: 0.8240 (m-80) REVERT: C 3992 PHE cc_start: 0.8637 (m-80) cc_final: 0.8004 (m-80) REVERT: C 4026 MET cc_start: 0.9291 (tmm) cc_final: 0.9010 (tmm) REVERT: C 4638 TYR cc_start: 0.5156 (p90) cc_final: 0.4368 (p90) REVERT: C 4798 MET cc_start: 0.8149 (mmt) cc_final: 0.7859 (mmt) REVERT: D 3968 TYR cc_start: 0.8496 (m-80) cc_final: 0.8239 (m-80) REVERT: D 3992 PHE cc_start: 0.8639 (m-80) cc_final: 0.8006 (m-80) REVERT: D 4026 MET cc_start: 0.9287 (tmm) cc_final: 0.9001 (tmm) REVERT: D 4638 TYR cc_start: 0.5157 (p90) cc_final: 0.4365 (p90) REVERT: D 4798 MET cc_start: 0.8145 (mmt) cc_final: 0.7855 (mmt) outliers start: 18 outliers final: 4 residues processed: 424 average time/residue: 0.3038 time to fit residues: 196.7141 Evaluate side-chains 398 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 394 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4993 MET Chi-restraints excluded: chain B residue 4993 MET Chi-restraints excluded: chain C residue 4993 MET Chi-restraints excluded: chain D residue 4993 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 87 optimal weight: 7.9990 chunk 211 optimal weight: 7.9990 chunk 235 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3998 HIS A4223 ASN ** A4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4933 GLN B3998 HIS B4223 ASN ** B4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3998 HIS C4223 ASN ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4933 GLN D3998 HIS D4223 ASN ** D4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.146231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.121907 restraints weight = 34752.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125005 restraints weight = 19174.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.127009 restraints weight = 13210.716| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 21088 Z= 0.138 Angle : 0.544 11.071 28448 Z= 0.277 Chirality : 0.038 0.150 3068 Planarity : 0.006 0.130 3600 Dihedral : 4.087 21.656 2700 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.51 % Favored : 97.33 % Rotamer: Outliers : 1.39 % Allowed : 13.24 % Favored : 85.38 % 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: 1.90 (0.17), residues: 2468 helix: 2.04 (0.12), residues: 1692 sheet: 0.21 (0.72), residues: 64 loop : -0.55 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C4701 HIS 0.003 0.001 HIS C4650 PHE 0.013 0.001 PHE B4921 TYR 0.021 0.002 TYR A5032 ARG 0.010 0.001 ARG D4892 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 1345) hydrogen bonds : angle 4.42266 ( 3963) metal coordination : bond 0.00725 ( 16) metal coordination : angle 2.46550 ( 8) SS BOND : bond 0.00072 ( 4) SS BOND : angle 0.76035 ( 8) covalent geometry : bond 0.00333 (21068) covalent geometry : angle 0.54260 (28432) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 408 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3968 TYR cc_start: 0.8510 (m-80) cc_final: 0.8278 (m-80) REVERT: A 3996 PHE cc_start: 0.7676 (m-80) cc_final: 0.7325 (m-80) REVERT: A 4000 MET cc_start: 0.6122 (ptm) cc_final: 0.5692 (ptm) REVERT: A 4021 LYS cc_start: 0.8585 (tmtt) cc_final: 0.7930 (tptt) REVERT: A 4207 MET cc_start: 0.8003 (mmt) cc_final: 0.7682 (mmt) REVERT: A 4638 TYR cc_start: 0.5066 (p90) cc_final: 0.4444 (p90) REVERT: A 4887 MET cc_start: 0.6325 (mmm) cc_final: 0.5711 (mtp) REVERT: B 3968 TYR cc_start: 0.8544 (m-80) cc_final: 0.8310 (m-80) REVERT: B 3996 PHE cc_start: 0.7673 (m-80) cc_final: 0.7321 (m-80) REVERT: B 4000 MET cc_start: 0.6120 (ptm) cc_final: 0.5694 (ptm) REVERT: B 4021 LYS cc_start: 0.8596 (tmtt) cc_final: 0.7941 (tptt) REVERT: B 4207 MET cc_start: 0.8013 (mmt) cc_final: 0.7684 (mmt) REVERT: B 4638 TYR cc_start: 0.5067 (p90) cc_final: 0.4448 (p90) REVERT: B 4887 MET cc_start: 0.6321 (mmm) cc_final: 0.5697 (mtp) REVERT: C 3968 TYR cc_start: 0.8546 (m-80) cc_final: 0.8311 (m-80) REVERT: C 3996 PHE cc_start: 0.7678 (m-80) cc_final: 0.7327 (m-80) REVERT: C 4000 MET cc_start: 0.6118 (ptm) cc_final: 0.5692 (ptm) REVERT: C 4021 LYS cc_start: 0.8592 (tmtt) cc_final: 0.7936 (tptt) REVERT: C 4207 MET cc_start: 0.8007 (mmt) cc_final: 0.7687 (mmt) REVERT: C 4638 TYR cc_start: 0.5076 (p90) cc_final: 0.4459 (p90) REVERT: C 4887 MET cc_start: 0.6312 (mmm) cc_final: 0.5702 (mtp) REVERT: D 3968 TYR cc_start: 0.8544 (m-80) cc_final: 0.8309 (m-80) REVERT: D 3996 PHE cc_start: 0.7678 (m-80) cc_final: 0.7323 (m-80) REVERT: D 4000 MET cc_start: 0.6121 (ptm) cc_final: 0.5691 (ptm) REVERT: D 4021 LYS cc_start: 0.8594 (tmtt) cc_final: 0.7939 (tptt) REVERT: D 4638 TYR cc_start: 0.5067 (p90) cc_final: 0.4449 (p90) REVERT: D 4887 MET cc_start: 0.6325 (mmm) cc_final: 0.5697 (mtp) outliers start: 31 outliers final: 14 residues processed: 420 average time/residue: 0.3165 time to fit residues: 201.7136 Evaluate side-chains 382 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 368 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3999 MET Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4993 MET Chi-restraints excluded: chain B residue 3999 MET Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4929 LEU Chi-restraints excluded: chain B residue 4993 MET Chi-restraints excluded: chain C residue 3999 MET Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4993 MET Chi-restraints excluded: chain D residue 3999 MET Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4929 LEU Chi-restraints excluded: chain D residue 4993 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 227 optimal weight: 0.9980 chunk 204 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 214 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4223 ASN ** A4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4223 ASN ** B4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4223 ASN ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4223 ASN ** D4806 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 = 0.3826 r_free = 0.3826 target = 0.146080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.121388 restraints weight = 35082.