Starting phenix.real_space_refine on Sat Jul 4 17:08:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qg1_53127/07_2026/9qg1_53127_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qg1_53127/07_2026/9qg1_53127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qg1_53127/07_2026/9qg1_53127_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qg1_53127/07_2026/9qg1_53127_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qg1_53127/07_2026/9qg1_53127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qg1_53127/07_2026/9qg1_53127.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.033 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 Fe 48 7.16 5 S 160 5.16 5 C 14160 2.51 5 N 3552 2.21 5 O 4048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21968 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1370 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "B" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1370 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "C" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1370 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "D" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1370 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "E" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1370 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "F" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1370 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "G" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1370 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "H" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1370 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "I" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1370 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "J" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1370 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "K" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1370 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "L" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1370 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "M" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1370 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "N" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1370 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "O" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1370 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "P" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1370 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' FE': 3} Chain breaks: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' FE': 3} Chain breaks: 3 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' FE': 2} Chain breaks: 2 Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' FE': 4} Chain breaks: 4 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' FE': 3} Chain breaks: 3 Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' FE': 3} Chain breaks: 3 Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' FE': 3} Chain breaks: 3 Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' FE': 3} Chain breaks: 3 Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' FE': 2} Chain breaks: 2 Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' FE': 4} Chain breaks: 4 Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' FE': 3} Chain breaks: 3 Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' FE': 3} Chain breaks: 3 Chain: "M" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' FE': 4} Chain breaks: 4 Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' FE': 2} Chain breaks: 2 Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' FE': 2} Chain breaks: 2 Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' FE': 4} Chain breaks: 4 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1150 SG CYS A 142 167.698 34.802 108.558 1.00139.43 S ATOM 1171 SG CYS A 145 165.871 37.940 108.989 1.00139.68 S ATOM 1262 SG CYS A 157 169.064 37.342 110.828 1.00144.72 S ATOM 1282 SG CYS A 160 166.130 34.517 111.888 1.00134.10 S ATOM 2541 SG CYS B 145 161.908 30.579 71.169 1.00148.73 S ATOM 2632 SG CYS B 157 163.862 28.845 69.175 1.00159.71 S ATOM 2652 SG CYS B 160 165.014 32.180 68.630 1.00160.57 S ATOM 3890 SG CYS C 142 117.132 55.207 72.599 1.00 90.15 S ATOM 3911 SG CYS C 145 120.376 54.207 71.874 1.00116.95 S ATOM 4002 SG CYS C 157 118.280 55.503 69.195 1.00103.17 S ATOM 4022 SG CYS C 160 117.124 52.211 69.987 1.00 82.46 S ATOM 5260 SG CYS D 142 122.715 65.111 107.866 1.00 89.78 S ATOM 5281 SG CYS D 145 125.454 62.779 108.853 1.00 99.88 S ATOM 5372 SG CYS D 157 123.254 64.026 111.346 1.00 92.55 S ATOM 5392 SG CYS D 160 125.753 66.578 110.449 1.00 91.22 S ATOM 6630 SG CYS E 142 120.668 64.321 162.942 1.00100.29 S ATOM 6651 SG CYS E 145 116.923 65.684 164.200 1.00114.02 S ATOM 6742 SG CYS E 157 120.947 66.783 165.795 1.00109.99 S ATOM 6762 SG CYS E 160 118.811 63.315 166.067 1.00117.69 S ATOM 8000 SG CYS F 142 121.693 67.998 126.534 1.00 88.16 S ATOM 8021 SG CYS F 145 118.558 67.725 125.715 1.00 88.66 S ATOM 8112 SG CYS F 157 121.179 66.088 123.539 1.00 90.94 S ATOM 9370 SG CYS G 142 69.070 83.423 126.356 1.00 95.40 S ATOM 9391 SG CYS G 145 71.524 79.805 125.296 1.00 86.87 S ATOM 9482 SG CYS G 157 69.808 82.580 123.107 1.00 95.69 S ATOM 10740 SG CYS H 142 69.860 84.594 162.829 1.00 98.75 S ATOM 10761 SG CYS H 145 72.467 82.224 163.517 1.00113.20 S ATOM 10852 SG CYS H 157 69.788 82.561 165.919 1.00107.07 S ATOM 10872 SG CYS H 160 71.793 85.852 166.052 1.00114.04 S ATOM 12110 SG CYS I 142 67.663 84.116 107.810 1.00 88.45 S ATOM 12131 SG CYS I 145 63.935 85.678 109.169 1.00103.53 S ATOM 12222 SG CYS I 157 67.475 85.189 111.258 1.00 93.62 S ATOM 12242 SG CYS I 160 64.880 82.589 110.479 1.00 91.56 S ATOM 13480 SG CYS J 142 73.515 94.062 72.635 1.00 87.11 S ATOM 13501 SG CYS J 145 70.238 94.930 71.852 1.00115.36 S ATOM 13592 SG CYS J 157 72.314 93.621 69.201 1.00 97.36 S ATOM 13612 SG CYS J 160 73.468 96.955 69.986 1.00 83.79 S ATOM 14871 SG CYS K 145 28.688 118.489 71.471 1.00151.88 S ATOM 14962 SG CYS K 157 26.607 120.252 69.105 1.00159.43 S ATOM 14982 SG CYS K 160 25.585 116.902 68.589 1.00161.92 S ATOM 16220 SG CYS L 142 22.687 114.463 108.613 1.00139.36 S ATOM 16241 SG CYS L 145 24.771 111.266 108.933 1.00137.21 S ATOM 16332 SG CYS L 157 21.693 111.816 110.987 1.00143.24 S ATOM 16352 SG CYS L 160 24.425 114.596 111.849 1.00135.63 S ATOM 17590 SG CYS M 142 113.870 54.753 54.076 1.00 95.16 S ATOM 17611 SG CYS M 145 112.278 58.156 55.050 1.00103.42 S ATOM 17702 SG CYS M 157 115.099 56.424 57.114 1.00103.55 S ATOM 17722 SG CYS M 160 111.558 54.487 56.905 1.00 94.90 S ATOM 18960 SG CYS N 142 115.967 57.687 17.998 1.00133.35 S ATOM 18981 SG CYS N 145 113.541 59.991 16.053 1.00148.46 S ATOM 19072 SG CYS N 157 114.456 56.098 14.675 1.00156.65 S ATOM 19092 SG CYS N 160 116.535 59.736 14.250 1.00153.19 S ATOM 20330 SG CYS O 142 74.630 91.492 17.805 1.00133.71 S ATOM 20351 SG CYS O 145 76.694 89.062 16.172 1.00144.88 S ATOM 20442 SG CYS O 157 76.137 93.178 14.618 1.00159.15 S ATOM 20462 SG CYS O 160 73.937 89.539 14.088 1.00158.32 S ATOM 21700 SG CYS P 142 76.731 94.276 54.054 1.00 93.70 S ATOM 21721 SG CYS P 145 79.441 91.490 55.443 1.00 96.50 S ATOM 21812 SG CYS P 157 75.471 92.846 57.106 1.00103.98 S ATOM 21832 SG CYS P 160 79.098 94.703 56.924 1.00 91.00 S Time building chain proxies: 4.74, per 1000 atoms: 0.22 Number of scatterers: 21968 At special positions: 0 Unit cell: (191.84, 150.42, 179.85, 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) Fe 48 26.01 S 160 16.00 O 4048 8.00 N 3552 7.00 C 14160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 795.4 milliseconds 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5152 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 15 sheets defined 72.0% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 5 through 36 removed outlier: 3.533A pdb=" N GLU A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 64 removed outlier: 3.616A pdb=" N ALA A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 64 " --> pdb=" O PHE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 86 removed outlier: 3.971A pdb=" N GLN A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 76 " --> pdb=" O ASN A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 99 removed outlier: 3.957A pdb=" N VAL A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 removed outlier: 3.535A pdb=" N GLU A 112 " --> pdb=" O HIS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 127 removed outlier: 4.611A pdb=" N ALA A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'B' and resid 5 through 36 removed outlier: 3.584A pdb=" N GLN B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 63 removed outlier: 3.583A pdb=" N LEU B 44 " --> pdb=" O ASN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 86 removed outlier: 3.799A pdb=" N GLN B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY B 76 " --> pdb=" O ASN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'B' and resid 100 through 112 Processing helix chain 'B' and resid 114 through 127 removed outlier: 4.542A pdb=" N ALA B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'C' and resid 5 through 35 removed outlier: 3.679A pdb=" N GLU C 31 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 63 removed outlier: 3.630A pdb=" N LEU C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 86 Processing helix chain 'C' and resid 86 through 99 removed outlier: 