Starting phenix.real_space_refine on Sun Aug 24 19:10:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qg1_53127/08_2025/9qg1_53127_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qg1_53127/08_2025/9qg1_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_53127/08_2025/9qg1_53127_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qg1_53127/08_2025/9qg1_53127_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qg1_53127/08_2025/9qg1_53127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qg1_53127/08_2025/9qg1_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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, 3 Unusual residues: {' FE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' FE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' FE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' FE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' FE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' FE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' FE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' FE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' FE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' FE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' FE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' FE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 5.38, per 1000 atoms: 0.24 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: 2.00 Conformation dependent library (CDL) restraints added in 854.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.75 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: 3.88 Time building geometry restraints manager: 2.50 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 2.260 nonbonded pdb=" OE1 GLU H 114 " pdb="FE FE H 203 " model vdw 1.629 2.260 nonbonded pdb=" OE2 GLU L 52 " pdb="FE FE L 201 " model vdw 1.718 2.260 nonbonded pdb="FE FE M 202 " pdb="FE FE M 203 " model vdw 1.786 1.480 nonbonded pdb=" OE2 GLU H 114 " pdb="FE FE G 203 " model vdw 1.787 2.260 ... (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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.860 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 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 aren 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 covalent geometry : bond 0.00437 (22416) covalent geometry : angle 0.66644 (30096) hydrogen bonds : bond 0.13946 ( 1486) hydrogen bonds : angle 4.22163 ( 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 : 0.837 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: 0.1303 (mtt) REVERT: I 150 VAL cc_start: 0.6686 (OUTLIER) cc_final: 0.6428 (t) REVERT: J 40 ASN cc_start: 0.6003 (t0) cc_final: 0.5715 (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: 0.6616 (t0) REVERT: K 1 MET cc_start: 0.3789 (pmm) cc_final: 0.2621 (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: 0.6335 (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: 0.7085 (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: 0.7439 (pt) cc_final: 0.7167 (tt) outliers start: 82 outliers final: 17 residues processed: 567 average time/residue: 0.1784 time to fit residues: 151.8511 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 : 1.063 ------------------------------------------------------------------------------- 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: 6.9990 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: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN D 98 GLN E 72 ASN F 58 ASN G 58 ASN K 40 ASN K 98 GLN M 55 HIS N 72 ASN N 98 GLN ** O 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.148014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.117863 restraints weight = 32842.917| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.65 r_work: 0.3607 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 22416 Z= 0.194 Angle : 0.629 9.078 30096 Z= 0.335 Chirality : 0.044 0.163 3152 Planarity : 0.005 0.068 3888 Dihedral : 5.605 88.995 2987 Min Nonbonded Distance : 1.196 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.70 % Favored : 96.15 % Rotamer: Outliers : 4.18 % Allowed : 24.91 % Favored : 70.91 % 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 aren not related in a simple way. whole: 1.59 (0.16), residues: 2704 helix: 2.38 (0.12), residues: 1792 sheet: -2.72 (0.38), residues: 144 loop : -1.50 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 5 TYR 0.019 0.002 TYR K 91 PHE 0.022 0.002 PHE M 97 HIS 0.008 0.001 HIS J 23 Details of bonding type rmsd covalent geometry : bond 0.00463 (22416) covalent geometry : angle 0.62944 (30096) hydrogen bonds : bond 0.05233 ( 1486) hydrogen bonds : angle 3.54465 ( 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 428 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 335 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6552 (mt-10) REVERT: A 75 MET cc_start: 0.7484 (tpp) cc_final: 0.7162 (ttm) REVERT: A 91 TYR cc_start: 0.6653 (m-10) cc_final: 0.6077 (m-10) REVERT: A 123 LYS cc_start: 0.6821 (mmtm) cc_final: 0.6578 (mmtm) REVERT: B 14 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6391 (tt0) REVERT: B 24 MET cc_start: 0.7243 (mmt) cc_final: 0.6840 (tpp) REVERT: B 71 GLU cc_start: 0.7692 (tp30) cc_final: 0.6835 (tm-30) REVERT: C 4 LYS cc_start: 0.8160 (mtpp) cc_final: 0.7622 (mtmm) REVERT: C 9 LYS cc_start: 0.8049 (ttpp) cc_final: 0.7558 (tptt) REVERT: D 151 ASP cc_start: 0.6763 (m-30) cc_final: 0.6500 (m-30) REVERT: D 152 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6697 (mm-30) REVERT: E 36 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6645 (mt-10) REVERT: E 123 LYS cc_start: 0.7921 (mmtt) cc_final: 0.7634 (mmmm) REVERT: F 9 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7642 (mttt) REVERT: F 101 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7827 (mmmt) REVERT: F 166 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7258 (mtpt) REVERT: G 26 TYR cc_start: 0.7754 (m-10) cc_final: 0.7454 (m-80) REVERT: H 87 MET cc_start: 0.7706 (ttm) cc_final: 0.7448 (ttp) REVERT: H 101 LYS cc_start: 0.8756 (mmmm) cc_final: 0.8527 (mmtt) REVERT: I 21 MET cc_start: 0.8436 (mtp) cc_final: 0.7994 (mtm) REVERT: I 75 MET cc_start: 0.6208 (ttt) cc_final: 0.5864 (mtp) REVERT: J 109 TYR cc_start: 0.7892 (m-10) cc_final: 0.7586 (m-10) REVERT: J 152 GLU cc_start: 0.7882 (pm20) cc_final: 0.7670 (tt0) REVERT: J 165 GLU cc_start: 0.7471 (pm20) cc_final: 0.7158 (pm20) REVERT: K 1 MET cc_start: 0.4112 (pmm) cc_final: 0.2760 (mmm) REVERT: K 75 MET cc_start: 0.6664 (ttt) cc_final: 0.6388 (ttp) REVERT: L 105 ARG cc_start: 0.7793 (ttm170) cc_final: 0.7581 (ttm170) REVERT: N 83 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7989 (mt-10) REVERT: N 152 GLU cc_start: 0.5905 (pm20) cc_final: 0.5686 (pm20) REVERT: O 1 MET cc_start: 0.6528 (pmm) cc_final: 0.6246 (pmm) REVERT: O 34 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7400 (tt0) REVERT: O 35 GLN cc_start: 0.6152 (tt0) cc_final: 0.5605 (mt0) REVERT: O 71 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7534 (mt-10) REVERT: O 72 ASN cc_start: 0.8690 (m-40) cc_final: 0.8487 (m-40) REVERT: P 63 LEU cc_start: 0.6311 (OUTLIER) cc_final: 0.5854 (mp) REVERT: P 87 MET cc_start: 0.7978 (mtp) cc_final: 0.7689 (mtm) REVERT: P 152 GLU cc_start: 0.7410 (pp20) cc_final: 0.6928 (pm20) outliers start: 93 outliers final: 47 residues processed: 408 average time/residue: 0.1387 time to fit residues: 88.6463 Evaluate side-chains 344 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 292 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 B residue 27 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 81 THR 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 D residue 152 GLU 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 111 LEU Chi-restraints excluded: chain F residue 166 LYS Chi-restraints excluded: chain G residue 3 VAL 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 115 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 G residue 145 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain I residue 31 GLU Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain I residue 136 ILE 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 L residue 107 THR Chi-restraints excluded: chain L residue 159 VAL 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 N residue 87 MET Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 12 LEU 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 169 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 160 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 chunk 156 optimal weight: 0.0570 chunk 229 