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.124498 restraints weight = 19293.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.126465 restraints weight = 13309.123| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 21088 Z= 0.135 Angle : 0.527 9.099 28448 Z= 0.265 Chirality : 0.037 0.144 3068 Planarity : 0.006 0.129 3600 Dihedral : 4.030 21.898 2700 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.76 % Favored : 97.08 % Rotamer: Outliers : 1.79 % Allowed : 15.03 % Favored : 83.18 % 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: 1.96 (0.17), residues: 2468 helix: 2.09 (0.12), residues: 1692 sheet: 0.49 (0.73), residues: 64 loop : -0.53 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A4701 HIS 0.003 0.001 HIS B4650 PHE 0.014 0.001 PHE D4921 TYR 0.019 0.001 TYR A5032 ARG 0.004 0.000 ARG A4892 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 1345) hydrogen bonds : angle 4.36469 ( 3963) metal coordination : bond 0.00803 ( 16) metal coordination : angle 2.56371 ( 8) SS BOND : bond 0.00076 ( 4) SS BOND : angle 0.80942 ( 8) covalent geometry : bond 0.00323 (21068) covalent geometry : angle 0.52475 (28432) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 416 time to evaluate : 2.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3996 PHE cc_start: 0.7560 (m-80) cc_final: 0.7279 (m-80) REVERT: A 4000 MET cc_start: 0.5803 (ptm) cc_final: 0.5290 (ptm) REVERT: A 4021 LYS cc_start: 0.8439 (tmtt) cc_final: 0.7813 (tptt) REVERT: A 4184 MET cc_start: 0.8504 (tpp) cc_final: 0.8266 (mmt) REVERT: A 4206 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: A 4207 MET cc_start: 0.7997 (mmt) cc_final: 0.7686 (mmt) REVERT: A 4638 TYR cc_start: 0.4571 (p90) cc_final: 0.4171 (p90) REVERT: A 4668 LEU cc_start: 0.8442 (tp) cc_final: 0.8043 (tp) REVERT: B 3996 PHE cc_start: 0.7557 (m-80) cc_final: 0.7277 (m-80) REVERT: B 4000 MET cc_start: 0.5802 (ptm) cc_final: 0.5283 (ptm) REVERT: B 4021 LYS cc_start: 0.8440 (tmtt) cc_final: 0.7811 (tptt) REVERT: B 4184 MET cc_start: 0.8508 (tpp) cc_final: 0.8272 (mmt) REVERT: B 4206 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: B 4207 MET cc_start: 0.8001 (mmt) cc_final: 0.7693 (mmt) REVERT: B 4638 TYR cc_start: 0.4574 (p90) cc_final: 0.4177 (p90) REVERT: B 4668 LEU cc_start: 0.8435 (tp) cc_final: 0.8035 (tp) REVERT: B 4933 GLN cc_start: 0.6959 (mt0) cc_final: 0.6369 (mt0) REVERT: C 3996 PHE cc_start: 0.7555 (m-80) cc_final: 0.7276 (m-80) REVERT: C 4000 MET cc_start: 0.5794 (ptm) cc_final: 0.5289 (ptm) REVERT: C 4021 LYS cc_start: 0.8440 (tmtt) cc_final: 0.7810 (tptt) REVERT: C 4184 MET cc_start: 0.8509 (tpp) cc_final: 0.8272 (mmt) REVERT: C 4206 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: C 4207 MET cc_start: 0.7995 (mmt) cc_final: 0.7687 (mmt) REVERT: C 4638 TYR cc_start: 0.4578 (p90) cc_final: 0.4182 (p90) REVERT: C 4668 LEU cc_start: 0.8440 (tp) cc_final: 0.8039 (tp) REVERT: D 3996 PHE cc_start: 0.7568 (m-80) cc_final: 0.7280 (m-80) REVERT: D 4000 MET cc_start: 0.5806 (ptm) cc_final: 0.5287 (ptm) REVERT: D 4021 LYS cc_start: 0.8445 (tmtt) cc_final: 0.7814 (tptt) REVERT: D 4184 MET cc_start: 0.8508 (tpp) cc_final: 0.8273 (mmt) REVERT: D 4206 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: D 4638 TYR cc_start: 0.4574 (p90) cc_final: 0.4179 (p90) REVERT: D 4668 LEU cc_start: 0.8425 (tp) cc_final: 0.8034 (tp) REVERT: D 4933 GLN cc_start: 0.6950 (mt0) cc_final: 0.6370 (mt0) outliers start: 40 outliers final: 16 residues processed: 437 average time/residue: 0.3113 time to fit residues: 206.3822 Evaluate side-chains 376 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 356 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4206 GLU Chi-restraints excluded: chain A residue 4796 MET Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4929 LEU Chi-restraints excluded: chain A residue 4993 MET Chi-restraints excluded: chain B residue 4206 GLU Chi-restraints excluded: chain B residue 4796 MET Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4929 LEU Chi-restraints excluded: chain B residue 4993 MET Chi-restraints excluded: chain C residue 4206 GLU Chi-restraints excluded: chain C residue 4796 MET Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4929 LEU Chi-restraints excluded: chain C residue 4993 MET Chi-restraints excluded: chain D residue 4206 GLU Chi-restraints excluded: chain D residue 4796 MET Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4929 LEU Chi-restraints excluded: chain D residue 4993 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 61 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 163 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 158 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4223 ASN ** A4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4223 ASN B4700 GLN ** B4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4223 ASN ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4223 ASN D4700 GLN ** D4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.145757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.120914 restraints weight = 35309.