Starting phenix.real_space_refine on Wed Nov 20 03:05:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sey_40433/11_2024/8sey_40433.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sey_40433/11_2024/8sey_40433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sey_40433/11_2024/8sey_40433.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sey_40433/11_2024/8sey_40433.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sey_40433/11_2024/8sey_40433.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sey_40433/11_2024/8sey_40433.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.123 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 160 5.16 5 C 13360 2.51 5 N 3280 2.21 5 O 3764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 20568 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5122 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "B" Number of atoms: 5122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5122 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "C" Number of atoms: 5122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5122 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "D" Number of atoms: 5122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5122 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {' ZN': 1, 'ADN%rna2p': 1} Classifications: {'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {' ZN': 1, 'ADN%rna2p': 1} Classifications: {'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {' ZN': 1, 'ADN%rna2p': 1} Classifications: {'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {' ZN': 1, 'ADN%rna2p': 1} Classifications: {'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4448 SG CYS A4958 56.002 81.276 88.845 1.00 44.66 S ATOM 4473 SG CYS A4961 58.248 82.388 91.794 1.00 41.54 S ATOM 9570 SG CYS B4958 60.404 56.002 88.845 1.00 44.78 S ATOM 9595 SG CYS B4961 59.292 58.248 91.794 1.00 41.58 S ATOM 14692 SG CYS C4958 85.678 60.404 88.845 1.00 44.43 S ATOM 14717 SG CYS C4961 83.432 59.292 91.794 1.00 41.45 S ATOM 19814 SG CYS D4958 81.277 85.678 88.845 1.00 44.61 S ATOM 19839 SG CYS D4961 82.388 83.432 91.794 1.00 41.80 S Time building chain proxies: 12.28, per 1000 atoms: 0.60 Number of scatterers: 20568 At special positions: 0 Unit cell: (142.968, 142.968, 135.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 160 16.00 O 3764 8.00 N 3280 7.00 C 13360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.03 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " distance=2.03 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " distance=2.03 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.02 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5102 " pdb="ZN ZN A5102 " - pdb=" ND1 HIS A4983 " pdb="ZN ZN A5102 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4958 " pdb=" ZN B5102 " pdb="ZN ZN B5102 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5102 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4958 " pdb=" ZN C5102 " pdb="ZN ZN C5102 " - pdb=" ND1 HIS C4983 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4958 " pdb=" ZN D5102 " pdb="ZN ZN D5102 " - pdb=" ND1 HIS D4983 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4958 " Number of angles added : 8 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4720 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 78.8% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 3950 through 3970 removed outlier: 3.532A pdb=" N VAL A3957 " --> pdb=" O LYS A3953 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A3969 " --> pdb=" O LEU A3965 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3983 removed outlier: 3.603A pdb=" N ALA A3981 " --> pdb=" O GLN A3977 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS A3982 " --> pdb=" O GLN A3978 " (cutoff:3.500A) Processing helix chain 'A' and resid 3984 through 4006 removed outlier: 4.015A pdb=" N HIS A3998 " --> pdb=" O HIS A3994 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A4005 " --> pdb=" O MET A4001 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP A4006 " --> pdb=" O LYS A4002 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4031 removed outlier: 3.951A pdb=" N GLU A4015 " --> pdb=" O GLU A4011 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A4031 " --> pdb=" O LEU A4027 " (cutoff:3.500A) Processing helix chain 'A' and resid 4038 through 4051 removed outlier: 3.504A pdb=" N ARG A4042 " --> pdb=" O GLY A4038 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A4043 " --> pdb=" O MET A4039 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4056 Processing helix chain 'A' and resid 4198 through 4207 Processing helix chain 'A' and resid 4207 through 4224 Processing helix chain 'A' and resid 4229 through 4252 Processing helix chain 'A' and resid 4544 through 4558 Processing helix chain 'A' and resid 4558 through 4578 Processing helix chain 'A' and resid 4638 through 4665 Processing helix chain 'A' and resid 4665 through 4683 Processing helix chain 'A' and resid 4696 through 4703 Processing helix chain 'A' and resid 4704 through 4708 removed outlier: 3.862A pdb=" N ASN A4707 " --> pdb=" O LEU A4704 " (cutoff:3.500A) Processing helix chain 'A' and resid 4719 through 4733 removed outlier: 5.207A pdb=" N ASP A4730 " --> pdb=" O ASP A4726 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE A4731 " --> pdb=" O LYS A4727 " (cutoff:3.500A) Processing helix chain 'A' and resid 4733 through 4742 Processing helix chain 'A' and resid 4744 through 4749 removed outlier: 3.655A pdb=" N SER A4747 " --> pdb=" O ASP A4744 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A4749 " --> pdb=" O ALA A4746 " (cutoff:3.500A) Processing helix chain 'A' and resid 4773 through 4786 Processing helix chain 'A' and resid 4786 through 4805 removed outlier: 3.775A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4813 Processing helix chain 'A' and resid 4814 through 4820 removed outlier: 4.288A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) Processing helix chain 'A' and resid 4820 through 4833 removed outlier: 3.697A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN A4833 " --> pdb=" O SER A4829 " (cutoff:3.500A) Processing helix chain 'A' and resid 4833 through 4859 Processing helix chain 'A' and resid 4860 through 4863 Processing helix chain 'A' and resid 4878 through 4893 removed outlier: 4.562A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG A4892 " --> pdb=" O TYR A4888 " (cutoff:3.500A) Processing helix chain 'A' and resid 4896 through 4900 Processing helix chain 'A' and resid 4909 through 4924 Processing helix chain 'A' and resid 4926 through 4957 removed outlier: 4.025A pdb=" N ILE A4932 " --> pdb=" O LEU A4928 " (cutoff:3.500A) Processing helix chain 'A' and resid 4964 through 4969 removed outlier: 3.984A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) Processing