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 ASN J 98 GLN K 40 ASN L 40 ASN N 40 ASN ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.154105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.123573 restraints weight = 32175.651| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.59 r_work: 0.3669 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.5136 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 : 0.494 8.440 30096 Z= 0.255 Chirality : 0.040 0.148 3152 Planarity : 0.005 0.072 3888 Dihedral : 4.625 56.841 2968 Min Nonbonded Distance : 1.245 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.29 % Favored : 96.63 % Rotamer: Outliers : 3.37 % Allowed : 25.00 % 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 aren not related in a simple way. whole: 2.50 (0.16), residues: 2704 helix: 2.80 (0.12), residues: 1792 sheet: None (None), residues: 0 loop : -0.79 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 105 TYR 0.023 0.001 TYR K 91 PHE 0.022 0.001 PHE I 97 HIS 0.005 0.001 HIS J 23 Details of bonding type rmsd covalent geometry : bond 0.00239 (22416) covalent geometry : angle 0.49401 (30096) hydrogen bonds : bond 0.03847 ( 1486) hydrogen bonds : angle 3.14173 ( 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 388 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 313 time to evaluate : 0.861 Fit side-chains REVERT: A 13 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6789 (mt-10) REVERT: A 75 MET cc_start: 0.7544 (tpp) cc_final: 0.7256 (ttm) REVERT: A 91 TYR cc_start: 0.6845 (m-10) cc_final: 0.6358 (m-10) REVERT: B 14 GLU cc_start: 0.7086 (tm-30) cc_final: 0.6363 (tt0) REVERT: B 24 MET cc_start: 0.7401 (mmt) cc_final: 0.7023 (tpp) REVERT: B 71 GLU cc_start: 0.7756 (tp30) cc_final: 0.6892 (tm-30) REVERT: B 87 MET cc_start: 0.7294 (ttm) cc_final: 0.6907 (ttp) REVERT: B 151 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.7057 (p0) REVERT: C 9 LYS cc_start: 0.8127 (ttpp) cc_final: 0.7613 (tptt) REVERT: E 36 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6505 (mt-10) REVERT: E 105 ARG cc_start: 0.7296 (ptm-80) cc_final: 0.7019 (ptt90) REVERT: F 9 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7370 (mttt) REVERT: F 40 ASN cc_start: 0.8477 (m-40) cc_final: 0.8148 (m-40) REVERT: F 101 LYS cc_start: 0.8041 (mmtt) cc_final: 0.7766 (mmmt) REVERT: G 24 MET cc_start: 0.8771 (tpp) cc_final: 0.8452 (tpp) REVERT: G 26 TYR cc_start: 0.7755 (m-10) cc_final: 0.7531 (m-80) REVERT: G 130 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.7013 (ptpp) REVERT: I 21 MET cc_start: 0.8449 (mtp) cc_final: 0.8136 (mtm) REVERT: I 75 MET cc_start: 0.6159 (ttt) cc_final: 0.5898 (mtp) REVERT: J 24 MET cc_start: 0.7958 (tpp) cc_final: 0.7671 (tpp) REVERT: J 109 TYR cc_start: 0.7913 (m-10) cc_final: 0.7697 (m-10) REVERT: J 152 GLU cc_start: 0.7872 (pm20) cc_final: 0.7609 (mp0) REVERT: J 165 GLU cc_start: 0.7369 (pm20) cc_final: 0.7022 (pm20) REVERT: K 1 MET cc_start: 0.4172 (pmm) cc_final: 0.3004 (mmm) REVERT: K 75 MET cc_start: 0.6655 (ttt) cc_final: 0.6429 (ttp) REVERT: M 21 MET cc_start: 0.7766 (mtm) cc_final: 0.7421 (mtm) REVERT: M 96 GLU cc_start: 0.8152 (tp30) cc_final: 0.7924 (tp30) REVERT: N 98 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8251 (mp10) REVERT: N 134 ILE cc_start: 0.6959 (tt) cc_final: 0.6746 (tp) REVERT: N 152 GLU cc_start: 0.5864 (pm20) cc_final: 0.5543 (pm20) REVERT: O 1 MET cc_start: 0.6665 (pmm) cc_final: 0.6373 (pmm) REVERT: O 7 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6712 (tpt) REVERT: O 24 MET cc_start: 0.7928 (mmm) cc_final: 0.7712 (tpp) REVERT: O 34 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7472 (tt0) REVERT: O 35 GLN cc_start: 0.6285 (tt0) cc_final: 0.5723 (mt0) REVERT: O 71 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7543 (mt-10) REVERT: O 72 ASN cc_start: 0.8810 (m-40) cc_final: 0.8485 (m-40) REVERT: P 63 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.5943 (mp) outliers start: 75 outliers final: 39 residues processed: 366 average time/residue: 0.1317 time to fit residues: 76.8101 Evaluate side-chains 336 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 290 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 151 ASP Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 31 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 