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124006 restraints weight = 19528.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.126007 restraints weight = 13555.107| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 21088 Z= 0.130 Angle : 0.521 8.744 28448 Z= 0.264 Chirality : 0.038 0.236 3068 Planarity : 0.005 0.127 3600 Dihedral : 4.002 21.722 2700 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.47 % Favored : 97.37 % Rotamer: Outliers : 2.06 % Allowed : 16.06 % Favored : 81.89 % 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: 2.01 (0.17), residues: 2468 helix: 2.16 (0.12), residues: 1684 sheet: 0.36 (0.70), residues: 64 loop : -0.59 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C4701 HIS 0.003 0.001 HIS C4650 PHE 0.016 0.001 PHE B4921 TYR 0.019 0.002 TYR D3968 ARG 0.006 0.001 ARG D4892 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 1345) hydrogen bonds : angle 4.35858 ( 3963) metal coordination : bond 0.00835 ( 16) metal coordination : angle 2.22936 ( 8) SS BOND : bond 0.00101 ( 4) SS BOND : angle 0.84200 ( 8) covalent geometry : bond 0.00311 (21068) covalent geometry : angle 0.51974 (28432) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 386 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3996 PHE cc_start: 0.7642 (m-80) cc_final: 0.7417 (m-80) REVERT: A 4021 LYS cc_start: 0.8529 (tmtt) cc_final: 0.7903 (tptt) REVERT: A 4184 MET cc_start: 0.8519 (tpp) cc_final: 0.8263 (mmt) REVERT: A 4206 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: A 4207 MET cc_start: 0.7999 (mmt) cc_final: 0.7688 (mmt) REVERT: A 4638 TYR cc_start: 0.4820 (p90) cc_final: 0.4423 (p90) REVERT: A 4887 MET cc_start: 0.6399 (mmm) cc_final: 0.5607 (mmp) REVERT: B 3968 TYR cc_start: 0.8453 (m-80) cc_final: 0.8253 (m-80) REVERT: B 3996 PHE cc_start: 0.7624 (m-80) cc_final: 0.7414 (m-80) REVERT: B 4021 LYS cc_start: 0.8530 (tmtt) cc_final: 0.7851 (tptt) REVERT: B 4184 MET cc_start: 0.8519 (tpp) cc_final: 0.8266 (mmt) REVERT: B 4206 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: B 4207 MET cc_start: 0.8006 (mmt) cc_final: 0.7690 (mmt) REVERT: B 4638 TYR cc_start: 0.4822 (p90) cc_final: 0.4427 (p90) REVERT: B 4887 MET cc_start: 0.6398 (mmm) cc_final: 0.5599 (mmp) REVERT: B 4933 GLN cc_start: 0.7083 (mt0) cc_final: 0.6532 (mt0) REVERT: C 3968 TYR cc_start: 0.8452 (m-80) cc_final: 0.8252 (m-80) REVERT: C 3996 PHE cc_start: 0.7629 (m-80) cc_final: 0.7417 (m-80) REVERT: C 4021 LYS cc_start: 0.8530 (tmtt) cc_final: 0.7850 (tptt) REVERT: C 4184 MET cc_start: 0.8518 (tpp) cc_final: 0.8265 (mmt) REVERT: C 4206 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: C 4207 MET cc_start: 0.7998 (mmt) cc_final: 0.7689 (mmt) REVERT: C 4638 TYR cc_start: 0.4824 (p90) cc_final: 0.4432 (p90) REVERT: C 4887 MET cc_start: 0.6394 (mmm) cc_final: 0.5594 (mmp) REVERT: D 3996 PHE cc_start: 0.7635 (m-80) cc_final: 0.7418 (m-80) REVERT: D 4021 LYS cc_start: 0.8534 (tmtt) cc_final: 0.7853 (tptt) REVERT: D 4184 MET cc_start: 0.8515 (tpp) cc_final: 0.8264 (mmt) REVERT: D 4206 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: D 4638 TYR cc_start: 0.4830 (p90) cc_final: 0.4437 (p90) REVERT: D 4887 MET cc_start: 0.6392 (mmm) cc_final: 0.5606 (mmp) REVERT: D 4933 GLN cc_start: 0.7068 (mt0) cc_final: 0.6530 (mt0) outliers start: 46 outliers final: 22 residues processed: 416 average time/residue: 0.3124 time to fit residues: 199.7972 Evaluate side-chains 395 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 369 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4206 GLU Chi-restraints excluded: chain A residue 4796 MET Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4929 LEU Chi-restraints excluded: chain A residue 4950 VAL Chi-restraints excluded: chain A residue 4993 MET Chi-restraints excluded: chain B residue 4046 ASP Chi-restraints excluded: chain B residue 4206 GLU Chi-restraints excluded: chain B residue 4796 MET Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4929 LEU Chi-restraints excluded: chain B residue 4950 VAL Chi-restraints excluded: chain B residue 4993 MET Chi-restraints excluded: chain C residue 4206 GLU Chi-restraints excluded: chain C residue 4796 MET Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4929 LEU Chi-restraints excluded: chain C residue 4950 VAL Chi-restraints excluded: chain C residue 4993 MET Chi-restraints excluded: chain D residue 4046 ASP Chi-restraints excluded: chain D residue 4206 GLU Chi-restraints excluded: chain D residue 4796 MET Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4929 LEU Chi-restraints excluded: chain D residue 4950 VAL Chi-restraints excluded: chain D residue 4993 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 10 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4223 ASN ** A4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4812 HIS B4223 ASN ** B4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4812 HIS C4223 ASN ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4812 HIS D4223 ASN ** D4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4812 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.140697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.115181 restraints weight = 34928.