helix chain 'A' and resid 4973 through 4981 Processing helix chain 'A' and resid 4984 through 4998 Processing helix chain 'A' and resid 5004 through 5016 Processing helix chain 'A' and resid 5027 through 5037 removed outlier: 6.525A pdb=" N ASP A5034 " --> pdb=" O LYS A5030 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLN A5035 " --> pdb=" O GLN A5031 " (cutoff:3.500A) Processing helix chain 'B' and resid 3951 through 3970 removed outlier: 3.534A pdb=" N VAL B3957 " --> pdb=" O LYS B3953 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B3969 " --> pdb=" O LEU B3965 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3983 removed outlier: 3.587A pdb=" N ALA B3981 " --> pdb=" O GLN B3977 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS B3982 " --> pdb=" O GLN B3978 " (cutoff:3.500A) Processing helix chain 'B' and resid 3984 through 4006 removed outlier: 4.001A pdb=" N HIS B3998 " --> pdb=" O HIS B3994 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET B4001 " --> pdb=" O ALA B3997 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN B4005 " --> pdb=" O MET B4001 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP B4006 " --> pdb=" O LYS B4002 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4031 removed outlier: 3.942A pdb=" N GLU B4015 " --> pdb=" O GLU B4011 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN B4020 " --> pdb=" O LEU B4016 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B4031 " --> pdb=" O LEU B4027 " (cutoff:3.500A) Processing helix chain 'B' and resid 4038 through 4051 Processing helix chain 'B' and resid 4051 through 4056 Processing helix chain 'B' and resid 4198 through 4207 Processing helix chain 'B' and resid 4207 through 4224 Processing helix chain 'B' and resid 4229 through 4252 Processing helix chain 'B' and resid 4544 through 4558 Processing helix chain 'B' and resid 4558 through 4578 Processing helix chain 'B' and resid 4638 through 4665 Processing helix chain 'B' and resid 4665 through 4683 Processing helix chain 'B' and resid 4696 through 4703 Processing helix chain 'B' and resid 4704 through 4708 removed outlier: 3.863A pdb=" N ASN B4707 " --> pdb=" O LEU B4704 " (cutoff:3.500A) Processing helix chain 'B' and resid 4719 through 4733 removed outlier: 5.207A pdb=" N ASP B4730 " --> pdb=" O ASP B4726 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE B4731 " --> pdb=" O LYS B4727 " (cutoff:3.500A) Processing helix chain 'B' and resid 4733 through 4742 Processing helix chain 'B' and resid 4744 through 4749 removed outlier: 3.655A pdb=" N SER B4747 " --> pdb=" O ASP B4744 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU B4749 " --> pdb=" O ALA B4746 " (cutoff:3.500A) Processing helix chain 'B' and resid 4773 through 4786 Processing helix chain 'B' and resid 4786 through 4805 removed outlier: 3.775A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4806 through 4813 Processing helix chain 'B' and resid 4814 through 4820 removed outlier: 4.289A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) Processing helix chain 'B' and resid 4820 through 4833 removed outlier: 3.696A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASN B4833 " --> pdb=" O SER B4829 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4859 Processing helix chain 'B' and resid 4860 through 4863 Processing helix chain 'B' and resid 4878 through 4893 removed outlier: 4.563A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG B4892 " --> pdb=" O TYR B4888 " (cutoff:3.500A) Processing helix chain 'B' and resid 4896 through 4900 Processing helix chain 'B' and resid 4909 through 4924 Processing helix chain 'B' and resid 4926 through 4957 removed outlier: 4.024A pdb=" N ILE B4932 " --> pdb=" O LEU B4928 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4969 removed outlier: 3.984A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4981 Processing helix chain 'B' and resid 4984 through 4998 Processing helix chain 'B' and resid 5004 through 5016 Processing helix chain 'B' and resid 5027 through 5037 removed outlier: 6.524A pdb=" N ASP B5034 " --> pdb=" O LYS B5030 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN B5035 " --> pdb=" O GLN B5031 " (cutoff:3.500A) Processing helix chain 'C' and resid 3951 through 3970 removed outlier: 3.534A pdb=" N VAL C3957 " --> pdb=" O LYS C3953 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C3969 " --> pdb=" O LEU C3965 " (cutoff:3.500A) Processing helix chain 'C' and resid 3973 through 3983 removed outlier: 3.587A pdb=" N ALA C3981 " --> pdb=" O GLN C3977 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS C3982 " --> pdb=" O GLN C3978 " (cutoff:3.500A) Processing helix chain 'C' and resid 3984 through 4006 removed outlier: 4.002A pdb=" N HIS C3998 " --> pdb=" O HIS C3994 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN C4005 " --> pdb=" O MET C4001 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP C4006 " --> pdb=" O LYS C4002 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4031 removed outlier: 3.942A pdb=" N GLU C4015 " --> pdb=" O GLU C4011 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN C4020 " --> pdb=" O LEU C4016 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C4031 " --> pdb=" O LEU C4027 " (cutoff:3.500A) Processing helix chain 'C' and resid 4038 through 4051 Processing helix chain 'C' and resid 4051 through 4056 Processing helix chain 'C' and resid 4198 through 4207 Processing helix chain 'C' and resid 4207 through 4224 Processing helix chain 'C' and resid 4229 through 4252 Processing helix chain 'C' and resid 4544 through 4558 Processing helix chain 'C' and resid 4558 through 4578 Processing helix chain 'C' and resid 4638 through 4665 Processing helix chain 'C' and resid 4665 through 4683 Processing helix chain 'C' and resid 4696 through 4703 Processing helix chain 'C' and resid 4704 through 4708 removed outlier: 3.863A pdb=" N ASN C4707 " --> pdb=" O LEU C4704 " (cutoff:3.500A) Processing helix chain 'C' and resid 4719 through 4733 removed outlier: 5.207A pdb=" N ASP C4730 " --> pdb=" O ASP C4726 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE C4731 " --> pdb=" O LYS C4727 " (cutoff:3.500A) Processing helix chain 'C' and resid 4733 through 4742 Processing helix chain 'C' and resid 4744 through 4749 removed outlier: 3.655A pdb=" N SER C4747 " --> pdb=" O ASP C4744 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU C4749 " --> pdb=" O ALA C4746 " (cutoff:3.500A) Processing helix chain 'C' and resid 4773 through 4786 Processing helix chain 'C' and resid 4786 through 4805 removed outlier: 3.775A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4806 through 4813 Processing helix chain 'C' and resid 4814 through 4820 removed outlier: 4.289A pdb=" N MET C4818 " --> pdb=" O LEU C4814 " (cutoff:3.500A) Processing helix chain 