3.792A pdb=" N VAL C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 112 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 116 through 127 removed outlier: 3.633A pdb=" N LEU C 120 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'D' and resid 5 through 35 removed outlier: 3.590A pdb=" N GLN D 35 " --> pdb=" O GLU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 63 removed outlier: 3.998A pdb=" N ALA D 42 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS D 43 " --> pdb=" O PRO D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 86 Processing helix chain 'D' and resid 86 through 99 removed outlier: 3.796A pdb=" N VAL D 90 " --> pdb=" O GLU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 114 Processing helix chain 'D' and resid 115 through 128 removed outlier: 4.457A pdb=" N GLU D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'E' and resid 5 through 36 removed outlier: 3.578A pdb=" N GLU E 31 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 64 removed outlier: 3.893A pdb=" N ALA E 42 " --> pdb=" O PHE E 38 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS E 43 " --> pdb=" O PRO E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 86 removed outlier: 4.489A pdb=" N GLN E 74 " --> pdb=" O PRO E 70 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N MET E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY E 76 " --> pdb=" O ASN E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 99 removed outlier: 3.677A pdb=" N VAL E 90 " --> pdb=" O GLU E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 114 removed outlier: 3.503A pdb=" N GLU E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA E 113 " --> pdb=" O TYR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 128 removed outlier: 4.234A pdb=" N GLU E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 167 Processing helix chain 'F' and resid 5 through 35 Processing helix chain 'F' and resid 39 through 63 removed outlier: 3.993A pdb=" N LYS F 43 " --> pdb=" O PRO F 39 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU F 44 " --> pdb=" O ASN F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 86 removed outlier: 3.762A pdb=" N GLN F 74 " --> pdb=" O PRO F 70 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY F 76 " --> pdb=" O ASN F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 99 removed outlier: 3.718A pdb=" N VAL F 90 " --> pdb=" O GLU F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 112 removed outlier: 3.610A pdb=" N VAL F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU F 112 " --> pdb=" O HIS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 129 removed outlier: 4.239A pdb=" N ALA F 118 " --> pdb=" O GLU F 114 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 167 removed outlier: 3.645A pdb=" N PHE F 167 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 36 removed outlier: 3.537A pdb=" N GLU G 31 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS G 32 " --> pdb=" O ILE G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 63 removed outlier: 3.740A pdb=" N LEU G 44 " --> pdb=" O ASN G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 86 Processing helix chain 'G' and resid 86 through 99 removed outlier: 3.772A pdb=" N VAL G 90 " --> pdb=" O GLU G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 114 removed outlier: 3.566A pdb=" N VAL G 104 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU G 112 " --> pdb=" O HIS G 108 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA G 113 " --> pdb=" O TYR G 109 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 129 removed outlier: 4.351A pdb=" N ALA G 118 " --> pdb=" O GLU G 114 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU G 119 " --> pdb=" O LYS G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 167 Processing helix chain 'H' and resid 5 through 35 removed outlier: 3.657A pdb=" N GLN H 35 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 64 removed outlier: 3.599A pdb=" N ALA H 42 " --> pdb=" O PHE H 38 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS H 43 " --> pdb=" O PRO H 39 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY H 64 " --> pdb=" O PHE H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 86 Processing helix chain 'H' and resid 86 through 99 removed outlier: 3.556A pdb=" N VAL H 90 " --> pdb=" O GLU H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 114 Processing helix chain 'H' and resid 115 through 126 removed outlier: 4.454A pdb=" N GLU H 119 " --> pdb=" O LYS H 115 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU H 126 " --> pdb=" O ARG H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 167 Processing helix chain 'I' and resid 5 through 36 Processing helix chain 'I' and resid 38 through 64 removed outlier: 4.111A pdb=" N ALA I 42 " --> pdb=" O PHE I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 86 removed outlier: 3.786A pdb=" N GLN I 74 " --> pdb=" O PRO I 70 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET I 75 " --> pdb=" O GLU I 71 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY I 76 " --> pdb=" O ASN I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 99 removed outlier: 3.953A pdb=" N VAL I 90 " --> pdb=" O GLU I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 114 removed outlier: 3.545A pdb=" N ALA I 113 " --> pdb=" O TYR I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 128 removed outlier: 4.580A pdb=" N ALA I 118 " --> pdb=" O GLU I 114 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU I 119 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 167 Processing helix chain 'J' and resid 5 through 36 Processing helix chain 'J' and resid 40 through 64 removed outlier: 3.784A pdb=" N LEU J 44 " --> pdb=" O ASN J 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY J 64 " --> pdb=" O PHE J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 86 removed outlier: 3.895A pdb=" N GLN J 74 " --> pdb=" O PRO J 70 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY J 76 " --> pdb=" O ASN J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 99 removed outlier: 3.895A pdb=" N VAL J 90 " --> pdb=" O GLU J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 112 Processing helix chain 'J' and resid 115 through 127 removed outlier: 4.631A pdb=" N GLU J 119 " --> pdb=" O LYS J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 167 removed outlier: 3.536A pdb=" N LYS J 166 " --> pdb=" O PRO J 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 36 removed outlier: 3.554A pdb=" N GLU K 31 " --> pdb=" O LEU K 27 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU K 36 " --> pdb=" O LYS K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 64 removed outlier: 3.705A pdb=" N ALA K 42 " --> pdb=" O PHE K 38 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS K 43 " --> pdb=" O PRO K 39 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU K 44 " --> pdb=" O ASN K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 86 Processing helix chain 'K' and resid 86 through 99 Processing helix chain 'K' and resid 100 through 112 Processing helix chain 'K' and resid 115 through 129 removed outlier: 4.291A pdb=" N GLU K 119 " --> pdb=" O LYS K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 167 removed outlier: 3.797A pdb=" N LYS K 166 " --> pdb=" O PRO K 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 36 removed outlier: 3.625A pdb=" N GLN L 35 " --> pdb=" O GLU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 63 removed outlier: 3.609A pdb=" N ALA L 42 " --> pdb=" O PHE L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 86 Processing helix chain 'L' and resid 86 through 99 removed outlier: 3.916A pdb=" N VAL L 90 " --> pdb=" O GLU L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 114 Processing helix chain 'L' and resid 116 through 127 Processing helix chain 'L' and resid 163 through 167 Processing helix chain 'M' and resid 5 through 36 Processing helix chain 'M' and resid 38 through 64 removed outlier: 3.773A pdb=" N ALA M 42 " --> pdb=" O PHE M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 86 removed outlier: 3.945A pdb=" N GLN M 74 " --> pdb=" O PRO M 70 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET M 75 " --> pdb=" O GLU M 71 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY M 76 " --> pdb=" O ASN M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 99 removed outlier: 3.632A pdb=" N VAL M 90 " --> pdb=" O GLU M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 112 removed outlier: 3.727A pdb=" N VAL M 104 " --> pdb=" O GLU M 100 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU M 112 " --> pdb=" O HIS M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 129 removed outlier: 4.374A pdb=" N ALA M 118 " --> pdb=" O GLU M 114 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU M 119 " --> pdb=" O LYS M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 167 Processing helix chain 'N' and resid 5 through 36 Processing helix chain 'N' and resid 40 through 63 removed outlier: 3.922A pdb=" N LEU N 44 " --> pdb=" O ASN N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 68 through 86 removed outlier: 3.917A pdb=" N GLN N 74 " --> pdb=" O PRO N 70 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET N 75 " --> pdb=" O GLU N 71 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY N 76 " --> pdb=" O ASN N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 99 Processing helix chain 'N' and resid 101 through 112 removed outlier: 3.590A pdb=" N GLU