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.118140 restraints weight = 19918.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.120042 restraints weight = 14046.802| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 21088 Z= 0.263 Angle : 0.660 10.563 28448 Z= 0.335 Chirality : 0.042 0.188 3068 Planarity : 0.006 0.133 3600 Dihedral : 4.443 23.643 2700 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.48 % Favored : 96.35 % Rotamer: Outliers : 1.70 % Allowed : 18.65 % Favored : 79.65 % 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: 1.43 (0.17), residues: 2468 helix: 1.72 (0.12), residues: 1672 sheet: 0.01 (0.69), residues: 64 loop : -0.74 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B4794 HIS 0.006 0.001 HIS A4812 PHE 0.025 0.002 PHE D4921 TYR 0.020 0.002 TYR C5032 ARG 0.003 0.001 ARG A4892 Details of bonding type rmsd hydrogen bonds : bond 0.04574 ( 1345) hydrogen bonds : angle 4.81827 ( 3963) metal coordination : bond 0.02152 ( 16) metal coordination : angle 4.98708 ( 8) SS BOND : bond 0.00065 ( 4) SS BOND : angle 1.11270 ( 8) covalent geometry : bond 0.00628 (21068) covalent geometry : angle 0.65443 (28432) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 361 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3996 PHE cc_start: 0.7754 (m-80) cc_final: 0.7334 (m-80) REVERT: A 4021 LYS cc_start: 0.8541 (tmtt) cc_final: 0.7820 (tptt) REVERT: A 4206 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: A 4207 MET cc_start: 0.7992 (mmt) cc_final: 0.7762 (mmt) REVERT: A 4976 GLU cc_start: 0.7524 (mp0) cc_final: 0.7288 (mt-10) REVERT: B 3996 PHE cc_start: 0.7533 (m-80) cc_final: 0.7161 (m-80) REVERT: B 4021 LYS cc_start: 0.8586 (tmtt) cc_final: 0.7860 (tptt) REVERT: B 4206 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: B 4207 MET cc_start: 0.7995 (mmt) cc_final: 0.7761 (mmt) REVERT: B 4976 GLU cc_start: 0.7523 (mp0) cc_final: 0.7286 (mt-10) REVERT: C 3996 PHE cc_start: 0.7755 (m-80) cc_final: 0.7341 (m-80) REVERT: C 4021 LYS cc_start: 0.8587 (tmtt) cc_final: 0.7861 (tptt) REVERT: C 4206 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: C 4207 MET cc_start: 0.7993 (mmt) cc_final: 0.7763 (mmt) REVERT: C 4976 GLU cc_start: 0.7525 (mp0) cc_final: 0.7287 (mt-10) REVERT: D 3968 TYR cc_start: 0.8571 (m-80) cc_final: 0.8280 (m-80) REVERT: D 3996 PHE cc_start: 0.7538 (m-80) cc_final: 0.7159 (m-80) REVERT: D 4021 LYS cc_start: 0.8589 (tmtt) cc_final: 0.7859 (tptt) REVERT: D 4206 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: D 4976 GLU cc_start: 0.7527 (mp0) cc_final: 0.7283 (mt-10) outliers start: 38 outliers final: 26 residues processed: 383 average time/residue: 0.3206 time to fit residues: 185.4968 Evaluate side-chains 379 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 349 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4046 ASP Chi-restraints excluded: chain A residue 4206 GLU Chi-restraints excluded: chain A residue 4555 LEU Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4892 ARG Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4950 VAL Chi-restraints excluded: chain A residue 4993 MET Chi-restraints excluded: chain B residue 4206 GLU Chi-restraints excluded: chain B residue 4555 LEU Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4892 ARG Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4950 VAL Chi-restraints excluded: chain B residue 4993 MET Chi-restraints excluded: chain C residue 4046 ASP Chi-restraints excluded: chain C residue 4206 GLU Chi-restraints excluded: chain C residue 4555 LEU Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4892 ARG Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4950 VAL Chi-restraints excluded: chain C residue 4993 MET Chi-restraints excluded: chain D residue 4206 GLU Chi-restraints excluded: chain D residue 4555 LEU Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4892 ARG Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4950 VAL Chi-restraints excluded: chain D residue 4993 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 155 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4223 ASN ** A4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4223 ASN ** B4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4223 ASN ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4223 ASN ** D4806 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 = 0.3811 r_free = 0.3811 target = 0.144747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.119664 restraints weight = 34515.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.122716 restraints weight = 19154.