'C' and resid 4820 through 4833 removed outlier: 3.695A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN C4833 " --> pdb=" O SER C4829 " (cutoff:3.500A) Processing helix chain 'C' and resid 4833 through 4859 Processing helix chain 'C' and resid 4860 through 4863 Processing helix chain 'C' and resid 4878 through 4893 removed outlier: 4.562A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG C4892 " --> pdb=" O TYR C4888 " (cutoff:3.500A) Processing helix chain 'C' and resid 4896 through 4900 Processing helix chain 'C' and resid 4909 through 4924 Processing helix chain 'C' and resid 4926 through 4957 removed outlier: 4.023A pdb=" N ILE C4932 " --> pdb=" O LEU C4928 " (cutoff:3.500A) Processing helix chain 'C' and resid 4964 through 4969 removed outlier: 3.984A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) Processing helix chain 'C' and resid 4973 through 4981 Processing helix chain 'C' and resid 4984 through 4998 Processing helix chain 'C' and resid 5004 through 5016 Processing helix chain 'C' and resid 5027 through 5037 removed outlier: 6.524A pdb=" N ASP C5034 " --> pdb=" O LYS C5030 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN C5035 " --> pdb=" O GLN C5031 " (cutoff:3.500A) Processing helix chain 'D' and resid 3951 through 3970 removed outlier: 3.534A pdb=" N VAL D3957 " --> pdb=" O LYS D3953 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D3969 " --> pdb=" O LEU D3965 " (cutoff:3.500A) Processing helix chain 'D' and resid 3973 through 3983 removed outlier: 3.587A pdb=" N ALA D3981 " --> pdb=" O GLN D3977 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS D3982 " --> pdb=" O GLN D3978 " (cutoff:3.500A) Processing helix chain 'D' and resid 3984 through 4006 removed outlier: 4.001A pdb=" N HIS D3998 " --> pdb=" O HIS D3994 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN D4005 " --> pdb=" O MET D4001 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP D4006 " --> pdb=" O LYS D4002 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4031 removed outlier: 3.942A pdb=" N GLU D4015 " --> pdb=" O GLU D4011 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN D4020 " --> pdb=" O LEU D4016 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU D4031 " --> pdb=" O LEU D4027 " (cutoff:3.500A) Processing helix chain 'D' and resid 4038 through 4051 Processing helix chain 'D' and resid 4051 through 4056 Processing helix chain 'D' and resid 4198 through 4207 Processing helix chain 'D' and resid 4207 through 4224 Processing helix chain 'D' and resid 4229 through 4252 Processing helix chain 'D' and resid 4544 through 4558 Processing helix chain 'D' and resid 4558 through 4578 Processing helix chain 'D' and resid 4638 through 4665 Processing helix chain 'D' and resid 4665 through 4683 Processing helix chain 'D' and resid 4696 through 4703 Processing helix chain 'D' and resid 4704 through 4708 removed outlier: 3.864A pdb=" N ASN D4707 " --> pdb=" O LEU D4704 " (cutoff:3.500A) Processing helix chain 'D' and resid 4719 through 4733 removed outlier: 5.207A pdb=" N ASP D4730 " --> pdb=" O ASP D4726 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE D4731 " --> pdb=" O LYS D4727 " (cutoff:3.500A) Processing helix chain 'D' and resid 4733 through 4742 Processing helix chain 'D' and resid 4744 through 4749 removed outlier: 3.655A pdb=" N SER D4747 " --> pdb=" O ASP D4744 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU D4749 " --> pdb=" O ALA D4746 " (cutoff:3.500A) Processing helix chain 'D' and resid 4773 through 4786 Processing helix chain 'D' and resid 4786 through 4805 removed outlier: 3.775A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4806 through 4813 Processing helix chain 'D' and resid 4814 through 4820 removed outlier: 4.288A pdb=" N MET D4818 " --> pdb=" O LEU D4814 " (cutoff:3.500A) Processing helix chain 'D' and resid 4820 through 4833 removed outlier: 3.695A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN D4833 " --> pdb=" O SER D4829 " (cutoff:3.500A) Processing helix chain 'D' and resid 4833 through 4859 Processing helix chain 'D' and resid 4860 through 4863 Processing helix chain 'D' and resid 4878 through 4893 removed outlier: 4.563A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG D4892 " --> pdb=" O TYR D4888 " (cutoff:3.500A) Processing helix chain 'D' and resid 4896 through 4900 Processing helix chain 'D' and resid 4909 through 4924 Processing helix chain 'D' and resid 4926 through 4957 removed outlier: 4.023A pdb=" N ILE D4932 " --> pdb=" O LEU D4928 " (cutoff:3.500A) Processing helix chain 'D' and resid 4964 through 4969 removed outlier: 3.984A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) Processing helix chain 'D' and resid 4973 through 4981 Processing helix chain 'D' and resid 4984 through 4998 Processing helix chain 'D' and resid 5004 through 5016 Processing helix chain 'D' and resid 5027 through 5037 removed outlier: 6.524A pdb=" N ASP D5034 " --> pdb=" O LYS D5030 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN D5035 " --> pdb=" O GLN D5031 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4181 through 4184 Processing sheet with id=AA2, first strand: chain 'A' and resid 4580 through 4583 Processing sheet with id=AA3, first strand: chain 'B' and resid 4181 through 4184 Processing sheet with id=AA4, first strand: chain 'B' and resid 4580 through 4583 Processing sheet with id=AA5, first strand: chain 'C' and resid 4181 through 4184 Processing sheet with id=AA6, first strand: chain 'C' and resid 4580 through 4583 Processing sheet with id=AA7, first strand: chain 'D' and resid 4181 through 4184 Processing sheet with id=AA8, first strand: chain 'D' and resid 4580 through 4583 1368 hydrogen bonds defined for protein. 3960 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.57 Time building geometry restraints manager: 5.