N 112 " --> pdb=" O HIS N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 114 through 128 removed outlier: 4.248A pdb=" N ALA N 118 " --> pdb=" O GLU N 114 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU N 119 " --> pdb=" O LYS N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 163 through 167 Processing helix chain 'O' and resid 5 through 36 removed outlier: 3.815A pdb=" N GLU O 31 " --> pdb=" O LEU O 27 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS O 32 " --> pdb=" O ILE O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 63 removed outlier: 3.950A pdb=" N LEU O 44 " --> pdb=" O ASN O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 86 Processing helix chain 'O' and resid 86 through 99 removed outlier: 3.609A pdb=" N VAL O 90 " --> pdb=" O GLU O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 112 removed outlier: 3.677A pdb=" N GLU O 112 " --> pdb=" O HIS O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 114 through 129 removed outlier: 4.427A pdb=" N ALA O 118 " --> pdb=" O GLU O 114 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU O 119 " --> pdb=" O LYS O 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 35 removed outlier: 3.662A pdb=" N GLN P 35 " --> pdb=" O GLU P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 63 removed outlier: 4.133A pdb=" N ALA P 42 " --> pdb=" O PHE P 38 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS P 43 " --> pdb=" O PRO P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 86 Processing helix chain 'P' and resid 86 through 99 removed outlier: 3.677A pdb=" N VAL P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 114 Processing helix chain 'P' and resid 114 through 127 removed outlier: 4.570A pdb=" N ALA P 118 " --> pdb=" O GLU P 114 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU P 119 " --> pdb=" O LYS P 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 167 Processing sheet with id=AA1, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.739A pdb=" N VAL B 139 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 141 " --> pdb=" O VAL B 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 148 through 149 Processing sheet with id=AA3, first strand: chain 'D' and resid 148 through 149 Processing sheet with id=AA4, first strand: chain 'E' and resid 139 through 141 Processing sheet with id=AA5, first strand: chain 'F' and resid 148 through 149 Processing sheet with id=AA6, first strand: chain 'G' and resid 139 through 141 Processing sheet with id=AA7, first strand: chain 'H' and resid 139 through 141 Processing sheet with id=AA8, first strand: chain 'I' and resid 148 through 149 removed outlier: 3.608A pdb=" N VAL I 139 " --> pdb=" O PHE I 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 148 through 149 Processing sheet with id=AB1, first strand: chain 'K' and resid 148 through 149 Processing sheet with id=AB2, first strand: chain 'L' and resid 139 through 141 removed outlier: 4.050A pdb=" N VAL L 139 " --> pdb=" O PHE L 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 148 through 150 Processing sheet with id=AB4, first strand: chain 'N' and resid 139 through 141 removed outlier: 3.559A pdb=" N VAL N 139 " --> pdb=" O PHE N 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 139 through 141 Processing sheet with id=AB6, first strand: chain 'P' and resid 139 through 141 1486 hydrogen bonds defined for protein. 4296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.60 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6993 1.34 - 1.46: 4875 1.46 - 1.58: 10292 1.58 - 1.70: 0 1.70 - 1.82: 256 Bond restraints: 22416 Sorted by residual: bond pdb=" N ILE D 144 " pdb=" CA ILE D 144 " ideal model delta sigma weight residual 1.457 1.499 -0.043 9.30e-03 1.16e+04 2.09e+01 bond pdb=" N ILE A 144 " pdb=" CA ILE A 144 " ideal model delta sigma weight residual 1.460 1.498 -0.038 8.60e-03 1.35e+04 1.98e+01 bond pdb=" N ILE C 144 " pdb=" CA ILE C 144 " ideal model delta sigma weight residual 1.455 1.499 -0.044 1.04e-02 9.25e+03 1.75e+01 bond pdb=" N ILE M 144 " pdb=" CA ILE M 144 " ideal model delta sigma weight residual 1.455 1.499 -0.044 1.06e-02 8.90e+03 1.70e+01 bond pdb=" N VAL G 84 " pdb=" CA VAL G 84 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.07e-02 8.73e+03 1.70e+01 ... (remaining 22411 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 29210 1.93 - 3.86: 775 3.86 - 5.80: 97 5.80 - 7.73: 12 7.73 - 9.66: 2 Bond angle restraints: 30096 Sorted by residual: angle pdb=" N LEU M 111 " pdb=" CA LEU M 111 " pdb=" C LEU M 111 " ideal model delta sigma weight residual 113.28 106.45 6.83 1.22e+00 6.72e-01 3.14e+01 angle pdb=" C GLY H 146 " pdb=" N TYR H 147 " pdb=" CA TYR H 147 " ideal model delta sigma weight residual 123.05 115.72 7.33 1.40e+00 5.10e-01 2.74e+01 angle pdb=" N LYS H 127 " pdb=" CA LYS H 127 " pdb=" C LYS H 127 " ideal model delta sigma weight residual 114.64 106.83 7.81 1.52e+00 4.33e-01 2.64e+01 angle pdb=" N GLU C 129 " pdb=" CA GLU C 129 " pdb=" C GLU C 129 " ideal model delta sigma weight residual 112.97 107.71 5.26 1.06e+00 8.90e-01 2.46e+01 angle pdb=" N GLU D 129 " pdb=" CA GLU D 129 " pdb=" C GLU D 129 " ideal model delta sigma weight residual 114.31 107.95 6.36 1.29e+00 6.01e-01 2.43e+01 ... (remaining 30091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 11319 17.96 - 35.91: 1667 35.91 - 53.87: 488 53.87 - 71.82: 113 71.82 - 89.78: 45 Dihedral angle restraints: 13632 sinusoidal: 5616 harmonic: 8016 Sorted by residual: dihedral pdb=" CA CYS I 145 " pdb=" C CYS I 145 " pdb=" N GLY I 146 " pdb=" CA GLY I 146 " ideal model delta harmonic sigma weight residual -180.00 -150.27 -29.73 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA CYS P 145 " pdb=" C CYS P 145 " pdb=" N GLY P 146 " pdb=" CA GLY P 146 " ideal model delta harmonic sigma weight residual -180.00 -153.42 -26.58 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA CYS E 145 " pdb=" C CYS E 145 " pdb=" N GLY E 146 " pdb=" CA GLY E 146 " ideal model delta harmonic sigma weight residual -180.00 -157.39 -22.61 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 13629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2562 0.056 - 0.112: 454 0.112 - 0.169: 105 0.169 - 0.225: 28 0.225 - 0.281: 3 Chirality restraints: 3152 Sorted by residual: chirality pdb=" CA ILE C 136 " pdb=" N ILE C 136 " pdb=" C ILE C 136 " pdb=" CB ILE C 136 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA ILE D 116 " pdb=" N ILE D 116 " pdb=" C ILE D 116 " pdb=" CB ILE D 116 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA VAL D 150 " pdb=" N VAL D 150 " pdb=" C VAL D 150 " pdb=" CB VAL D 150 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 3149 not shown) Planarity restraints: 3888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA L 149 " -0.015 2.00e-02 2.50e+03 3.10e-02 9.58e+00 pdb=" C ALA L 149 " 0.054 2.00e-02 2.50e+03 pdb=" O ALA L 149 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL L 150 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 82 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C PHE G 82 " 0.042 2.00e-02 2.50e+03 pdb=" O PHE G 82 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU G 83 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE F 38 " -0.038 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO F 39 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO F 39 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 39 " -0.032 5.00e-02 4.00e+02 ... (remaining 3885 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 37 2.08 - 2.78: 5048 2.78 - 3.49: 30565 3.49 - 4.19: 47704 4.19 - 4.90: 90779 Nonbonded interactions: 174133 Sorted by model distance: nonbonded pdb=" OE2 GLU H 52 " pdb="FE FE H 201 " model vdw 1.372 3.000 nonbonded pdb=" OE1 GLU H 114 " pdb="FE FE H 203 " model vdw 1.629 3.000 nonbonded pdb=" OE2 GLU L 52 " pdb="FE FE L 201 " model vdw 1.718 3.000 nonbonded pdb="FE FE M 202 " pdb="FE FE M 203 " model vdw 1.786 2.960 nonbonded pdb=" OE2 GLU H 114 " pdb="FE FE G 203 " model vdw 1.787 3.000 ... (remaining 174128 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 202) selection = (chain 'B' and resid 1 through 202) selection = chain 'C' selection = (chain 'D' and resid 1 through 202) selection = (chain 'E' and resid 1 through 202) selection = (chain 'F' and resid 1 through 202) selection = (chain 'G' and resid 1 through 202) selection = (chain 'H' and resid 1 through 202) selection = chain 'I' selection = (chain 'J' and resid 1 through 202) selection = (chain 'K' and resid 1 through 202) selection = (chain 'L' and resid 1 through 202) selection = (chain 'M' and resid 1 through 202) selection = chain 'N' selection = chain 'O' selection = (chain 'P' and resid 1 through 202) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.380 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 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 : 0.004 0.051 22416 Z= 0.296 Angle : 0.666 9.660 30096 Z= 0.427 Chirality : 0.049 0.281 3152 Planarity : 0.005 0.058 3888 Dihedral : 19.111 89.776 8480 Min Nonbonded Distance : 1.372 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.67 % Allowed : 4.29 % Favored : 95.04 % Rotamer: Outliers : 3.69 % Allowed : 25.09 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.17), residues: 2704 helix: 2.55 (0.12), residues: 1760 sheet: None (None), residues: 0 loop : -1.22 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 46 TYR 0.021 0.001 TYR O 147 PHE 0.013 0.001 PHE D 97 HIS 0.004 0.001 HIS N 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.30 (22416) covalent geometry : angle 0.66644 / 0.43 (30096) hydrogen bonds : bond 0.13946 / 9.14 ( 1486) hydrogen bonds : angle 4.22163 / 2.97 ( 4296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 513 time to evaluate : 0.728 Fit side-chains REVERT: B 35 GLN cc_start: 0.7736 (pp30) cc_final: 0.7520 (pp30) REVERT: C 4 LYS cc_start: 0.7679 (mtpp) cc_final: 0.7012 (mtmm) REVERT: C 98 GLN cc_start: 0.7147 (mt0) cc_final: 0.6478 (mm-40) REVERT: F 1 MET cc_start: 0.5690 (tpp) cc_final: 0.5371 (ptt) REVERT: F 152 GLU cc_start: 0.6953 (pm20) cc_final: 0.6692 (pm20) REVERT: H 104 VAL cc_start: 0.8087 (t) cc_final: 0.7675 (m) REVERT: H 127 LYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6621 (ttpp) REVERT: I 1 MET cc_start: 0.3025 (pmm) cc_final: 0.1306 (mtt) REVERT: I 150 VAL cc_start: 0.6686 (OUTLIER) cc_final: 0.6430 (t) REVERT: J 40 ASN cc_start: 0.6003 (t0) cc_final: 0.5718 (t0) REVERT: J 48 ILE cc_start: 0.7761 (mt) cc_final: 0.7477 (mt) REVERT: J 133 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.6617 (t0) REVERT: K 1 MET cc_start: 0.3789 (pmm) cc_final: 0.2620 (ttp) REVERT: K 71 GLU cc_start: 0.7320 (mm-30) cc_final: 0.6693 (tm-30) REVERT: K 78 GLU cc_start: 0.7188 (tm-30) cc_final: 0.5968 (mt-10) REVERT: K 126 GLU cc_start: 0.7890 (tp30) cc_final: 0.7574 (pt0) REVERT: K 165 GLU cc_start: 0.7417 (pp20) cc_final: 0.6990 (pp20) REVERT: K 169 VAL cc_start: 0.7005 (m) cc_final: 0.6792 (t) REVERT: L 140 TYR cc_start: 0.7452 (m-80) cc_final: 0.6987 (m-80) REVERT: M 81 THR cc_start: 0.8481 (m) cc_final: 0.8095 (p) REVERT: M 111 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7105 (pp) REVERT: N 96 GLU cc_start: 0.6628 (mt-10) cc_final: 0.6334 (mt-10) REVERT: N 105 ARG cc_start: 0.7919 (ttp80) cc_final: 0.7681 (ttp80) REVERT: N 164 LYS cc_start: 0.7321 (tptp) cc_final: 0.7086 (tptt) REVERT: O 34 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6692 (tt0) REVERT: O 71 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7167 (mp0) REVERT: O 78 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6995 (mm-30) REVERT: P 134 ILE cc_start: 0.7438 (pt) cc_final: 0.7167 (tt) outliers start: 82 outliers final: 17 residues processed: 567 average time/residue: 0.1575 time to fit residues: 135.0305 Evaluate side-chains 337 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 316 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 127 LYS Chi-restraints excluded: chain H residue 147 TYR Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain J residue 133 ASP Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain K residue 144 ILE Chi-restraints excluded: chain K residue 147 TYR Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain P residue 169 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 108 HIS C 92 ASN E 72 ASN F 58 ASN G 58 ASN K 40 ASN K 98 GLN M 55 HIS ** N 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 ASN N 98 GLN N 117 HIS ** O 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.150769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.121402 restraints weight = 32972.690| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.48 r_work: 0.3684 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22416 Z= 0.171 Angle : 0.622 9.400 30096 Z= 0.331 Chirality : 0.043 0.164 3152 Planarity : 0.005 0.055 3888 Dihedral : 5.626 96.286 2987 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.29 % Favored : 96.56 % Rotamer: Outliers : 4.09 % Allowed : 24.96 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.16), residues: 2704 helix: 2.40 (0.12), residues: 1792 sheet: -2.72 (0.38), residues: 144 loop : -1.53 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 105 TYR 0.017 0.002 TYR D 91 PHE 0.022 0.002 PHE M 97 HIS 0.009 0.001 HIS J 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (22416) covalent geometry : angle 0.62244 / 0.33 (30096) hydrogen bonds : bond 0.04595 / 3.10 ( 1486) hydrogen bonds : angle 3.47464 / 2.46 ( 4296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 356 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6496 (mt-10) REVERT: A 75 MET cc_start: 0.7261 (tpp) cc_final: 0.6917 (ttm) REVERT: A 91 TYR cc_start: 0.6443 (m-10) cc_final: 0.5869 (m-10) REVERT: A 111 LEU cc_start: 0.7709 (pp) cc_final: 0.7446 (tp) REVERT: A 157 CYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7799 (t) REVERT: B 14 GLU cc_start: 0.6494 (tm-30) cc_final: 0.5966 (tt0) REVERT: B 71 GLU cc_start: 0.7469 (tp30) cc_final: 0.6541 (tm-30) REVERT: B 144 ILE cc_start: 0.7616 (tt) cc_final: 0.7414 (pt) REVERT: C 4 LYS cc_start: 0.8123 (mtpp) cc_final: 0.7431 (mtmm) REVERT: C 9 LYS cc_start: 0.7764 (ttpp) cc_final: 0.7311 (tptt) REVERT: C 145 CYS cc_start: 0.7600 (p) cc_final: 0.7282 (p) REVERT: D 145 CYS cc_start: 0.7711 (p) cc_final: 0.7404 (p) REVERT: D 151 ASP cc_start: 0.6488 (m-30) cc_final: 0.6193 (m-30) REVERT: E 36 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6410 (mt-10) REVERT: F 9 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7104 (mttt) REVERT: F 54 VAL cc_start: 0.7713 (t) cc_final: 0.7499 (p) REVERT: F 166 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7237 (mtpt) REVERT: G 26 TYR cc_start: 0.7368 (m-10) cc_final: 0.7107 (m-80) REVERT: H 87 MET cc_start: 0.7474 (ttm) cc_final: 0.7066 (ttp) REVERT: H 101 LYS cc_start: 0.8770 (mmmm) cc_final: 0.8501 (mmtt) REVERT: I 21 MET cc_start: 0.8084 (mtp) cc_final: 0.7640 (mtm) REVERT: I 24 MET cc_start: 0.8186 (tpp) cc_final: 0.7752 (tpp) REVERT: I 75 MET cc_start: 0.5775 (ttt) cc_final: 0.5449 (mtp) REVERT: J 152 GLU cc_start: 0.7731 (pm20) cc_final: 0.7424 (tt0) REVERT: J 165 GLU cc_start: 0.7295 (pm20) cc_final: 0.6980 (pm20) REVERT: K 1 MET cc_start: 0.4151 (pmm) cc_final: 0.2796 (mmm) REVERT: K 75 MET cc_start: 0.6364 (ttt) cc_final: 0.6092 (ttp) REVERT: K 126 GLU cc_start: 0.8014 (tp30) cc_final: 0.7668 (pt0) REVERT: L 105 ARG cc_start: 0.7580 (ttm170) cc_final: 0.7257 (ttp-170) REVERT: M 81 THR cc_start: 0.8555 (m) cc_final: 0.7995 (p) REVERT: N 63 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.5909 (mp) REVERT: N 111 LEU cc_start: 0.5879 (OUTLIER) cc_final: 0.5629 (pt) REVERT: N 121 TYR cc_start: 0.7703 (m-10) cc_final: 0.7494 (m-80) REVERT: O 1 MET cc_start: 0.6556 (pmm) cc_final: 0.6257 (pmm) REVERT: O 34 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7214 (tt0) REVERT: O 35 GLN cc_start: 0.5913 (tt0) cc_final: 0.5335 (mt0) REVERT: O 71 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7470 (mt-10) REVERT: P 63 LEU cc_start: 0.5771 (OUTLIER) cc_final: 0.5419 (mp) REVERT: P 87 MET cc_start: 0.7525 (mtp) cc_final: 0.7265 (mtm) REVERT: P 157 CYS cc_start: 0.7919 (t) cc_final: 0.7515 (t) outliers start: 91 outliers final: 42 residues processed: 427 average time/residue: 0.1421 time to fit residues: 96.0841 Evaluate side-chains 350 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 301 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 9 LYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 166 LYS Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 145 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain K residue 144 ILE Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 111 LEU Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 20 SER Chi-restraints excluded: chain O residue 150 VAL Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 133 ASP Chi-restraints excluded: chain P residue 169 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 200 optimal weight: 0.6980 chunk 150 optimal weight: 0.8980 chunk 156 optimal weight: 0.0980 chunk 229 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 GLN E 72 ASN K 40 ASN N 40 ASN O 40 ASN O 98 GLN P 40 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.151936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.121375 restraints weight = 32914.714| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.68 r_work: 0.3697 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 22416 Z= 0.107 Angle : 0.488 8.310 30096 Z= 0.252 Chirality : 0.040 0.160 3152 Planarity : 0.004 0.056 3888 Dihedral : 4.548 52.949 2966 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.51 % Favored : 96.41 % Rotamer: Outliers : 3.24 % Allowed : 25.13 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.17), residues: 2704 helix: 2.70 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -0.56 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 105 TYR 0.019 0.001 TYR K 91 PHE 0.020 0.001 PHE I 97 HIS 0.006 0.001 HIS H 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (22416) covalent geometry : angle 0.48803 / 0.25 (30096) hydrogen bonds : bond 0.03644 / 2.43 ( 1486) hydrogen bonds : angle 3.10654 / 2.20 ( 4296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 308 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6439 (mt-10) REVERT: A 21 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7535 (mtm) REVERT: A 24 MET cc_start: 0.7430 (tpp) cc_final: 0.7193 (mmp) REVERT: A 75 MET cc_start: 0.7309 (tpp) cc_final: 0.7082 (ttm) REVERT: A 91 TYR cc_start: 0.6479 (m-10) cc_final: 0.5961 (m-10) REVERT: A 111 LEU cc_start: 0.7778 (pp) cc_final: 0.7400 (tp) REVERT: B 14 GLU cc_start: 0.6733 (tm-30) cc_final: 0.6064 (tt0) REVERT: B 71 GLU cc_start: 0.7541 (tp30) cc_final: 0.6539 (tm-30) REVERT: B 75 MET cc_start: 0.6234 (mtm) cc_final: 0.5985 (mtm) REVERT: B 87 MET cc_start: 0.6740 (ttm) cc_final: 0.6331 (ttp) REVERT: B 98 GLN cc_start: 0.6549 (OUTLIER) cc_final: 0.3675 (mp-120) REVERT: B 151 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7223 (p0) REVERT: C 9 LYS cc_start: 0.7742 (ttpp) cc_final: 0.7180 (tptt) REVERT: C 87 MET cc_start: 0.8802 (ttt) cc_final: 0.8580 (ttm) REVERT: D 145 CYS cc_start: 0.7729 (p) cc_final: 0.7390 (p) REVERT: D 151 ASP cc_start: 0.6577 (m-30) cc_final: 0.6295 (m-30) REVERT: E 36 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6338 (mt-10) REVERT: E 127 LYS cc_start: 0.7717 (mmtm) cc_final: 0.7400 (mmtm) REVERT: F 1 MET cc_start: 0.5042 (tpp) cc_final: 0.4246 (tmm) REVERT: F 9 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.7059 (mttt) REVERT: F 101 LYS cc_start: 0.8013 (mmtt) cc_final: 0.7789 (mmmt) REVERT: F 102 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6308 (mp0) REVERT: G 26 TYR cc_start: 0.7373 (m-10) cc_final: 0.7164 (m-80) REVERT: G 130 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6918 (ptpp) REVERT: H 116 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7140 (tp) REVERT: I 21 MET cc_start: 0.8156 (mtp) cc_final: 0.7873 (mtm) REVERT: I 24 MET cc_start: 0.8247 (tpp) cc_final: 0.7716 (tpp) REVERT: I 75 MET cc_start: 0.5741 (ttt) cc_final: 0.5463 (mtp) REVERT: I 83 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6743 (mt-10) REVERT: J 109 TYR cc_start: 0.7571 (m-10) cc_final: 0.7370 (m-10) REVERT: J 152 GLU cc_start: 0.7720 (pm20) cc_final: 0.7437 (mp0) REVERT: J 165 GLU cc_start: 0.7305 (pm20) cc_final: 0.6910 (pm20) REVERT: K 1 MET cc_start: 0.4105 (pmm) cc_final: 0.2872 (mmm) REVERT: M 21 MET cc_start: 0.7479 (mtm) cc_final: 0.7214 (mtm) REVERT: M 96 GLU cc_start: 0.7922 (tp30) cc_final: 0.7690 (tp30) REVERT: M 157 CYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7302 (t) REVERT: N 111 LEU cc_start: 0.6044 (OUTLIER) cc_final: 0.5736 (pt) REVERT: O 1 MET cc_start: 0.6577 (pmm) cc_final: 0.6289 (pmm) REVERT: O 7 MET cc_start: 0.7052 (tpt) cc_final: 0.6577 (tpt) REVERT: O 40 ASN cc_start: 0.6423 (OUTLIER) cc_final: 0.5686 (t0) REVERT: O 71 GLU cc_start: 0.7683 (mm-30) cc_final: 0.6811 (tm-30) REVERT: P 63 LEU cc_start: 0.5879 (OUTLIER) cc_final: 0.5528 (mp) REVERT: P 75 MET cc_start: 0.7343 (mtm) cc_final: 0.7139 (ttp) REVERT: P 157 CYS cc_start: 0.8053 (t) cc_final: 0.7542 (t) outliers start: 72 outliers final: 35 residues processed: 362 average time/residue: 0.1334 time to fit residues: 77.8107 Evaluate side-chains 335 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 287 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain F residue 9 LYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 145 CYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 87 MET Chi-restraints excluded: chain K residue 144 ILE Chi-restraints excluded: chain K residue 147 TYR Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 157 CYS Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 40 ASN Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 111 LEU Chi-restraints excluded: chain O residue 40 ASN Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 133 ASP Chi-restraints excluded: chain P residue 169 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 20 optimal weight: 7.9990 chunk 181 optimal weight: 9.9990 chunk 201 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 202 optimal weight: 0.0010 chunk 97 optimal weight: 0.3980 chunk 121 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 overall best weight: 1.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 98 GLN K 40 ASN N 40 ASN N 98 GLN O 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.149515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.119592 restraints weight = 32864.262| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.69 r_work: 0.3634 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.6120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 22416 Z= 0.129 Angle : 0.506 7.928 30096 Z= 0.266 Chirality : 0.041 0.186 3152 Planarity : 0.004 0.053 3888 Dihedral : 4.433 55.304 2960 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.71 % Rotamer: Outliers : 3.55 % Allowed : 25.63 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.17), residues: 2704 helix: 2.75 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -0.57 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 122 TYR 0.027 0.001 TYR K 91 PHE 0.015 0.001 PHE I 60 HIS 0.005 0.001 HIS F 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (22416) covalent geometry : angle 0.50592 / 0.27 (30096) hydrogen bonds : bond 0.04143 / 2.78 ( 1486) hydrogen bonds : angle 3.13859 / 2.22 ( 4296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 302 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6538 (mt-10) REVERT: A 75 MET cc_start: 0.7340 (tpp) cc_final: 0.6919 (ttm) REVERT: A 91 TYR cc_start: 0.6969 (m-10) cc_final: 0.6482 (m-10) REVERT: A 111 LEU cc_start: 0.7832 (pp) cc_final: 0.7279 (tp) REVERT: B 14 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6400 (tt0) REVERT: B 71 GLU cc_start: 0.7563 (tp30) cc_final: 0.6755 (tm-30) REVERT: B 75 MET cc_start: 0.6287 (mtm) cc_final: 0.5979 (mtm) REVERT: B 87 MET cc_start: 0.7043 (ttm) cc_final: 0.6521 (ttp) REVERT: D 145 CYS cc_start: 0.7939 (p) cc_final: 0.7658 (p) REVERT: E 36 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6379 (mt-10) REVERT: E 75 MET cc_start: 0.6550 (ttm) cc_final: 0.6198 (ttm) REVERT: E 88 TYR cc_start: 0.8960 (OUTLIER) cc_final: 0.8366 (m-10) REVERT: E 127 LYS cc_start: 0.7501 (mmtm) cc_final: 0.6887 (tttp) REVERT: F 40 ASN cc_start: 0.8443 (m-40) cc_final: 0.8203 (m-40) REVERT: F 101 LYS cc_start: 0.8168 (mmtt) cc_final: 0.7898 (mmmt) REVERT: G 21 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.6944 (mtp) REVERT: G 26 TYR cc_start: 0.7775 (m-10) cc_final: 0.7540 (m-80) REVERT: H 81 THR cc_start: 0.7618 (m) cc_final: 0.7264 (p) REVERT: H 98 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8022 (mt0) REVERT: H 127 LYS cc_start: 0.7737 (mtpp) cc_final: 0.7384 (ttmt) REVERT: I 7 MET cc_start: 0.7283 (mmm) cc_final: 0.7060 (mmt) REVERT: I 21 MET cc_start: 0.8361 (mtp) cc_final: 0.8056 (mtm) REVERT: I 75 MET cc_start: 0.5867 (ttt) cc_final: 0.5562 (mtp) REVERT: J 75 MET cc_start: 0.7134 (ttm) cc_final: 0.6921 (mtp) REVERT: J 152 GLU cc_start: 0.7792 (pm20) cc_final: 0.7556 (mp0) REVERT: J 165 GLU cc_start: 0.7319 (pm20) cc_final: 0.6939 (pm20) REVERT: K 1 MET cc_start: 0.4200 (pmm) cc_final: 0.3037 (mmm) REVERT: K 122 ARG cc_start: 0.6220 (ptp-110) cc_final: 0.5819 (mtm110) REVERT: K 137 LYS cc_start: 0.7952 (mmmm) cc_final: 0.7741 (mmmt) REVERT: M 21 MET cc_start: 0.7531 (mtm) cc_final: 0.7255 (mtm) REVERT: M 157 CYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7723 (t) REVERT: N 24 MET cc_start: 0.7999 (tpp) cc_final: 0.7706 (mmt) REVERT: N 40 ASN cc_start: 0.7581 (OUTLIER) cc_final: 0.6613 (t0) REVERT: N 63 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6233 (mt) REVERT: N 111 LEU cc_start: 0.6258 (OUTLIER) cc_final: 0.5864 (pt) REVERT: O 1 MET cc_start: 0.6769 (pmm) cc_final: 0.6416 (pmm) REVERT: O 71 GLU cc_start: 0.7816 (mm-30) cc_final: 0.6805 (tm-30) REVERT: O 75 MET cc_start: 0.5109 (ttt) cc_final: 0.4901 (ttt) REVERT: O 78 GLU cc_start: 0.8085 (pt0) cc_final: 0.7840 (pt0) REVERT: P 21 MET cc_start: 0.7118 (mpp) cc_final: 0.6902 (mmm) REVERT: P 63 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5701 (mp) REVERT: P 157 CYS cc_start: 0.8334 (t) cc_final: 0.7819 (t) outliers start: 79 outliers final: 43 residues processed: 358 average time/residue: 0.1313 time to fit residues: 75.1426 Evaluate side-chains 323 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 271 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 88 TYR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 145 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 9 LYS Chi-restraints excluded: chain H residue 98 GLN Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 144 ILE Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain L residue 136 ILE Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 157 CYS Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 40 ASN Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 111 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 133 ASP Chi-restraints excluded: chain P residue 169 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 110 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 138 optimal weight: 0.5980 chunk 259 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 224 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 35 GLN H 98 GLN J 98 GLN K 40 ASN N 40 ASN O 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.155359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.127916 restraints weight = 31538.773| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.04 r_work: 0.3717 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.6567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22416 Z= 0.113 Angle : 0.474 6.797 30096 Z= 0.248 Chirality : 0.040 0.173 3152 Planarity : 0.004 0.051 3888 Dihedral : 4.138 53.250 2953 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.14 % Favored : 96.82 % Rotamer: Outliers : 3.10 % Allowed : 26.21 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.17), residues: 2704 helix: 2.81 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -0.54 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 46 TYR 0.012 0.001 TYR B 91 PHE 0.014 0.001 PHE A 60 HIS 0.004 0.001 HIS H 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (22416) covalent geometry : angle 0.47413 / 0.25 (30096) hydrogen bonds : bond 0.03704 / 2.48 ( 1486) hydrogen bonds : angle 3.06447 / 2.17 ( 4296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 286 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7185 (mt-10) REVERT: A 21 MET cc_start: 0.8216 (ttp) cc_final: 0.7824 (mtm) REVERT: A 75 MET cc_start: 0.7661 (tpp) cc_final: 0.7311 (ttm) REVERT: A 91 TYR cc_start: 0.7407 (m-10) cc_final: 0.6877 (m-10) REVERT: B 14 GLU cc_start: 0.7794 (tm-30) cc_final: 0.6950 (tt0) REVERT: B 71 GLU cc_start: 0.7796 (tp30) cc_final: 0.7037 (tm-30) REVERT: B 75 MET cc_start: 0.6780 (mtm) cc_final: 0.6501 (mtm) REVERT: B 87 MET cc_start: 0.7767 (ttm) cc_final: 0.7432 (ttp) REVERT: D 152 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7288 (mm-30) REVERT: E 36 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6384 (mt-10) REVERT: E 75 MET cc_start: 0.6984 (ttm) cc_final: 0.6585 (ttm) REVERT: E 88 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8388 (m-10) REVERT: E 127 LYS cc_start: 0.7731 (mmtm) cc_final: 0.7051 (tttp) REVERT: F 1 MET cc_start: 0.5043 (tpp) cc_final: 0.3897 (tmm) REVERT: F 101 LYS cc_start: 0.8044 (mmtt) cc_final: 0.7843 (mmmt) REVERT: F 102 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.6654 (mp0) REVERT: G 21 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7392 (mtp) REVERT: G 26 TYR cc_start: 0.8062 (m-10) cc_final: 0.7815 (m-80) REVERT: H 127 LYS cc_start: 0.8086 (mtpp) cc_final: 0.7754 (ttmt) REVERT: I 21 MET cc_start: 0.8671 (mtp) cc_final: 0.8418 (mtm) REVERT: I 24 MET cc_start: 0.8711 (tpp) cc_final: 0.8339 (mmm) REVERT: I 75 MET cc_start: 0.6666 (ttt) cc_final: 0.6384 (mtp) REVERT: J 75 MET cc_start: 0.7865 (ttm) cc_final: 0.7632 (mtp) REVERT: J 165 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7259 (pm20) REVERT: K 1 MET cc_start: 0.4312 (pmm) cc_final: 0.3045 (mmm) REVERT: K 122 ARG cc_start: 0.6639 (ptp-110) cc_final: 0.6318 (mtm110) REVERT: K 135 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6456 (mm-30) REVERT: M 21 MET cc_start: 0.8117 (mtm) cc_final: 0.7795 (mtm) REVERT: M 157 CYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7845 (t) REVERT: N 63 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6424 (mt) REVERT: N 111 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6451 (pt) REVERT: O 1 MET cc_start: 0.7020 (pmm) cc_final: 0.6665 (pmm) REVERT: O 71 GLU cc_start: 0.7953 (mm-30) cc_final: 0.6916 (tm-30) REVERT: O 75 MET cc_start: 0.5514 (ttt) cc_final: 0.5287 (ttt) REVERT: O 78 GLU cc_start: 0.8324 (pt0) cc_final: 0.8117 (pt0) REVERT: P 21 MET cc_start: 0.7593 (mpp) cc_final: 0.7368 (mmm) REVERT: P 63 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6246 (mp) REVERT: P 157 CYS cc_start: 0.8170 (t) cc_final: 0.7817 (t) outliers start: 69 outliers final: 48 residues processed: 336 average time/residue: 0.1321 time to fit residues: 71.7694 Evaluate side-chains 327 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 269 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 88 TYR Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 145 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 98 GLN Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain J residue 133 ASP Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 136 ILE Chi-restraints excluded: chain M residue 157 CYS Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 111 LEU Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain O residue 150 VAL Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 133 ASP Chi-restraints excluded: chain P residue 169 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 65 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 105 optimal weight: 0.2980 chunk 139 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 92 ASN H 35 GLN H 98 GLN K 40 ASN N 40 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.153595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.126704 restraints weight = 31542.346| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.91 r_work: 0.3698 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.6981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22416 Z= 0.118 Angle : 0.483 7.103 30096 Z= 0.251 Chirality : 0.040 0.145 3152 Planarity : 0.004 0.051 3888 Dihedral : 4.128 54.584 2951 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.00 % Favored : 96.97 % Rotamer: Outliers : 3.55 % Allowed : 25.76 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.17), residues: 2704 helix: 2.73 (0.12), residues: 1904 sheet: None (None), residues: 0 loop : -0.48 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 46 TYR 0.012 0.001 TYR B 91 PHE 0.012 0.001 PHE F 97 HIS 0.005 0.001 HIS F 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (22416) covalent geometry : angle 0.48278 / 0.25 (30096) hydrogen bonds : bond 0.03864 / 2.59 ( 1486) hydrogen bonds : angle 3.05517 / 2.16 ( 4296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 281 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8328 (ttp) cc_final: 0.7982 (mtm) REVERT: A 75 MET cc_start: 0.7995 (tpp) cc_final: 0.7590 (ttm) REVERT: A 91 TYR cc_start: 0.7444 (m-10) cc_final: 0.6893 (m-10) REVERT: B 14 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7047 (tt0) REVERT: B 71 GLU cc_start: 0.7709 (tp30) cc_final: 0.7091 (tm-30) REVERT: B 75 MET cc_start: 0.6951 (mtm) cc_final: 0.6677 (mtm) REVERT: B 122 ARG cc_start: 0.7328 (mtm110) cc_final: 0.7114 (mtm110) REVERT: C 1 MET cc_start: 0.4475 (tmm) cc_final: 0.4138 (tmm) REVERT: D 160 CYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7734 (p) REVERT: E 36 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6394 (mt-10) REVERT: E 75 MET cc_start: 0.7185 (ttm) cc_final: 0.6793 (ttm) REVERT: E 88 TYR cc_start: 0.8887 (OUTLIER) cc_final: 0.8075 (m-10) REVERT: E 127 LYS cc_start: 0.7696 (mmtm) cc_final: 0.7049 (tttp) REVERT: F 1 MET cc_start: 0.4925 (tpp) cc_final: 0.3735 (tmm) REVERT: F 102 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.6741 (mp0) REVERT: G 21 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7519 (mtp) REVERT: G 26 TYR cc_start: 0.8197 (m-10) cc_final: 0.7935 (m-80) REVERT: H 46 ARG cc_start: 0.7732 (tpt170) cc_final: 0.7406 (mtp180) REVERT: H 127 LYS cc_start: 0.8180 (mtpp) cc_final: 0.7887 (ttmm) REVERT: I 21 MET cc_start: 0.8661 (mtp) cc_final: 0.8427 (mtm) REVERT: I 24 MET cc_start: 0.8774 (tpp) cc_final: 0.8407 (mmm) REVERT: I 75 MET cc_start: 0.6816 (ttt) cc_final: 0.6562 (mtp) REVERT: I 87 MET cc_start: 0.8443 (ttp) cc_final: 0.8165 (ttm) REVERT: J 75 MET cc_start: 0.8034 (ttm) cc_final: 0.7803 (mtp) REVERT: J 165 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7216 (pm20) REVERT: K 1 MET cc_start: 0.4683 (pmm) cc_final: 0.3432 (mmm) REVERT: K 122 ARG cc_start: 0.6816 (ptp-110) cc_final: 0.6402 (mtm110) REVERT: K 135 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6332 (mm-30) REVERT: K 165 GLU cc_start: 0.7711 (pp20) cc_final: 0.7329 (pp20) REVERT: M 21 MET cc_start: 0.8216 (mtm) cc_final: 0.7903 (mtm) REVERT: M 157 CYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7852 (t) REVERT: N 14 GLU cc_start: 0.7579 (tp30) cc_final: 0.7370 (tp30) REVERT: N 40 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7296 (t0) REVERT: N 63 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6506 (mt) REVERT: N 111 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6569 (pt) REVERT: O 1 MET cc_start: 0.7164 (pmm) cc_final: 0.6782 (pmm) REVERT: O 71 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7573 (mt-10) REVERT: O 75 MET cc_start: 0.5732 (ttt) cc_final: 0.5498 (ttt) REVERT: P 21 MET cc_start: 0.7659 (mpp) cc_final: 0.7436 (mmm) REVERT: P 63 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6544 (mp) REVERT: P 157 CYS cc_start: 0.8072 (t) cc_final: 0.7832 (t) outliers start: 79 outliers final: 45 residues processed: 339 average time/residue: 0.1324 time to fit residues: 71.9989 Evaluate side-chains 325 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 269 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 88 TYR Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 145 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain J residue 133 ASP Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain J residue 152 GLU Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 157 CYS Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 40 ASN Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 111 LEU Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain O residue 150 VAL Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 133 ASP Chi-restraints excluded: chain P residue 169 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 109 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 194 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 260 optimal weight: 0.7980 chunk 262 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 257 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 40 ASN K 40 ASN N 40 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.153902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.126267 restraints weight = 31592.848| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.02 r_work: 0.3711 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.7241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22416 Z= 0.110 Angle : 0.475 6.655 30096 Z= 0.247 Chirality : 0.040 0.143 3152 Planarity : 0.004 0.051 3888 Dihedral : 4.052 53.539 2949 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.96 % Favored : 97.00 % Rotamer: Outliers : 3.24 % Allowed : 25.49 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.17), residues: 