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 84 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 171 GLU 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 H residue 150 VAL Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain K residue 144 ILE Chi-restraints excluded: chain K residue 147 TYR 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 27 LEU Chi-restraints excluded: chain N residue 40 ASN Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 98 GLN Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 7 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 20 optimal weight: 3.9990 chunk 181 optimal weight: 10.0000 chunk 201 optimal weight: 6.9990 chunk 214 optimal weight: 1.9990 chunk 226 optimal weight: 0.5980 chunk 202 optimal weight: 8.9990 chunk 97 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN K 98 GLN L 40 ASN N 98 GLN O 40 ASN P 40 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.150713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.123350 restraints weight = 31161.202| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.92 r_work: 0.3659 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.6729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22416 Z= 0.159 Angle : 0.551 8.401 30096 Z= 0.290 Chirality : 0.042 0.159 3152 Planarity : 0.005 0.058 3888 Dihedral : 4.609 56.189 2962 Min Nonbonded Distance : 1.038 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 4.23 % Allowed : 24.33 % Favored : 71.45 % 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 aren not related in a simple way. whole: 1.97 (0.17), residues: 2704 helix: 2.61 (0.12), residues: 1808 sheet: -2.58 (0.38), residues: 144 loop : -1.26 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 25 TYR 0.017 0.002 TYR K 91 PHE 0.018 0.002 PHE N 60 HIS 0.007 0.001 HIS F 23 Details of bonding type rmsd covalent geometry : bond 0.00385 (22416) covalent geometry : angle 0.55134 (30096) hydrogen bonds : bond 0.04958 ( 1486) hydrogen bonds : angle 3.31030 ( 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 383 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 289 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8475 (ttp) cc_final: 0.8184 (mtm) REVERT: A 24 MET cc_start: 0.8368 (tpp) cc_final: 0.7789 (mmp) REVERT: A 75 MET cc_start: 0.7949 (tpp) cc_final: 0.7557 (ttm) REVERT: A 91 TYR cc_start: 0.7396 (m-10) cc_final: 0.6990 (m-10) REVERT: B 14 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7010 (tt0) REVERT: B 24 MET cc_start: 0.7877 (mmt) cc_final: 0.7522 (tpp) REVERT: B 71 GLU cc_start: 0.7739 (tp30) cc_final: 0.7084 (tm-30) REVERT: B 75 MET cc_start: 0.7010 (mtm) cc_final: 0.6768 (mtm) REVERT: B 87 MET cc_start: 0.7987 (ttm) cc_final: 0.7489 (ttp) REVERT: D 152 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7238 (mm-30) REVERT: E 36 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6688 (mt-10) REVERT: E 75 MET cc_start: 0.7379 (ttm) cc_final: 0.6989 (ttm) REVERT: E 88 TYR cc_start: 0.8999 (OUTLIER) cc_final: 0.8261 (m-10) REVERT: E 105 ARG cc_start: 0.7744 (ptm-80) cc_final: 0.7298 (ttt90) REVERT: F 9 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8159 (mttp) REVERT: F 26 TYR cc_start: 0.8381 (m-10) cc_final: 0.8139 (m-80) REVERT: F 101 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7837 (mmmt) REVERT: G 24 MET cc_start: 0.8866 (tpp) cc_final: 0.8367 (tpp) REVERT: I 7 MET cc_start: 0.8135 (mmm) cc_final: 0.7914 (mmt) REVERT: I 21 MET cc_start: 0.8691 (mtp) cc_final: 0.8488 (mtm) REVERT: I 75 MET cc_start: 0.6951 (ttt) cc_final: 0.6661 (mtp) REVERT: I 87 MET cc_start: 0.8605 (ttp) cc_final: 0.8299 (ttm) REVERT: J 75 MET cc_start: 0.8043 (ttm) cc_final: 0.7815 (mtp) REVERT: J 152 GLU cc_start: 0.7943 (pm20) cc_final: 0.7731 (mp0) REVERT: J 155 GLU cc_start: 0.7927 (tp30) cc_final: 0.7481 (mm-30) REVERT: K 1 MET cc_start: 0.4577 (pmm) cc_final: 0.3362 (mmm) REVERT: K 85 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: K 122 ARG cc_start: 0.6699 (ptp-110) cc_final: 0.6381 (mtm110) REVERT: N 21 MET cc_start: 0.7910 (mtp) cc_final: 0.7697 (mtp) REVERT: N 152 GLU cc_start: 0.6323 (pm20) cc_final: 0.6032 (pm20) REVERT: O 1 MET cc_start: 0.7032 (pmm) cc_final: 0.6656 (pmm) REVERT: O 21 MET cc_start: 0.8153 (ttm) cc_final: 0.7819 (mtp) REVERT: O 34 