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6489 1.34 - 1.46: 4662 1.46 - 1.58: 9621 1.58 - 1.69: 0 1.69 - 1.81: 276 Bond restraints: 21048 Sorted by residual: bond pdb=" C5 ADN D5101 " pdb=" N7 ADN D5101 " ideal model delta sigma weight residual 1.371 1.387 -0.016 2.00e-02 2.50e+03 6.31e-01 bond pdb=" C5 ADN C5101 " pdb=" N7 ADN C5101 " ideal model delta sigma weight residual 1.371 1.387 -0.016 2.00e-02 2.50e+03 6.31e-01 bond pdb=" C5 ADN B5101 " pdb=" N7 ADN B5101 " ideal model delta sigma weight residual 1.371 1.387 -0.016 2.00e-02 2.50e+03 6.31e-01 bond pdb=" C5 ADN A5101 " pdb=" N7 ADN A5101 " ideal model delta sigma weight residual 1.371 1.387 -0.016 2.00e-02 2.50e+03 6.31e-01 bond pdb=" C GLY D4225 " pdb=" O GLY D4225 " ideal model delta sigma weight residual 1.237 1.230 0.007 9.70e-03 1.06e+04 5.97e-01 ... (remaining 21043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 27276 0.96 - 1.92: 866 1.92 - 2.89: 157 2.89 - 3.85: 81 3.85 - 4.81: 32 Bond angle restraints: 28412 Sorted by residual: angle pdb=" C GLU C4900 " pdb=" N ILE C4901 " pdb=" CA ILE C4901 " ideal model delta sigma weight residual 122.48 119.40 3.08 1.13e+00 7.83e-01 7.44e+00 angle pdb=" C GLU A4900 " pdb=" N ILE A4901 " pdb=" CA ILE A4901 " ideal model delta sigma weight residual 122.48 119.40 3.08 1.13e+00 7.83e-01 7.44e+00 angle pdb=" C GLU D4900 " pdb=" N ILE D4901 " pdb=" CA ILE D4901 " ideal model delta sigma weight residual 122.48 119.45 3.03 1.13e+00 7.83e-01 7.20e+00 angle pdb=" C GLU B4900 " pdb=" N ILE B4901 " pdb=" CA ILE B4901 " ideal model delta sigma weight residual 122.48 119.50 2.98 1.13e+00 7.83e-01 6.96e+00 angle pdb=" C ASN B4857 " pdb=" N PHE B4858 " pdb=" CA PHE B4858 " ideal model delta sigma weight residual 122.58 118.33 4.25 2.07e+00 2.33e-01 4.22e+00 ... (remaining 28407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 11298 16.69 - 33.37: 946 33.37 - 50.06: 113 50.06 - 66.75: 68 66.75 - 83.44: 35 Dihedral angle restraints: 12460 sinusoidal: 5140 harmonic: 7320 Sorted by residual: dihedral pdb=" CA GLY D3971 " pdb=" C GLY D3971 " pdb=" N PRO D3972 " pdb=" CA PRO D3972 " ideal model delta harmonic sigma weight residual -180.00 -150.34 -29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLY A3971 " pdb=" C GLY A3971 " pdb=" N PRO A3972 " pdb=" CA PRO A3972 " ideal model delta harmonic sigma weight residual -180.00 -150.34 -29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLY C3971 " pdb=" C GLY C3971 " pdb=" N PRO C3972 " pdb=" CA PRO C3972 " ideal model delta harmonic sigma weight residual -180.00 -150.38 -29.62 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 12457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1946 0.029 - 0.058: 850 0.058 - 0.088: 230 0.088 - 0.117: 50 0.117 - 0.146: 12 Chirality restraints: 3088 Sorted by residual: chirality pdb=" CA MET D5013 " pdb=" N MET D5013 " pdb=" C MET D5013 " pdb=" CB MET D5013 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA MET A5013 " pdb=" N MET A5013 " pdb=" C MET A5013 " pdb=" CB MET A5013 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA MET C5013 " pdb=" N MET C5013 " pdb=" C MET C5013 " pdb=" CB MET C5013 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 3085 not shown) Planarity restraints: 3592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B4666 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO B4667 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B4667 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B4667 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C4666 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO C4667 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO C4667 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C4667 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A4666 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.66e+00 pdb=" N PRO A4667 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A4667 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A4667 " 0.018 5.00e-02 4.00e+02 ... (remaining 3589 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3640 2.76 - 3.29: 19983 3.29 - 3.83: 34719 3.83 - 4.36: 40004 4.36 - 4.90: 69643 Nonbonded interactions: 167989 Sorted by model distance: nonbonded pdb=" OD2 ASP A4917 " pdb=" OH TYR D4888 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR C4888 " pdb=" OD2 ASP D4917 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR B4888 " pdb=" OD2 ASP C4917 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR A4888 " pdb=" OD2 ASP B4917 " model vdw 2.224 3.040 nonbonded pdb=" O THR A4825 " pdb=" OG SER A4828 " model vdw 2.235 3.040 ... (remaining 167984 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.110 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: 0.710 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 48.970 Find NCS groups from input model: 0.950 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: 0.010 Load rotamer database and sin/cos tables:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21048 Z= 0.140 Angle : 0.461 4.812 28412 Z= 0.258 Chirality : 0.036 0.146 3088 Planarity : 0.003 0.041 3592 Dihedral : 13.633 83.436 7728 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.17), residues: 2464 helix: 2.01 (0.13), residues: 1652 sheet: -1.32 (0.52), residues: 112 loop : -0.49 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B5011 HIS 0.004 0.001 HIS D5003 PHE 0.011 0.001 PHE A4916 TYR 0.008 0.001 TYR A4994 ARG 0.002 0.000 ARG C4913 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 2.419 Fit side-chains REVERT: A 4026 MET cc_start: 0.7916 (ttp) cc_final: 0.7621 (ttm) REVERT: A 4949 GLN cc_start: 0.7719 (tt0) cc_final: 0.7432 (tt0) REVERT: A 4953 ASP cc_start: 0.7014 (m-30) cc_final: 0.6771 (m-30) REVERT: B 4026 MET cc_start: 0.7890 (ttp) cc_final: 0.7601 (ttm) REVERT: B 4196 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6604 (mm-30) REVERT: B 4949 GLN cc_start: 0.7716 (tt0) cc_final: 0.7429 (tt0) REVERT: B 4953 ASP cc_start: 0.7011 (m-30) cc_final: 0.6768 (m-30) REVERT: C 4026 MET cc_start: 0.7889 (ttp) cc_final: 0.7602 (ttm) REVERT: C 4196 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6600 (mm-30) REVERT: C 4949 GLN cc_start: 0.7724 (tt0) cc_final: 0.7436 (tt0) REVERT: C 4953 ASP cc_start: 0.7014 (m-30) cc_final: 0.6772 (m-30) REVERT: D 4026 MET cc_start: 0.7889 (ttp) cc_final: 0.7603 (ttm) REVERT: D 4949 GLN cc_start: 0.7725 (tt0) cc_final: 0.7434 (tt0) REVERT: D 4953 ASP cc_start: 0.7011 (m-30) cc_final: 0.6769 (m-30) outliers start: 0 outliers final: 4 residues processed: 349 average time/residue: 1.5125 time to fit residues: 590.9659 Evaluate side-chains 254 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 250 time to evaluate : 3.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4777 ILE Chi-restraints excluded: chain B residue 4777 ILE Chi-restraints excluded: chain C residue 4777 ILE Chi-restraints excluded: chain D residue 4777 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.0570 chunk 187 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 225 optimal weight: 0.8980 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3950 ASN A4020 GLN B3950 ASN B4020 GLN C3950 ASN C4020 GLN D3950 ASN D4020 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21048 Z= 0.217 Angle : 0.498 9.683 28412 Z= 0.266 Chirality : 0.037 0.129 3088 Planarity : 0.004 0.059 3592 Dihedral : 8.772 71.674 2792 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.55 % Allowed : 7.60 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.17), residues: 2464 helix: 2.17 (0.12), residues: 1652 sheet: -1.74 (0.49), residues: 112 loop : -0.39 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C4701 HIS 0.003 0.001 HIS D3994 PHE 0.015 0.001 PHE B4916 TYR 0.009 0.001 TYR C4994 ARG 0.006 0.001 ARG C4913 