2704 helix: 2.77 (0.12), residues: 1904 sheet: None (None), residues: 0 loop : -0.45 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 46 TYR 0.010 0.001 TYR H 121 PHE 0.013 0.001 PHE F 97 HIS 0.003 0.001 HIS H 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (22416) covalent geometry : angle 0.47518 / 0.25 (30096) hydrogen bonds : bond 0.03642 / 2.44 ( 1486) hydrogen bonds : angle 3.01960 / 2.14 ( 4296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 288 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.7892 (tpp) cc_final: 0.7425 (ttm) REVERT: A 91 TYR cc_start: 0.7410 (m-10) cc_final: 0.6868 (m-10) REVERT: B 14 GLU cc_start: 0.7788 (tm-30) cc_final: 0.6935 (tt0) REVERT: B 71 GLU cc_start: 0.7751 (tp30) cc_final: 0.7038 (tm-30) REVERT: B 75 MET cc_start: 0.6789 (mtm) cc_final: 0.6527 (mtm) REVERT: C 165 GLU cc_start: 0.7420 (pm20) cc_final: 0.7099 (pm20) REVERT: D 35 GLN cc_start: 0.6455 (mp10) cc_final: 0.6057 (mt0) REVERT: D 160 CYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7693 (p) REVERT: E 36 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6390 (mt-10) REVERT: E 75 MET cc_start: 0.7200 (ttm) cc_final: 0.6731 (ttm) REVERT: E 88 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.8076 (m-10) REVERT: E 111 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8158 (tt) REVERT: E 127 LYS cc_start: 0.7626 (mmtm) cc_final: 0.6971 (tttp) REVERT: F 26 TYR cc_start: 0.8150 (m-80) cc_final: 0.7905 (m-80) REVERT: F 102 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: G 21 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7474 (mtp) REVERT: H 46 ARG cc_start: 0.7735 (tpt170) cc_final: 0.7310 (mtp180) REVERT: H 127 LYS cc_start: 0.8147 (mtpp) cc_final: 0.7867 (ttmm) REVERT: I 21 MET cc_start: 0.8655 (mtp) cc_final: 0.8350 (mtm) REVERT: I 24 MET cc_start: 0.8722 (tpp) cc_final: 0.8402 (tpp) REVERT: I 75 MET cc_start: 0.6681 (ttt) cc_final: 0.6418 (mtp) REVERT: I 87 MET cc_start: 0.8386 (ttp) cc_final: 0.8137 (ttm) REVERT: J 75 MET cc_start: 0.7925 (ttm) cc_final: 0.7686 (mtp) REVERT: K 1 MET cc_start: 0.4662 (pmm) cc_final: 0.3419 (mmm) REVERT: K 122 ARG cc_start: 0.6709 (ptp-110) cc_final: 0.6302 (mtm110) REVERT: K 135 GLU cc_start: 0.6573 (mm-30) cc_final: 0.6352 (mm-30) REVERT: M 21 MET cc_start: 0.8138 (mtm) cc_final: 0.7854 (mtm) REVERT: M 121 TYR cc_start: 0.8706 (m-80) cc_final: 0.8363 (m-80) REVERT: M 157 CYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8027 (t) REVERT: N 14 GLU cc_start: 0.7566 (tp30) cc_final: 0.7341 (tp30) REVERT: N 34 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7118 (tt0) REVERT: N 40 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7120 (t0) REVERT: N 63 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6397 (mt) REVERT: N 111 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6486 (pt) REVERT: O 1 MET cc_start: 0.7233 (pmm) cc_final: 0.6874 (pmm) REVERT: O 71 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7573 (mt-10) REVERT: P 21 MET cc_start: 0.7628 (mpp) cc_final: 0.7415 (mmm) REVERT: P 63 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6371 (mp) REVERT: P 157 CYS cc_start: 0.8168 (t) cc_final: 0.7914 (t) outliers start: 72 outliers final: 47 residues processed: 338 average time/residue: 0.1321 time to fit residues: 71.4400 Evaluate side-chains 331 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 273 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 88 TYR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 145 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain J residue 133 ASP Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain J residue 152 GLU Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 144 ILE Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 157 CYS Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 40 ASN Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 111 LEU Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain O residue 150 VAL Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 133 ASP Chi-restraints excluded: chain P residue 169 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 153 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 193 optimal weight: 8.9990 chunk 191 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 ASN K 40 ASN N 40 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.145895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.118357 restraints weight = 31804.075| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.95 r_work: 0.3606 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.7845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 22416 Z= 0.223 Angle : 0.601 8.298 30096 Z= 0.319 Chirality : 0.044 0.170 3152 Planarity : 0.005 0.047 3888 Dihedral : 4.514 55.885 2949 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.51 % Favored : 96.38 % Rotamer: Outliers : 3.73 % Allowed : 25.22 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.16), residues: 2704 helix: 2.36 (0.12), residues: 1824 sheet: None (None), residues: 0 loop : -0.88 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 25 TYR 0.017 0.002 TYR H 109 PHE 0.025 0.002 PHE H 60 HIS 0.009 0.001 HIS F 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.22 (22416) covalent geometry : angle 0.60075 / 0.32 (30096) hydrogen bonds : bond 0.05772 / 3.88 ( 1486) hydrogen bonds : angle 3.51289 / 2.49 ( 4296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 269 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8255 (tpp) cc_final: 0.7841 (ttm) REVERT: A 167 PHE cc_start: 0.8399 (m-10) cc_final: 0.8177 (m-10) REVERT: B 14 GLU cc_start: 0.7853 (tm-30) cc_final: 0.6941 (tt0) REVERT: B 21 MET cc_start: 0.8299 (mtt) cc_final: 0.8090 (mtp) REVERT: B 71 GLU cc_start: 0.7632 (tp30) cc_final: 0.7259 (tm-30) REVERT: B 122 ARG cc_start: 0.7154 (mtm110) cc_final: 0.6937 (mtm110) REVERT: C 9 LYS cc_start: 0.8570 (ttpp) cc_final: 0.8089 (tptt) REVERT: C 121 TYR cc_start: 0.8602 (m-80) cc_final: 0.8345 (m-80) REVERT: E 1 MET cc_start: 0.3122 (ppp) cc_final: 0.2196 (ppp) REVERT: E 36 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6823 (mt-10) REVERT: E 75 MET cc_start: 0.7508 (ttm) cc_final: 0.7159 (ttm) REVERT: E 88 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.8065 (m-10) REVERT: E 111 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8359 (tt) REVERT: E 127 LYS cc_start: 0.7664 (mmtm) cc_final: 0.7183 (tttp) REVERT: F 102 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.6637 (mp0) REVERT: I 24 MET cc_start: 0.8746 (tpp) cc_final: 0.8447 (mmm) REVERT: I 75 MET cc_start: 0.7014 (ttt) cc_final: 0.6422 (mtt) REVERT: K 1 MET cc_start: 0.4947 (pmm) cc_final: 0.3506 (mmm) REVERT: K 122 ARG cc_start: 0.6618 (ptp-110) cc_final: 0.6127 (mtm110) REVERT: K 135 GLU cc_start: 0.6709 (mm-30) cc_final: 0.6410 (mm-30) REVERT: L 145 CYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6982 (p) REVERT: N 40 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7024 (t0) REVERT: N 111 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6645 (pt) REVERT: O 1 MET cc_start: 0.6989 (pmm) cc_final: 0.6638 (pmm) REVERT: O 71 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7720 (mt-10) REVERT: P 21 MET cc_start: 0.7801 (mpp) cc_final: 0.7467 (mmm) REVERT: P 63 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.6836 (mp) outliers start: 83 outliers final: 58 residues processed: 331 average time/residue: 0.1212 time to fit residues: 64.5463 Evaluate side-chains 321 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 255 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 88 TYR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 145 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain J residue 116 ILE Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain J residue 133 ASP Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain J residue 152 GLU Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain K residue 144 ILE Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain L residue 145 CYS Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain N residue 40 ASN Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 111 LEU Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 168 VAL Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 150 VAL Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 169 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 124 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 240 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 ASN K 40 ASN N 40 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.150954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.123257 restraints weight = 31795.988| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.04 r_work: 0.3671 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.7926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22416 Z= 0.120 Angle : 0.511 9.497 30096 Z= 0.265 Chirality : 0.040 0.228 3152 Planarity : 0.004 0.057 3888 Dihedral : 4.301 54.850 2949 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.01 % Allowed : 25.94 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.17), residues: 2704 helix: 2.60 (0.12), residues: 1904 sheet: None (None), residues: 0 loop : -0.53 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 46 TYR 0.012 0.001 TYR F 26 PHE 0.014 0.001 PHE F 97 HIS 0.008 0.001 HIS F 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (22416) covalent geometry : angle 0.51109 / 0.27 (30096) hydrogen bonds : bond 0.04065 / 2.72 ( 