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7630 (tt0) REVERT: O 40 ASN cc_start: 0.7582 (OUTLIER) cc_final: 0.7002 (t0) REVERT: O 71 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7718 (mp0) REVERT: O 78 GLU cc_start: 0.8074 (pt0) cc_final: 0.7869 (pt0) REVERT: P 21 MET cc_start: 0.7754 (mpp) cc_final: 0.7457 (mmm) REVERT: P 63 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6573 (mp) REVERT: P 75 MET cc_start: 0.8027 (mtm) cc_final: 0.7807 (ttp) REVERT: P 152 GLU cc_start: 0.7194 (pp20) cc_final: 0.6816 (pm20) outliers start: 94 outliers final: 51 residues processed: 363 average time/residue: 0.1322 time to fit residues: 76.9363 Evaluate side-chains 318 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 260 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 63 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 155 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 152 GLU 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 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 171 GLU 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 169 VAL Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 85 GLU 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 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 27 LEU Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 20 SER Chi-restraints excluded: chain O residue 40 ASN 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 169 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 110 optimal weight: 0.8980 chunk 217 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 238 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 259 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN G 92 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN N 40 ASN N 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.151246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.123679 restraints weight = 30564.790| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.92 r_work: 0.3679 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.7116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22416 Z= 0.138 Angle : 0.504 8.721 30096 Z= 0.263 Chirality : 0.041 0.153 3152 Planarity : 0.005 0.054 3888 Dihedral : 4.380 55.721 2955 Min Nonbonded Distance : 1.179 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.14 % Favored : 96.82 % Rotamer: Outliers : 3.64 % Allowed : 25.04 % Favored : 71.31 % 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 aren not related in a simple way. whole: 2.63 (0.17), residues: 2704 helix: 2.64 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -0.46 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 46 TYR 0.014 0.001 TYR K 91 PHE 0.013 0.001 PHE D 60 HIS 0.005 0.001 HIS H 23 Details of bonding type rmsd covalent geometry : bond 0.00335 (22416) covalent geometry : angle 0.50400 (30096) hydrogen bonds : bond 0.04340 ( 1486) hydrogen bonds : angle 3.19535 ( 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 354 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 273 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.8242 (ttp) cc_final: 0.7842 (mtm) REVERT: A 24 MET cc_start: 0.8482 (tpp) cc_final: 0.7855 (mmp) REVERT: A 75 MET cc_start: 0.8033 (tpp) cc_final: 0.7576 (ttm) REVERT: B 14 GLU cc_start: 0.7800 (tm-30) cc_final: 0.6943 (tt0) REVERT: B 24 MET cc_start: 0.7866 (mmt) cc_final: 0.7497 (tpp) REVERT: B 71 GLU cc_start: 0.7709 (tp30) cc_final: 0.7123 (tm-30) REVERT: B 75 MET cc_start: 0.6696 (mtm) cc_final: 0.6459 (mtm) REVERT: B 87 MET cc_start: 0.7875 (ttm) cc_final: 0.7529 (ttp) REVERT: D 152 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7209 (mm-30) REVERT: E 36 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6597 (mt-10) REVERT: E 75 MET cc_start: 0.7440 (ttm) cc_final: 0.7030 (ttm) REVERT: E 88 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.8170 (m-10) REVERT: E 105 ARG cc_start: 0.7643 (ptm-80) cc_final: 0.7387 (ttp80) REVERT: E 127 LYS cc_start: 0.7686 (mmtm) cc_final: 0.7019 (tttp) REVERT: F 9 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8044 (mttp) REVERT: F 26 TYR cc_start: 0.8356 (m-10) cc_final: 0.8112 (m-80) REVERT: F 101 LYS cc_start: 0.8047 (mmtt) cc_final: 0.7826 (mmmt) REVERT: F 102 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: G 24 MET cc_start: 0.8899 (tpp) cc_final: 