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 275 time to evaluate : 2.559 Fit side-chains REVERT: A 4949 GLN cc_start: 0.7704 (tt0) cc_final: 0.7396 (tt0) REVERT: A 5034 ASP cc_start: 0.6330 (OUTLIER) cc_final: 0.5998 (p0) REVERT: B 4949 GLN cc_start: 0.7704 (tt0) cc_final: 0.7394 (tt0) REVERT: B 4953 ASP cc_start: 0.7083 (m-30) cc_final: 0.6883 (m-30) REVERT: B 5034 ASP cc_start: 0.6338 (OUTLIER) cc_final: 0.6009 (p0) REVERT: C 4949 GLN cc_start: 0.7709 (tt0) cc_final: 0.7400 (tt0) REVERT: C 5034 ASP cc_start: 0.6339 (OUTLIER) cc_final: 0.6010 (p0) REVERT: D 4949 GLN cc_start: 0.7712 (tt0) cc_final: 0.7403 (tt0) REVERT: D 5034 ASP cc_start: 0.6336 (OUTLIER) cc_final: 0.6008 (p0) outliers start: 57 outliers final: 23 residues processed: 315 average time/residue: 1.3332 time to fit residues: 469.0967 Evaluate side-chains 277 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 250 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4777 ILE Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain A residue 5034 ASP Chi-restraints excluded: chain B residue 3951 PHE Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4777 ILE Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain B residue 5034 ASP Chi-restraints excluded: chain C residue 3951 PHE Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4777 ILE Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain C residue 5034 ASP Chi-restraints excluded: chain D residue 3951 PHE Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4777 ILE Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5001 THR Chi-restraints excluded: chain D residue 5034 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 153 optimal weight: 0.4980 chunk 62 optimal weight: 10.0000 chunk 225 optimal weight: 0.9990 chunk 243 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4020 GLN ** B4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4020 GLN ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4020 GLN ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21048 Z= 0.175 Angle : 0.462 5.958 28412 Z= 0.249 Chirality : 0.036 0.130 3088 Planarity : 0.003 0.056 3592 Dihedral : 8.740 72.145 2792 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.42 % Allowed : 10.11 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.17), residues: 2464 helix: 2.31 (0.12), residues: 1668 sheet: -1.92 (0.48), residues: 112 loop : -0.30 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D4701 HIS 0.003 0.001 HIS A3994 PHE 0.015 0.001 PHE B3996 TYR 0.010 0.001 TYR A5009 ARG 0.003 0.000 ARG C4913 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 263 time to evaluate : 2.416 Fit side-chains REVERT: A 4011 GLU cc_start: 0.6538 (pm20) cc_final: 0.6322 (pm20) REVERT: A 4026 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7686 (ttm) REVERT: B 4026 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7620 (ttm) REVERT: B 4949 GLN cc_start: 0.7709 (tt0) cc_final: 0.7384 (tt0) REVERT: B 4953 ASP cc_start: 0.7073 (m-30) cc_final: 0.6871 (m-30) REVERT: C 4026 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7619 (ttm) REVERT: D 4026 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7623 (ttm) outliers start: 54 outliers final: 16 residues processed: 289 average time/residue: 1.5306 time to fit residues: 494.9722 Evaluate side-chains 277 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 257 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4026 MET Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4777 ILE Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain B residue 4026 MET Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4777 ILE Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain C residue 4026 MET Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4777 ILE Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain D residue 4026 MET Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4777 ILE Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5001 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 117 optimal weight: 0.0020 chunk 24 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 226 optimal weight: 4.9990 chunk 239 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4201 ASN C4020 GLN ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4201 ASN D4020 GLN ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4201 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21048 Z= 0.202 Angle : 0.458 6.202 28412 Z= 0.245 Chirality : 0.036 0.132 3088 Planarity : 0.003 0.061 3592 Dihedral : 8.712 72.357 2792 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.73 % Allowed : 11.45 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.17), residues: 2464 helix: 2.25 (0.12), residues: 1664 sheet: -1.98 (0.49), residues: 112 loop : -0.30 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D4701 HIS 0.003 0.001 HIS C4803 PHE 0.015 0.001 PHE B3996 TYR 0.009 0.001 TYR B5009 ARG 0.003 0.000 ARG C4913 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 266 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3999 MET cc_start: 0.8166 (mmp) cc_final: 0.7913 (mmm) REVERT: A 4887 MET cc_start: 0.8575 (tpt) cc_final: 0.8221 (tpt) REVERT: A 4949 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.7101 (tt0) REVERT: A 4980 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8249 (tp) REVERT: B 3999 MET cc_start: 0.8270 (mmp) cc_final: 0.8033 (mmm) REVERT: B 4011 GLU cc_start: 0.6534 (pm20) cc_final: 0.6230 (pm20) REVERT: B 4887 MET cc_start: 0.8573 (tpt) cc_final: 0.8226 (tpt) REVERT: B 4949 GLN cc_start: 0.7725 (tt0) cc_final: 0.7398 (tt0) REVERT: B 4953 ASP cc_start: 0.7090 (m-30) cc_final: 0.6871 (m-30) REVERT: B 4980 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8245 (tp) REVERT: C 3999 MET cc_start: 0.8280 (mmp) cc_final: 0.8037 (mmm) REVERT: C 4011 GLU cc_start: 0.6528 (pm20) cc_final: 0.6223 (pm20) REVERT: C 4887 MET cc_start: 0.8570 (tpt) cc_final: 0.8217 (tpt) REVERT: C 4949 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7102 (tt0) REVERT: C 4980 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8246 (tp) REVERT: D 3999 MET cc_start: 0.8277 (mmp) cc_final: 0.8035 (mmm) REVERT: D 4011 GLU cc_start: 0.6534 (pm20) cc_final: 0.6229 (pm20) REVERT: D 4887 MET cc_start: 0.8569 (tpt) cc_final: 0.8206 (tpt) REVERT: D 4949 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7104 (tt0) REVERT: D 4980 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8249 (tp) outliers start: 61 outliers final: 22 residues processed: 296 average time/residue: 1.5255 time to fit residues: 504.5311 Evaluate side-chains 282 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 253 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3951 PHE Chi-restraints excluded: chain A residue 4247 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4949 