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124648 restraints weight = 13323.338| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21088 Z= 0.117 Angle : 0.532 8.838 28448 Z= 0.268 Chirality : 0.038 0.184 3068 Planarity : 0.005 0.127 3600 Dihedral : 4.154 22.749 2700 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.89 % Rotamer: Outliers : 2.28 % Allowed : 19.19 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.88 (0.17), residues: 2468 helix: 2.06 (0.12), residues: 1688 sheet: 0.09 (0.69), residues: 64 loop : -0.62 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A4794 HIS 0.002 0.001 HIS C4978 PHE 0.012 0.001 PHE D4921 TYR 0.025 0.001 TYR A3968 ARG 0.002 0.000 ARG A4736 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 1345) hydrogen bonds : angle 4.42636 ( 3963) metal coordination : bond 0.00426 ( 16) metal coordination : angle 2.25551 ( 8) SS BOND : bond 0.00176 ( 4) SS BOND : angle 0.91776 ( 8) covalent geometry : bond 0.00278 (21068) covalent geometry : angle 0.53021 (28432) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 395 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3996 PHE cc_start: 0.7655 (m-80) cc_final: 0.7365 (m-80) REVERT: A 3999 MET cc_start: 0.8052 (ttm) cc_final: 0.7783 (ttp) REVERT: A 4021 LYS cc_start: 0.8539 (tmtt) cc_final: 0.7872 (tptt) REVERT: A 4207 MET cc_start: 0.7939 (mmt) cc_final: 0.7703 (mmt) REVERT: B 3996 PHE cc_start: 0.7643 (m-80) cc_final: 0.7366 (m-80) REVERT: B 3999 MET cc_start: 0.8073 (ttm) cc_final: 0.7806 (ttp) REVERT: B 4021 LYS cc_start: 0.8543 (tmtt) cc_final: 0.7871 (tptt) REVERT: B 4207 MET cc_start: 0.7946 (mmt) cc_final: 0.7705 (mmt) REVERT: B 4933 GLN cc_start: 0.7138 (mt0) cc_final: 0.6604 (mt0) REVERT: C 3996 PHE cc_start: 0.7645 (m-80) cc_final: 0.7365 (m-80) REVERT: C 3999 MET cc_start: 0.8063 (ttm) cc_final: 0.7794 (ttp) REVERT: C 4021 LYS cc_start: 0.8543 (tmtt) cc_final: 0.7867 (tptt) REVERT: C 4207 MET cc_start: 0.7938 (mmt) cc_final: 0.7707 (mmt) REVERT: D 3996 PHE cc_start: 0.7652 (m-80) cc_final: 0.7370 (m-80) REVERT: D 3999 MET cc_start: 0.8074 (ttm) cc_final: 0.7806 (ttp) REVERT: D 4021 LYS cc_start: 0.8543 (tmtt) cc_final: 0.7867 (tptt) REVERT: D 4933 GLN cc_start: 0.7130 (mt0) cc_final: 0.6599 (mt0) outliers start: 51 outliers final: 27 residues processed: 422 average time/residue: 0.3233 time to fit residues: 206.3843 Evaluate side-chains 399 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 372 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4046 ASP Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4796 MET Chi-restraints excluded: chain A residue 4826 ILE Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4950 VAL Chi-restraints excluded: chain A residue 4993 MET Chi-restraints excluded: chain B residue 4046 ASP Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4796 MET Chi-restraints excluded: chain B residue 4826 ILE Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4950 VAL Chi-restraints excluded: chain B residue 4993 MET Chi-restraints excluded: chain C residue 4046 ASP Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4796 MET Chi-restraints excluded: chain C residue 4826 ILE Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4950 VAL Chi-restraints excluded: chain C residue 4993 MET Chi-restraints excluded: chain D residue 4046 ASP Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4796 MET Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4950 VAL Chi-restraints excluded: chain D residue 4993 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 112 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4223 ASN ** A4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4223 ASN ** B4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4223 ASN ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4223 ASN ** D4806 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 = 0.3807 r_free = 0.3807 target = 0.144595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.119722 restraints weight = 34929.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.122778 restraints weight = 19407.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.124726 restraints weight = 13482.896| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 21088 Z= 0.129 Angle : 0.575 9.101 28448 Z= 0.287 Chirality : 0.039 0.285 3068 Planarity : 0.005 0.125 3600 Dihedral : 4.099 20.915 2700 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.55 % Favored : 97.29 % Rotamer: Outliers : 2.28 % Allowed : 18.47 % Favored : 79.25 % 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: 1.87 (0.17), residues: 2468 helix: 2.08 (0.12), residues: 1680 sheet: 0.05 (0.68), residues: 64 loop : -0.66 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D4205 HIS 0.003 0.001 HIS C4650 PHE 0.016 0.001 PHE C4921 TYR 0.027 0.001 TYR A3968 ARG 0.003 0.000 ARG A4736 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 1345) hydrogen bonds : angle 4.39917 ( 3963) metal coordination : bond 0.00724 ( 16) metal coordination : angle 2.92219 ( 8) SS BOND : bond 0.00199 ( 4) SS BOND : angle 0.85519 ( 8) covalent geometry : bond 0.00313 (21068) covalent geometry : angle 0.57263 (28432) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 376 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3996 PHE cc_start: 0.7608 (m-80) cc_final: 0.7338 (m-80) REVERT: A 3999 MET cc_start: 0.8045 (ttm) cc_final: 0.7788 (ttp) REVERT: A 4021 LYS cc_start: 0.8559 (tmtt) cc_final: 0.7831 (tptt) REVERT: A 4184 MET cc_start: 0.8480 (tpp) cc_final: 0.8208 (mmt) REVERT: A 4207 MET cc_start: 0.7943 (mmt) cc_final: 0.7711 (mmt) REVERT: B 3996 PHE cc_start: 0.7605 (m-80) cc_final: 0.7339 (m-80) REVERT: B 3999 MET cc_start: 0.8071 (ttm) cc_final: 0.7805 (ttp) REVERT: B 4021 LYS cc_start: 0.8568 (tmtt) cc_final: 0.7839 (tptt) REVERT: B 4184 MET cc_start: 0.8484 (tpp) cc_final: 0.8209 (mmt) REVERT: B 4207 MET cc_start: 0.7952 (mmt) cc_final: 0.7711 (mmt) REVERT: B 4933 GLN cc_start: 0.7151 (mt0) cc_final: 0.6671 (mt0) REVERT: C 3996 PHE cc_start: 0.7602 (m-80) cc_final: 0.7336 (m-80) REVERT: C 3999 MET cc_start: 0.8063 (ttm) cc_final: 0.7805 (ttp) REVERT: C 4021 LYS cc_start: 0.8563 (tmtt) cc_final: 0.7833 (tptt) REVERT: C 4184 MET cc_start: 0.8482 (tpp) cc_final: 0.8207 (mmt) REVERT: C 4207 MET cc_start: 0.7942 (mmt) cc_final: 0.7711 (mmt) REVERT: D 3996 PHE cc_start: 0.7613 (m-80) cc_final: 0.7342 (m-80) REVERT: D 3999 MET cc_start: 0.8067 (ttm) cc_final: 0.7809 (ttp) REVERT: D 4021 LYS cc_start: 0.8565 (tmtt) cc_final: 0.7829 (tptt) REVERT: D 4184 MET cc_start: 0.8479 (tpp) cc_final: 0.8210 (mmt) REVERT: D 4933 GLN cc_start: 0.7140 (mt0) cc_final: 0.6666 (mt0) outliers start: 51 outliers final: 42 residues processed: 400 average time/residue: 0.3179 time to fit residues: 193.7728 Evaluate side-chains 399 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 357 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4046 ASP Chi-restraints excluded: chain A residue 4199 GLU Chi-restraints excluded: chain A residue 4555 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4796 MET Chi-restraints excluded: chain A residue 4826 ILE Chi-restraints excluded: chain A residue 4892 ARG Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4929 LEU Chi-restraints excluded: chain A residue 4950 VAL Chi-restraints excluded: chain A residue 4993 MET Chi-restraints excluded: chain B residue 4046 ASP Chi-restraints excluded: chain B residue 4199 GLU Chi-restraints excluded: chain B residue 4555 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4796 MET Chi-restraints excluded: chain B residue 4826 ILE Chi-restraints excluded: chain B residue 4892 ARG Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4950 VAL Chi-restraints excluded: chain B residue 4993 MET Chi-restraints excluded: chain C residue 4046 ASP Chi-restraints excluded: chain C residue 4199 GLU Chi-restraints excluded: chain C residue 4555 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4796 MET Chi-restraints excluded: chain C residue 4826 ILE Chi-restraints excluded: chain C residue 4892 ARG Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4929 LEU Chi-restraints excluded: chain C residue 4950 VAL Chi-restraints excluded: chain C residue 4993 MET Chi-restraints excluded: chain D residue 4046 ASP Chi-restraints excluded: chain D residue 4199 GLU Chi-restraints excluded: chain D residue 4555 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4796 MET Chi-restraints excluded: chain D residue 4826 ILE Chi-restraints excluded: chain D residue 4892 ARG Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4950 VAL Chi-restraints excluded: chain D residue 4993 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 33 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 247 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4223 ASN ** A4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4223 ASN ** B4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4223 ASN ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4223 ASN ** D4806 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 = 0.3795 r_free = 0.3795 target = 0.143572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.118585 restraints weight = 34825.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.121605 restraints weight = 19495.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.123494 restraints weight = 13609.582| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 21088 Z= 0.150 Angle : 0.579 8.172 28448 Z= 0.290 Chirality : 0.039 0.203 3068 Planarity : 0.006 0.126 3600 Dihedral : 4.135 20.335 2700 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.31 % Favored : 97.53 % Rotamer: Outliers : 2.50 % Allowed : 18.16 % Favored : 79.34 % 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: 1.81 (0.17), residues: 2468 helix: 2.05 (0.12), residues: 1676 sheet: -0.03 (0.67), residues: 64 loop : -0.72 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D4205 HIS 0.004 0.001 HIS B4650 PHE 0.018 0.001 PHE C4921 TYR 0.029 0.002 TYR D3968 ARG 0.003 0.000 ARG B4736 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 1345) hydrogen bonds : angle 4.45693 ( 3963) metal coordination : bond 0.00979 ( 16) metal coordination : angle 3.29643 ( 8) SS BOND : bond 0.00124 ( 4) SS BOND : angle 0.82658 ( 8) covalent geometry : bond 0.00364 (21068) covalent geometry : angle 0.57593 (28432) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 373 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3968 TYR cc_start: 0.8372 (m-80) cc_final: 0.7949 (m-80) REVERT: A 3996 PHE cc_start: 0.7644 (m-80) cc_final: 0.7349 (m-80) REVERT: A 3999 MET cc_start: 0.8085 (ttm) cc_final: 0.7826 (ttp) REVERT: A 4021 LYS cc_start: 0.8537 (tmtt) cc_final: 0.7805 (tptt) REVERT: A 4184 MET cc_start: 0.8416 (tpp) cc_final: 0.8143 (mmt) REVERT: A 4207 MET cc_start: 0.8091 (mmt) cc_final: 0.7787 (mmt) REVERT: B 3968 TYR cc_start: 0.8372 (m-80) cc_final: 0.8092 (m-80) REVERT: B 3996 PHE cc_start: 0.7635 (m-80) cc_final: 0.7354 (m-80) REVERT: B 3999 MET cc_start: 0.8097 (ttm) cc_final: 