1486) hydrogen bonds : angle 3.18717 / 2.26 ( 4296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 275 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8536 (tpp) cc_final: 0.7956 (mmp) REVERT: A 75 MET cc_start: 0.8185 (tpp) cc_final: 0.7706 (ttm) REVERT: A 167 PHE cc_start: 0.8397 (m-10) cc_final: 0.8189 (m-10) REVERT: B 14 GLU cc_start: 0.7844 (tm-30) cc_final: 0.6885 (tt0) REVERT: B 71 GLU cc_start: 0.7729 (tp30) cc_final: 0.7182 (tm-30) REVERT: C 155 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7902 (mm-30) REVERT: C 165 GLU cc_start: 0.7326 (pm20) cc_final: 0.6910 (pm20) REVERT: E 1 MET cc_start: 0.3079 (ppp) cc_final: 0.2017 (ppp) REVERT: E 36 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6707 (mt-10) REVERT: E 75 MET cc_start: 0.7364 (ttm) cc_final: 0.7020 (ttm) REVERT: E 88 TYR cc_start: 0.8900 (OUTLIER) cc_final: 0.7940 (m-10) REVERT: E 111 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8313 (tt) REVERT: E 127 LYS cc_start: 0.7625 (mmtm) cc_final: 0.7152 (tttp) REVERT: F 102 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.6540 (mp0) REVERT: H 127 LYS cc_start: 0.8254 (mtpp) cc_final: 0.7825 (ttmm) REVERT: I 21 MET cc_start: 0.8689 (mtp) cc_final: 0.8462 (mtm) REVERT: I 24 MET cc_start: 0.8756 (tpp) cc_final: 0.8411 (mmm) REVERT: I 75 MET cc_start: 0.6788 (ttt) cc_final: 0.6263 (mtt) REVERT: I 87 MET cc_start: 0.8499 (ttp) cc_final: 0.8288 (ttm) REVERT: J 165 GLU cc_start: 0.7242 (pm20) cc_final: 0.7002 (pm20) REVERT: K 1 MET cc_start: 0.5064 (pmm) cc_final: 0.3615 (mmm) REVERT: K 122 ARG cc_start: 0.6584 (ptp-110) cc_final: 0.6022 (mtm110) REVERT: K 135 GLU cc_start: 0.6583 (mm-30) cc_final: 0.6281 (mm-30) REVERT: K 138 LYS cc_start: 0.7095 (tptt) cc_final: 0.6660 (tppt) REVERT: K 165 GLU cc_start: 0.7673 (pp20) cc_final: 0.7302 (pp20) REVERT: L 145 CYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7201 (p) REVERT: M 121 TYR cc_start: 0.8692 (m-80) cc_final: 0.8403 (m-80) REVERT: M 126 GLU cc_start: 0.7740 (tp30) cc_final: 0.7115 (tm-30) REVERT: N 27 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7699 (mp) REVERT: N 34 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7189 (tt0) REVERT: N 63 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6578 (mt) REVERT: N 111 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6577 (pt) REVERT: O 1 MET cc_start: 0.7092 (pmm) cc_final: 0.6720 (pmm) REVERT: O 71 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7692 (mt-10) REVERT: P 63 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6683 (mp) REVERT: P 121 TYR cc_start: 0.8396 (m-80) cc_final: 0.8094 (m-80) outliers start: 67 outliers final: 47 residues processed: 333 average time/residue: 0.1367 time to fit residues: 73.7099 Evaluate side-chains 324 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 267 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 88 TYR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 147 TYR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 145 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain J residue 116 ILE Chi-restraints excluded: chain J residue 133 ASP Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain J residue 152 GLU Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain L residue 145 CYS Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 111 LEU Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 168 VAL Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain O residue 150 VAL Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 145 optimal weight: 6.9990 chunk 184 optimal weight: 0.4980 chunk 217 optimal weight: 3.9990 chunk 242 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 198 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 203 optimal weight: 0.0570 chunk 101 optimal weight: 4.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 40 ASN J 23 HIS K 40 ASN K 55 HIS K 98 GLN N 40 ASN O 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.154335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.126322 restraints weight = 31602.470| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.05 r_work: 0.3727 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.8031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 22416 Z= 0.102 Angle : 0.492 11.886 30096 Z= 0.252 Chirality : 0.039 0.208 3152 Planarity : 0.004 0.050 3888 Dihedral : 4.025 58.609 2947 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.25 % Allowed : 26.80 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.17), residues: 2704 helix: 2.89 (0.12), residues: 1872 sheet: None (None), residues: 0 loop : -0.57 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 122 TYR 0.019 0.001 TYR J 121 PHE 0.015 0.001 PHE F 97 HIS 0.006 0.001 HIS F 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (22416) covalent geometry : angle 0.49197 / 0.25 (30096) hydrogen bonds : bond 0.03374 / 2.25 ( 1486) hydrogen bonds : angle 3.04181 / 2.15 ( 4296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 281 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8462 (tpp) cc_final: 0.7862 (mmp) REVERT: A 75 MET cc_start: 0.8087 (tpp) cc_final: 0.7625 (ttm) REVERT: A 140 TYR cc_start: 0.7736 (m-80) cc_final: 0.7407 (m-80) REVERT: B 14 GLU cc_start: 0.7759 (tm-30) cc_final: 0.6783 (tt0) REVERT: B 71 GLU cc_start: 0.7686 (tp30) cc_final: 0.7117 (tm-30) REVERT: B 122 ARG cc_start: 0.6934 (mtm110) cc_final: 0.6494 (ptm-80) REVERT: C 1 MET cc_start: 0.4470 (tmm) cc_final: 0.3911 (tmm) REVERT: C 155 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7944 (mm-30) REVERT: C 165 GLU cc_start: 0.7204 (pm20) cc_final: 0.6824 (pm20) REVERT: E 1 MET cc_start: 0.3107 (ppp) cc_final: 0.2829 (ppp) REVERT: E 13 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7024 (mt-10) REVERT: E 36 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6491 (mt-10) REVERT: E 75 MET cc_start: 0.7298 (ttm) cc_final: 0.6963 (ttm) REVERT: E 88 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.7912 (m-10) REVERT: E 111 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8133 (tt) REVERT: E 127 LYS cc_start: 0.7605 (mmtm) cc_final: 0.7125 (tttp) REVERT: G 26 TYR cc_start: 0.8229 (m-10) cc_final: 0.8015 (m-80) REVERT: H 127 LYS cc_start: 0.8132 (mtpp) cc_final: 0.7790 (ttmm) REVERT: H 140 TYR cc_start: 0.7940 (m-80) cc_final: 0.7561 (m-80) REVERT: I 21 MET cc_start: 0.8613 (mtp) cc_final: 0.8380 (mtm) REVERT: I 24 MET cc_start: 0.8650 (tpp) cc_final: 0.8371 (tpp) REVERT: I 75 MET cc_start: 0.6705 (ttt) cc_final: 0.6099 (mtt) REVERT: J 165 GLU cc_start: 0.7341 (pm20) cc_final: 0.7112 (pm20) REVERT: K 1 MET cc_start: 0.5132 (pmm) cc_final: 0.3699 (mmm) REVERT: K 21 MET cc_start: 0.8679 (mtp) cc_final: 0.8375 (mtm) REVERT: K 122 ARG cc_start: 0.6507 (ptp-110) cc_final: 0.5946 (mtm110) REVERT: K 138 LYS cc_start: 0.6977 (tptt) cc_final: 0.6631 (tppt) REVERT: K 140 TYR cc_start: 0.8249 (m-80) cc_final: 0.7829 (m-80) REVERT: L 140 TYR cc_start: 0.7955 (m-80) cc_final: 0.7472 (m-80) REVERT: L 145 CYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6949 (p) REVERT: M 126 GLU cc_start: 0.7785 (tp30) cc_final: 0.7149 (tm-30) REVERT: N 34 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7046 (tt0) REVERT: N 63 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6343 (mt) REVERT: O 1 MET cc_start: 0.7106 (pmm) cc_final: 0.6735 (pmm) REVERT: O 71 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7688 (mt-10) REVERT: P 63 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6316 (mp) outliers start: 50 outliers final: 38 residues processed: 321 average time/residue: 0.1408 time to fit residues: 73.0416 Evaluate side-chains 314 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 269 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 88 TYR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 147 TYR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 40 ASN Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 145 CYS Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain J residue 133 ASP Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 152 GLU Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain L residue 145 CYS Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 168 VAL Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 176 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 ASN E 72 ASN G 40 ASN K 40 ASN L 40 ASN O 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.151547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.124109 restraints weight = 31488.148| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.95 r_work: 0.3684 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.8080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22416 Z= 0.134 Angle : 0.531 13.311 30096 Z= 0.272 Chirality : 0.041 0.224 3152 Planarity : 0.004 0.051 3888 Dihedral : 4.088 59.691 2947 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.65 % Allowed : 26.62 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.17), residues: 2704 helix: 2.75 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -0.53 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 122 TYR 0.012 0.001 TYR M 121 PHE 0.014 0.001 PHE H 60 HIS 0.007 0.001 HIS F 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.13 (22416) covalent geometry : angle 0.53123 / 0.27 (30096) hydrogen bonds : bond 0.04079 / 2.74 ( 1486) hydrogen bonds : angle 3.14351 / 2.22 ( 4296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5754.32 seconds wall clock time: 99 minutes 34.01 seconds (5974.01 seconds total)