GLN Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain B residue 3951 PHE Chi-restraints excluded: chain B residue 4043 GLN Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain C residue 3951 PHE Chi-restraints excluded: chain C residue 4043 GLN Chi-restraints excluded: chain C residue 4247 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4949 GLN Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain D residue 3951 PHE Chi-restraints excluded: chain D residue 4043 GLN Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4949 GLN Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5001 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 204 optimal weight: 0.8980 chunk 165 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4201 ASN B4020 GLN ** B4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4020 GLN ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4020 GLN ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21048 Z= 0.310 Angle : 0.522 7.733 28412 Z= 0.278 Chirality : 0.038 0.141 3088 Planarity : 0.004 0.070 3592 Dihedral : 8.751 72.803 2784 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.53 % Allowed : 11.67 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.17), residues: 2464 helix: 2.16 (0.12), residues: 1640 sheet: -2.12 (0.48), residues: 112 loop : -0.37 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B4778 HIS 0.005 0.001 HIS B4803 PHE 0.019 0.002 PHE C4916 TYR 0.011 0.002 TYR C4994 ARG 0.003 0.000 ARG B4913 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 274 time to evaluate : 2.452 Fit side-chains REVERT: A 3999 MET cc_start: 0.8164 (mmp) cc_final: 0.7927 (mmm) REVERT: A 4011 GLU cc_start: 0.6505 (pm20) cc_final: 0.6262 (pm20) REVERT: A 4015 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6836 (pm20) REVERT: A 4735 GLU cc_start: 0.8141 (tp30) cc_final: 0.7911 (tp30) REVERT: A 4949 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7137 (tt0) REVERT: A 5034 ASP cc_start: 0.6357 (OUTLIER) cc_final: 0.6061 (p0) REVERT: B 3999 MET cc_start: 0.8251 (mmp) cc_final: 0.8024 (mmm) REVERT: B 4735 GLU cc_start: 0.8150 (tp30) cc_final: 0.7920 (tp30) REVERT: B 5034 ASP cc_start: 0.6352 (OUTLIER) cc_final: 0.6063 (p0) REVERT: C 3999 MET cc_start: 0.8259 (mmp) cc_final: 0.8026 (mmm) REVERT: C 4735 GLU cc_start: 0.8146 (tp30) cc_final: 0.7915 (tp30) REVERT: C 4949 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7138 (tt0) REVERT: C 5034 ASP cc_start: 0.6356 (OUTLIER) cc_final: 0.6064 (p0) REVERT: D 3999 MET cc_start: 0.8264 (mmp) cc_final: 0.8028 (mmm) REVERT: D 4735 GLU cc_start: 0.8148 (tp30) cc_final: 0.7921 (tp30) REVERT: D 4949 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7144 (tt0) REVERT: D 5034 ASP cc_start: 0.6356 (OUTLIER) cc_final: 0.6061 (p0) outliers start: 79 outliers final: 34 residues processed: 318 average time/residue: 1.4963 time to fit residues: 532.6074 Evaluate side-chains 310 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 268 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3951 PHE Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4247 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4949 GLN Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 4981 GLU Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain A residue 5034 ASP Chi-restraints excluded: chain B residue 3951 PHE Chi-restraints excluded: chain B residue 4048 LEU Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 4981 GLU Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain B residue 5034 ASP Chi-restraints excluded: chain C residue 3951 PHE Chi-restraints excluded: chain C residue 4048 LEU Chi-restraints excluded: chain C residue 4247 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4949 GLN Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 4981 GLU Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain C residue 5034 ASP Chi-restraints excluded: chain D residue 3951 PHE Chi-restraints excluded: chain D residue 4048 LEU Chi-restraints excluded: chain D residue 4247 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4949 GLN Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5001 THR Chi-restraints excluded: chain D residue 5034 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 59 optimal weight: 0.0870 chunk 239 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 125 optimal weight: 0.3980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4020 GLN B4054 ASN C4020 GLN C4054 ASN D4020 GLN D4054 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21048 Z= 0.149 Angle : 0.458 8.836 28412 Z= 0.243 Chirality : 0.035 0.144 3088 Planarity : 0.003 0.056 3592 Dihedral : 8.564 71.899 2784 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.86 % Allowed : 12.66 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.17), residues: 2464 helix: 2.36 (0.12), residues: 1656 sheet: -2.05 (0.49), residues: 112 loop : -0.37 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D5011 HIS 0.003 0.001 HIS B4812 PHE 0.015 0.001 PHE C3996 TYR 0.015 0.001 TYR A4804 ARG 0.002 0.000 ARG C4913 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 275 time to evaluate : 2.412 Fit side-chains REVERT: A 3999 MET cc_start: 0.8293 (mmp) cc_final: 0.8003 (mmm) REVERT: A 4011 GLU cc_start: 0.6601 (pm20) cc_final: 0.6361 (pm20) REVERT: A 4735 GLU cc_start: 0.8128 (tp30) cc_final: 0.7891 (tp30) REVERT: A 4887 MET cc_start: 0.8565 (tpt) cc_final: 0.8190 (tpt) REVERT: A 4980 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8252 (tp) REVERT: B 3999 MET cc_start: 0.8263 (mmp) cc_final: 0.8028 (mmm) REVERT: B 4011 GLU cc_start: 0.6608 (pm20) cc_final: 0.6267 (pm20) REVERT: B 4735 GLU cc_start: 0.8134 (tp30) cc_final: 0.7898 (tp30) REVERT: B 4887 MET cc_start: 0.8562 (tpt) cc_final: 0.8185 (tpt) REVERT: B 4948 GLU cc_start: 0.7464 (mp0) cc_final: 0.7241 (mp0) REVERT: B 4953 ASP cc_start: 0.7180 (m-30) cc_final: 0.6860 (m-30) REVERT: C 3999 MET cc_start: 0.8269 (mmp) cc_final: 0.8027 (mmm) REVERT: C 4011 GLU cc_start: 0.6611 (pm20) cc_final: 0.6270 (pm20) REVERT: C 4735 GLU cc_start: 0.8128 (tp30) cc_final: 0.7890 (tp30) REVERT: C 4887 MET cc_start: 0.8561 (tpt) cc_final: 0.8184 (tpt) REVERT: D 3999 MET cc_start: 0.8272 (mmp) cc_final: 0.8029 (mmm) REVERT: D 4011 GLU cc_start: 0.6612 (pm20) cc_final: 0.6273 (pm20) REVERT: D 4735 GLU cc_start: 0.8136 (tp30) cc_final: 0.7898 (tp30) REVERT: D 4887 MET cc_start: 0.8560 (tpt) cc_final: 0.8175 (tpt) outliers start: 64 outliers final: 18 residues processed: 310 average time/residue: 1.5260 time to fit residues: 528.7899 Evaluate side-chains 280 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 261 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3951 PHE Chi-restraints excluded: chain A residue 4247 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain B residue 3951 PHE Chi-restraints