0.7831 (ttp) REVERT: B 4021 LYS cc_start: 0.8575 (tmtt) cc_final: 0.7827 (tptt) REVERT: B 4050 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8146 (tm-30) REVERT: B 4184 MET cc_start: 0.8412 (tpp) cc_final: 0.8140 (mmt) REVERT: B 4207 MET cc_start: 0.8099 (mmt) cc_final: 0.7784 (mmt) REVERT: B 4933 GLN cc_start: 0.7191 (mt0) cc_final: 0.6715 (mt0) REVERT: C 3968 TYR cc_start: 0.8367 (m-80) cc_final: 0.8087 (m-80) REVERT: C 3996 PHE cc_start: 0.7632 (m-80) cc_final: 0.7353 (m-80) REVERT: C 3999 MET cc_start: 0.8088 (ttm) cc_final: 0.7824 (ttp) REVERT: C 4021 LYS cc_start: 0.8574 (tmtt) cc_final: 0.7823 (tptt) REVERT: C 4184 MET cc_start: 0.8410 (tpp) cc_final: 0.8138 (mmt) REVERT: C 4207 MET cc_start: 0.8091 (mmt) cc_final: 0.7786 (mmt) REVERT: D 3996 PHE cc_start: 0.7641 (m-80) cc_final: 0.7355 (m-80) REVERT: D 3999 MET cc_start: 0.8093 (ttm) cc_final: 0.7831 (ttp) REVERT: D 4021 LYS cc_start: 0.8574 (tmtt) cc_final: 0.7824 (tptt) REVERT: D 4050 GLU cc_start: 0.8387 (tm-30) cc_final: 0.8143 (tm-30) REVERT: D 4184 MET cc_start: 0.8414 (tpp) cc_final: 0.8143 (mmt) REVERT: D 4933 GLN cc_start: 0.7181 (mt0) cc_final: 0.6709 (mt0) outliers start: 56 outliers final: 44 residues processed: 404 average time/residue: 0.3109 time to fit residues: 193.3642 Evaluate side-chains 403 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 359 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4046 ASP Chi-restraints excluded: chain A residue 4199 GLU Chi-restraints excluded: chain A residue 4555 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4796 MET Chi-restraints excluded: chain A residue 4826 ILE Chi-restraints excluded: chain A residue 4892 ARG Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4929 LEU Chi-restraints excluded: chain A residue 4950 VAL Chi-restraints excluded: chain A residue 4993 MET Chi-restraints excluded: chain B residue 4046 ASP Chi-restraints excluded: chain B residue 4199 GLU Chi-restraints excluded: chain B residue 4555 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4796 MET Chi-restraints excluded: chain B residue 4826 ILE Chi-restraints excluded: chain B residue 4892 ARG Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4929 LEU Chi-restraints excluded: chain B residue 4950 VAL Chi-restraints excluded: chain B residue 4993 MET Chi-restraints excluded: chain C residue 4046 ASP Chi-restraints excluded: chain C residue 4199 GLU Chi-restraints excluded: chain C residue 4555 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4826 ILE Chi-restraints excluded: chain C residue 4892 ARG Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4929 LEU Chi-restraints excluded: chain C residue 4950 VAL Chi-restraints excluded: chain C residue 4993 MET Chi-restraints excluded: chain D residue 4046 ASP Chi-restraints excluded: chain D residue 4199 GLU Chi-restraints excluded: chain D residue 4555 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4796 MET Chi-restraints excluded: chain D residue 4822 THR Chi-restraints excluded: chain D residue 4826 ILE Chi-restraints excluded: chain D residue 4892 ARG Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4929 LEU Chi-restraints excluded: chain D residue 4950 VAL Chi-restraints excluded: chain D residue 4993 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 152 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 123 optimal weight: 0.0270 chunk 76 optimal weight: 4.9990 chunk 217 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 0.0770 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4223 ASN ** A4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4223 ASN ** B4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4223 ASN ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4223 ASN ** D4806 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 = 0.3831 r_free = 0.3831 target = 0.146599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.121965 restraints weight = 34815.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.125023 restraints weight = 19203.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.127005 restraints weight = 13322.198| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 21088 Z= 0.109 Angle : 0.545 8.220 28448 Z= 0.272 Chirality : 0.037 0.193 3068 Planarity : 0.005 0.125 3600 Dihedral : 3.998 19.313 2700 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.59 % Favored : 97.24 % Rotamer: Outliers : 1.97 % Allowed : 18.38 % Favored : 79.65 % 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: 2.07 (0.17), residues: 2468 helix: 2.25 (0.12), residues: 1680 sheet: 0.07 (0.67), residues: 64 loop : -0.65 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A4205 HIS 0.002 0.000 HIS A4978 PHE 0.012 0.001 PHE D4921 TYR 0.029 0.001 TYR D3968 ARG 0.002 0.000 ARG B4736 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 1345) hydrogen bonds : angle 4.33607 ( 3963) metal coordination : bond 0.00249 ( 16) metal coordination : angle 2.16533 ( 8) SS BOND : bond 0.00279 ( 4) SS BOND : angle 0.72374 ( 8) covalent geometry : bond 0.00262 (21068) covalent geometry : angle 0.54388 (28432) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 393 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3968 TYR cc_start: 0.8293 (m-80) cc_final: 0.7828 (m-80) REVERT: A 3999 MET cc_start: 0.7698 (ttm) cc_final: 