excluded: chain B residue 4048 LEU Chi-restraints excluded: chain B residue 4247 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain C residue 3951 PHE Chi-restraints excluded: chain C residue 4048 LEU Chi-restraints excluded: chain C residue 4247 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain D residue 3951 PHE Chi-restraints excluded: chain D residue 4048 LEU Chi-restraints excluded: chain D residue 4247 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4980 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 201 optimal weight: 0.4980 chunk 133 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 110 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4020 GLN ** B4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4020 GLN ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4020 GLN D4054 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21048 Z= 0.143 Angle : 0.471 7.513 28412 Z= 0.247 Chirality : 0.035 0.140 3088 Planarity : 0.003 0.055 3592 Dihedral : 8.499 71.753 2784 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.01 % Allowed : 14.27 % Favored : 83.72 % 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: 2.24 (0.17), residues: 2464 helix: 2.45 (0.12), residues: 1656 sheet: -2.07 (0.49), residues: 112 loop : -0.27 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B4794 HIS 0.003 0.000 HIS A4812 PHE 0.012 0.001 PHE C4916 TYR 0.015 0.001 TYR D5009 ARG 0.002 0.000 ARG B4913 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 267 time to evaluate : 2.376 Fit side-chains REVERT: A 3999 MET cc_start: 0.8287 (mmp) cc_final: 0.8037 (mmm) REVERT: A 4571 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7246 (t80) REVERT: A 4735 GLU cc_start: 0.8174 (tp30) cc_final: 0.7956 (tp30) REVERT: A 4887 MET cc_start: 0.8534 (tpt) cc_final: 0.8198 (tpt) REVERT: A 4980 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8256 (tp) REVERT: B 4011 GLU cc_start: 0.6555 (pm20) cc_final: 0.6344 (pm20) REVERT: B 4571 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7246 (t80) REVERT: B 4735 GLU cc_start: 0.8182 (tp30) cc_final: 0.7963 (tp30) REVERT: B 4887 MET cc_start: 0.8536 (tpt) cc_final: 0.8196 (tpt) REVERT: C 4011 GLU cc_start: 0.6556 (pm20) cc_final: 0.6340 (pm20) REVERT: C 4571 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7235 (t80) REVERT: C 4735 GLU cc_start: 0.8175 (tp30) cc_final: 0.7957 (tp30) REVERT: C 4887 MET cc_start: 0.8533 (tpt) cc_final: 0.8192 (tpt) REVERT: D 4011 GLU cc_start: 0.6559 (pm20) cc_final: 0.6347 (pm20) REVERT: D 4571 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7242 (t80) REVERT: D 4735 GLU cc_start: 0.8179 (tp30) cc_final: 0.7964 (tp30) REVERT: D 4887 MET cc_start: 0.8531 (tpt) cc_final: 0.8187 (tpt) outliers start: 45 outliers final: 15 residues processed: 293 average time/residue: 1.6150 time to fit residues: 528.1312 Evaluate side-chains 274 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 254 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3951 PHE Chi-restraints excluded: chain A residue 4571 PHE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain B residue 3951 PHE Chi-restraints excluded: chain B residue 4571 PHE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain C residue 3951 PHE Chi-restraints excluded: chain C residue 4571 PHE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain D residue 3951 PHE Chi-restraints excluded: chain D residue 4571 PHE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5001 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 0.0020 chunk 95 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 187 optimal weight: 3.9990 chunk 217 optimal weight: 0.3980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4020 GLN C4020 GLN D4020 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21048 Z= 0.137 Angle : 0.465 8.545 28412 Z= 0.244 Chirality : 0.035 0.135 3088 Planarity : 0.003 0.054 3592 Dihedral : 8.463 71.715 2784 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.19 % Allowed : 14.58 % Favored : 83.23 % 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: 2.30 (0.17), residues: 2464 helix: 2.48 (0.12), residues: 1656 sheet: -1.99 (0.49), residues: 112 loop : -0.22 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C5011 HIS 0.003 0.000 HIS A4812 PHE 0.012 0.001 PHE A4916 TYR 0.016 0.001 TYR B4804 ARG 0.002 0.000 ARG B4913 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 267 time to evaluate : 2.542 Fit side-chains REVERT: A 3999 MET cc_start: 0.8289 (mmp) cc_final: 0.8040 (mmm) REVERT: A 4224 GLU cc_start: 0.7011 (pm20) cc_final: 0.6808 (pm20) REVERT: A 4571 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7243 (t80) REVERT: A 4887 MET cc_start: 0.8511 (tpt) cc_final: 0.8272 (tpt) REVERT: A 4980 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8251 (tp) REVERT: B 4571 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7243 (t80) REVERT: B 4735 GLU cc_start: 0.8183 (tp30) cc_final: 0.7982 (tp30) REVERT: B 4887 MET cc_start: 0.8511 (tpt) cc_final: 0.8267 (tpt) REVERT: B 4953 ASP cc_start: 0.7149 (t0) cc_final: 0.6946 (m-30) REVERT: C 4224 GLU cc_start: 0.7046 (pm20) cc_final: 0.6827 (pm20) REVERT: C 4571 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7232 (t80) REVERT: C 4735 GLU cc_start: 0.8177 (tp30) cc_final: 0.7975 (tp30) REVERT: C 4887 MET cc_start: 0.8510 (tpt) cc_final: 0.8263 (tpt) REVERT: D 3998 HIS cc_start: 0.8030 (m-70) cc_final: 0.7703 (m-70) REVERT: D 4224 GLU cc_start: 0.7034 (pm20) cc_final: 0.6818 (pm20) REVERT: D 4571 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7238 (t80) REVERT: D 4887 MET cc_start: 0.8507 (tpt) cc_final: 0.8260 (tpt) outliers start: 49 outliers final: 24 residues processed: 303 average time/residue: 1.5569 time to fit residues: 526.1030 Evaluate side-chains 290 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 261 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3951 PHE Chi-restraints excluded: chain A residue 4026 MET Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4571 PHE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain B residue 4184 MET Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4571 PHE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain C residue 4184 MET Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4571 PHE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain D residue 4184 MET Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4571 PHE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5001 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 201 optimal weight: 2.9990 chunk 210 optimal weight: 0.6980 chunk 221 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN A4054 ASN B4020 GLN B4054 ASN C4020 GLN C4054 ASN D4020 GLN D4054 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21048 Z= 0.174 Angle : 0.497 9.536 28412 Z= 0.259 Chirality : 0.036 0.157 3088 Planarity : 0.003 0.057 3592 Dihedral : 8.493 71.899 2784 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.06 % Allowed : 15.21 % Favored : 82.74 % 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: 2.28 (0.17), residues: 2464 helix: 2.47 (0.12), residues: 1652 sheet: -1.94 (0.50), residues: 112 loop : -0.23 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B4701 HIS 0.002 0.000 HIS D4803 PHE 0.013 0.001 PHE A4916 TYR 0.015 0.001 TYR B5009 ARG 0.002 0.000 ARG C4913 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 274 time to evaluate : 2.315 Fit side-chains REVERT: A 3999 MET cc_start: 0.8282 (mmp) cc_final: 0.8041 (mmm) REVERT: A 4571 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7247 (t80) REVERT: A 4887 MET cc_start: 0.8523 (tpt) cc_final: 0.8264 (tpt) REVERT: A 4980 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8260 (tp) REVERT: B 4571 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7246 (t80) REVERT: B 4735 GLU cc_start: 0.8255 (tp30) cc_final: 0.8055 (tp30) REVERT: B 4887 MET cc_start: 0.8524 (tpt) cc_final: 0.8260 (tpt) REVERT: C 4571 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7235 (t80) REVERT: C 4887 MET cc_start: 0.8522 (tpt) cc_final: 0.8255 (tpt) REVERT: D 3998 HIS cc_start: 0.7999 (m-70) cc_final: 0.7591 (m-70) REVERT: D 4571 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7242 (t80) REVERT: D 4887 MET cc_start: 0.8519 (tpt) cc_final: 0.8253 (tpt) outliers start: 46 outliers final: 29 residues processed: 300 average time/residue: 1.5494 time to fit residues: 519.1176 Evaluate side-chains 298 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 264 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3951 PHE Chi-restraints excluded: chain A residue 4026 MET Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4571 PHE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain B residue 3951 PHE Chi-restraints excluded: chain B residue 4184 MET Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4571 PHE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain C residue 3951 PHE Chi-restraints excluded: chain C residue 4184 MET Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4571 PHE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain D residue 3951 PHE Chi-restraints excluded: chain D residue 4184 MET Chi-restraints excluded: chain D residue 4247 ILE Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4571 PHE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5000 GLU Chi-restraints excluded: chain D residue 5001 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 111 optimal weight: 0.0170 chunk 163 optimal weight: 0.9980 chunk 247 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 196 optimal weight: 0.0000 chunk 20 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 overall best weight: 0.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN B4020 GLN C4020 GLN D4020 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21048 Z= 0.137 Angle : 0.488 10.861 28412 Z= 0.253 Chirality : 0.035 0.146 3088 Planarity : 0.003 0.054 3592 Dihedral : 8.449 71.646 2784 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.88 % Allowed : 15.92 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.17), residues: 2464 helix: 2.48 (0.12), residues: 1652 sheet: -1.87 (0.50), residues: 112 loop : -0.13 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C5011 HIS 0.002 0.000 HIS D4812 PHE 0.011 0.001 PHE B4916 TYR 0.017 0.001 TYR D4804 ARG 0.003 0.000 ARG C4736 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 264 time to evaluate : 2.470 Fit side-chains REVERT: A 3999 MET cc_start: 0.8277 (mmp) cc_final: 0.8042 (mmm) REVERT: A 4011 GLU cc_start: 0.6434 (pm20) cc_final: 0.6020 (pm20) REVERT: A 4571 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7233 (t80) REVERT: A 4887 MET cc_start: 0.8517 (tpt) cc_final: 0.8249 (tpt) REVERT: A 4980 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8239 (tp) REVERT: B 3998 HIS cc_start: 0.8055 (m-70) cc_final: 0.7650 (m-70) REVERT: B 4571 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7233 (t80) REVERT: B 4735 GLU cc_start: 0.8164 (tp30) cc_final: 0.7940 (tp30) REVERT: B 4887 MET cc_start: 0.8515 (tpt) cc_final: 0.8241 (tpt) REVERT: C 3998 HIS cc_start: 0.8055 (m-70) cc_final: 0.7647 (m-70) REVERT: C 4571 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7221 (t80) REVERT: C 4887 MET cc_start: 0.8515 (tpt) cc_final: 0.8237 (tpt) REVERT: D 3998 HIS cc_start: 0.7991 (m-70) cc_final: 0.7625 (m-70) REVERT: D 4571 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7231 (t80) REVERT: D 4887 MET cc_start: 0.8513 (tpt) cc_final: 0.8235 (tpt) outliers start: 42 outliers final: 28 residues processed: 293 average time/residue: 1.6073 time to fit residues: 523.9565 Evaluate side-chains 291 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 258 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3951 PHE Chi-restraints excluded: chain A residue 4026 MET Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4571 PHE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain B residue 3951 PHE Chi-restraints excluded: chain B residue 4184 MET Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4571 PHE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain C residue 3951 PHE Chi-restraints excluded: chain C residue 4184 MET Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4571 PHE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain D residue 3951 PHE Chi-restraints excluded: chain D residue 4184 MET Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4571 PHE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5000 GLU Chi-restraints excluded: chain D residue 5001 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN A4054 ASN B4020 GLN C4020 GLN C4707 ASN D4020 GLN D4054 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.144929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.114805 restraints weight = 26255.009| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.55 r_work: 0.3065 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21048 Z= 0.174 Angle : 0.525 12.544 28412 Z= 0.271 Chirality : 0.036 0.160 3088 Planarity : 0.003 0.056 3592 Dihedral : 8.487 71.867 2784 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.97 % Allowed : 15.79 % Favored : 82.25 % 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: 2.28 (0.17), residues: 2464 helix: 2.44 (0.12), residues: 1652 sheet: -1.87 (0.50), residues: 112 loop : -0.13 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B4701 HIS 0.002 0.000 HIS C4803 PHE 0.013 0.001 PHE C4916 TYR 0.016 0.001 TYR D5009 ARG 0.006 0.000 ARG A4042 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7913.95 seconds wall clock time: 235 minutes 15.67 seconds (14115.67 seconds total)