0.7427 (ttp) REVERT: A 4021 LYS cc_start: 0.8372 (tmtt) cc_final: 0.7706 (tptt) REVERT: A 4184 MET cc_start: 0.8460 (tpp) cc_final: 0.8092 (mmt) REVERT: A 4199 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6600 (mt-10) REVERT: A 4207 MET cc_start: 0.8066 (mmt) cc_final: 0.7782 (mmt) REVERT: A 4668 LEU cc_start: 0.8324 (tp) cc_final: 0.8039 (tp) REVERT: B 3968 TYR cc_start: 0.8310 (m-80) cc_final: 0.7834 (m-80) REVERT: B 3996 PHE cc_start: 0.7537 (m-80) cc_final: 0.7298 (m-80) REVERT: B 3999 MET cc_start: 0.7962 (ttm) cc_final: 0.7665 (ttp) REVERT: B 4021 LYS cc_start: 0.8503 (tmtt) cc_final: 0.7749 (tptt) REVERT: B 4184 MET cc_start: 0.8458 (tpp) cc_final: 0.8092 (mmt) REVERT: B 4199 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6598 (mt-10) REVERT: B 4207 MET cc_start: 0.8072 (mmt) cc_final: 0.7781 (mmt) REVERT: B 4668 LEU cc_start: 0.8321 (tp) cc_final: 0.8034 (tp) REVERT: B 4933 GLN cc_start: 0.7375 (mt0) cc_final: 0.6957 (mt0) REVERT: C 3968 TYR cc_start: 0.8312 (m-80) cc_final: 0.7835 (m-80) REVERT: C 3996 PHE cc_start: 0.7541 (m-80) cc_final: 0.7301 (m-80) REVERT: C 3999 MET cc_start: 0.7955 (ttm) cc_final: 0.7663 (ttp) REVERT: C 4021 LYS cc_start: 0.8506 (tmtt) cc_final: 0.7749 (tptt) REVERT: C 4184 MET cc_start: 0.8455 (tpp) cc_final: 0.8087 (mmt) REVERT: C 4199 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6598 (mt-10) REVERT: C 4207 MET cc_start: 0.8062 (mmt) cc_final: 0.7778 (mmt) REVERT: C 4668 LEU cc_start: 0.8324 (tp) cc_final: 0.8037 (tp) REVERT: D 3968 TYR cc_start: 0.8352 (m-80) cc_final: 0.7778 (m-80) REVERT: D 3996 PHE cc_start: 0.7550 (m-80) cc_final: 0.7296 (m-80) REVERT: D 3999 MET cc_start: 0.7975 (ttm) cc_final: 0.7676 (ttp) REVERT: D 4021 LYS cc_start: 0.8517 (tmtt) cc_final: 0.7785 (tptt) REVERT: D 4050 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8196 (tm-30) REVERT: D 4184 MET cc_start: 0.8456 (tpp) cc_final: 0.8086 (mmt) REVERT: D 4199 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6544 (mt-10) REVERT: D 4668 LEU cc_start: 0.8305 (tp) cc_final: 0.8025 (tp) REVERT: D 4933 GLN cc_start: 0.7362 (mt0) cc_final: 0.6948 (mt0) outliers start: 44 outliers final: 22 residues processed: 414 average time/residue: 0.3287 time to fit residues: 204.8708 Evaluate side-chains 395 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 369 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4199 GLU Chi-restraints excluded: chain A residue 4555 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4796 MET Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4950 VAL Chi-restraints excluded: chain A residue 4993 MET Chi-restraints excluded: chain B residue 4199 GLU Chi-restraints excluded: chain B residue 4555 LEU Chi-restraints excluded: chain B residue 4796 MET Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4950 VAL Chi-restraints excluded: chain B residue 4993 MET Chi-restraints excluded: chain C residue 4199 GLU Chi-restraints excluded: chain C residue 4555 LEU Chi-restraints excluded: chain C residue 4796 MET Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4950 VAL Chi-restraints excluded: chain C residue 4993 MET Chi-restraints excluded: chain D residue 4199 GLU Chi-restraints excluded: chain D residue 4555 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4796 MET Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4950 VAL Chi-restraints excluded: chain D residue 4993 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 186 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 210 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 221 optimal weight: 1.9990 chunk 213 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4223 ASN ** A4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4223 ASN ** B4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4223 ASN ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4223 ASN ** D4806 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 = 0.3819 r_free = 0.3819 target = 0.145693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.120826 restraints weight = 34960.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123884 restraints weight = 19422.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.125839 restraints weight = 13510.531| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 21088 Z= 0.120 Angle : 0.565 8.129 28448 Z= 0.283 Chirality : 0.039 0.256 3068 Planarity : 0.006 0.124 3600 Dihedral : 4.010 19.134 2700 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.76 % Favored : 97.08 % Rotamer: Outliers : 1.79 % Allowed : 18.20 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.01 (0.17), residues: 2468 helix: 2.17 (0.12), residues: 1688 sheet: 0.10 (0.68), residues: 64 loop : -0.62 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D4205 HIS 0.002 0.001 HIS A3998 PHE 0.035 0.001 PHE A3996 TYR 0.028 0.001 TYR D3968 ARG 0.004 0.000 ARG A4679 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 1345) hydrogen bonds : angle 4.40432 ( 3963) metal coordination : bond 0.00468 ( 16) metal coordination : angle 2.54777 ( 8) SS BOND : bond 0.00179 ( 4) SS BOND : angle 0.70155 ( 8) covalent geometry : bond 0.00294 (21068) covalent geometry : angle 0.56369 (28432) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6428.79 seconds wall clock time: 113 minutes 23.32 seconds (6803.32 seconds total)