0.8370 (tpp) REVERT: H 127 LYS cc_start: 0.8137 (mtpp) cc_final: 0.7745 (ttmm) REVERT: I 75 MET cc_start: 0.6938 (ttt) cc_final: 0.6656 (mtp) REVERT: J 75 MET cc_start: 0.8043 (ttm) cc_final: 0.7820 (mtp) REVERT: J 152 GLU cc_start: 0.7827 (pm20) cc_final: 0.7597 (mp0) REVERT: J 155 GLU cc_start: 0.7822 (tp30) cc_final: 0.7452 (mm-30) REVERT: K 1 MET cc_start: 0.4695 (pmm) cc_final: 0.3472 (mmm) REVERT: K 85 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: K 122 ARG cc_start: 0.6544 (ptp-110) cc_final: 0.6236 (mtm110) REVERT: K 165 GLU cc_start: 0.7771 (pp20) cc_final: 0.7336 (pp20) REVERT: N 21 MET cc_start: 0.7865 (mtp) cc_final: 0.7658 (mtp) REVERT: N 40 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7018 (t0) REVERT: N 152 GLU cc_start: 0.6182 (pm20) cc_final: 0.5893 (pm20) REVERT: O 1 MET cc_start: 0.7163 (pmm) cc_final: 0.6806 (pmm) REVERT: O 7 MET cc_start: 0.7491 (tpt) cc_final: 0.6892 (tpt) REVERT: O 21 MET cc_start: 0.8001 (ttm) cc_final: 0.7732 (mtp) REVERT: O 34 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7644 (tt0) REVERT: O 71 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7731 (mp0) REVERT: P 21 MET cc_start: 0.7637 (mpp) cc_final: 0.7363 (mmm) REVERT: P 63 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6596 (mp) outliers start: 81 outliers final: 52 residues processed: 336 average time/residue: 0.1511 time to fit residues: 81.3485 Evaluate side-chains 324 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 264 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 63 LEU 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 144 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 69 THR Chi-restraints excluded: chain E residue 88 TYR Chi-restraints excluded: chain E residue 116 ILE 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 102 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 171 GLU 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 165 GLU Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 85 GLU 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 M residue 84 VAL Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 40 ASN Chi-restraints excluded: chain N residue 87 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 65 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 205 optimal weight: 7.9990 chunk 189 optimal weight: 7.9990 chunk 196 optimal weight: 0.3980 chunk 53 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN H 98 GLN J 40 ASN K 40 ASN N 40 ASN N 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.150625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.122945 restraints weight = 30820.256| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.95 r_work: 0.3663 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.7469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22416 Z= 0.142 Angle : 0.516 10.784 30096 Z= 0.269 Chirality : 0.041 0.149 3152 Planarity : 0.005 0.053 3888 Dihedral : 4.405 56.083 2955 Min Nonbonded Distance : 1.183 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.18 % Favored : 96.78 % Rotamer: Outliers : 4.09 % Allowed : 24.69 % Favored : 71.22 % 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 aren not related in a simple way. whole: 2.64 (0.17), residues: 2704 helix: 2.64 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -0.45 (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 K 91 PHE 0.014 0.001 PHE H 60 HIS 0.005 0.001 HIS H 23 Details of bonding type rmsd covalent geometry : bond 0.00346 (22416) covalent geometry : angle 0.51636 (30096) hydrogen bonds : bond 0.04482 ( 1486) hydrogen bonds : angle 3.18935 ( 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: 91 poor density : 269 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8227 (ttp) cc_final: 0.7877 (mtm) REVERT: A 24 MET cc_start: 0.8484 (tpp) cc_final: 0.8129 (mmp) REVERT: A 75 MET cc_start: 0.8199 (tpp) cc_final: 0.7716 (ttm) REVERT: B 14 GLU cc_start: 0.7801 (tm-30) cc_final: 0.6906 (tt0) REVERT: B 24 MET cc_start: 0.7807 (mmt) cc_final: 0.7506 (tpp) REVERT: B 71 GLU cc_start: 0.7708 (tp30) cc_final: 0.7105 (tm-30) REVERT: B 75 MET cc_start: 0.6921 (mtm) cc_final: 0.6677 (mtm) REVERT: C 1 MET cc_start: 0.4896 (OUTLIER) cc_final: 0.4377 (tmm) REVERT: D 152 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7211 (mm-30) REVERT: E 1 MET cc_start: 0.3018 (ppp) cc_final: 0.2079 (ppp) REVERT: E 36 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6705 (mt-10) REVERT: E 75 MET cc_start: 0.7431 (ttm) cc_final: 0.7068 (ttm) REVERT: E 88 TYR cc_start: 0.8931 (OUTLIER) cc_final: 0.8121 (m-10) REVERT: E 105 ARG cc_start: 0.7696 (ptm-80) cc_final: 0.7452 (ttp80) REVERT: E 127 LYS cc_start: 0.7639 (mmtm) cc_final: 0.7067 (tttp) REVERT: F 9 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8117 (mttp) REVERT: F 101 LYS cc_start: 0.8011 (mmtt) cc_final: 0.7807 (mmmt) REVERT: F 102 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: G 24 MET cc_start: 0.8884 (tpp) cc_final: 0.8579 (mmm) REVERT: H 98 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8315 (mt0) REVERT: H 127 LYS cc_start: 0.8190 (mtpp) cc_final: 0.7769 (ttmm) REVERT: I 24 MET cc_start: 0.8897 (tpp) cc_final: 0.8642 (tpp) REVERT: I 75 MET cc_start: 0.6882 (ttt) cc_final: 0.6607 (mtp) REVERT: J 75 MET cc_start: 0.8039 (ttm) cc_final: 0.7809 (mtp) REVERT: J 152 GLU cc_start: 0.7819 (pm20) cc_final: 0.7608 (mp0) REVERT: J 155 GLU cc_start: 0.7854 (tp30) cc_final: 0.7505 (mm-30) REVERT: K 1 MET cc_start: 0.4901 (pmm) cc_final: 0.3573 (mmm) REVERT: K 85 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: K 122 ARG cc_start: 0.6552 (ptp-110) cc_final: 0.6210 (mtm110) REVERT: K 165 GLU cc_start: 0.7854 (pp20) cc_final: 0.7451 (pp20) REVERT: M 121 TYR cc_start: 0.8692 (m-80) cc_final: 0.8368 (m-80) REVERT: N 24 MET cc_start: 0.8295 (tpp) cc_final: 0.8057 (mmm) REVERT: N 40 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7015 (t160) REVERT: N 111 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6543 (pt) REVERT: N 152 GLU cc_start: 0.6137 (pm20) cc_final: 0.5844 (pm20) REVERT: O 1 MET cc_start: 0.7164 (pmm) cc_final: 0.6834 (pmm) REVERT: O 21 MET cc_start: 0.7981 (ttm) cc_final: 0.7722 (mtp) REVERT: O 34 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7633 (tt0) REVERT: O 71 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7772 (mp0) REVERT: P 21 MET cc_start: 0.7750 (mpp) cc_final: 0.7409 (mmm) REVERT: P 63 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6673 (mp) REVERT: P 152 GLU cc_start: 0.7153 (pp20) cc_final: 0.6316 (mp0) outliers start: 91 outliers final: 64 residues processed: 341 average time/residue: 0.1367 time to fit residues: 74.4731 Evaluate side-chains 335 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 260 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 63 LEU 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 1 MET 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 84 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 144 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 69 THR Chi-restraints excluded: chain E residue 88 TYR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 136 ILE 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 102 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 171 GLU 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 98 GLN 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 I residue 115 LYS Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 85 GLU 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 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 12 LEU 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 136 ILE Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 147 TYR Chi-restraints excluded: chain N residue 165 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 109 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 174 optimal weight: 5.9990 chunk 260 optimal weight: 4.9990 chunk 262 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN H 98 GLN K 40 ASN ** N 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.151547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.124073 restraints weight = 30526.707| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 1.92 r_work: 0.3683 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.7633 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= 0.122 Angle : 0.494 12.406 30096 Z= 0.256 Chirality : 0.040 0.146 3152 Planarity : 0.004 0.054 3888 Dihedral : 4.316 55.293 2955 Min Nonbonded Distance : 1.207 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.07 % Favored : 96.89 % Rotamer: Outliers : 3.37 % Allowed : 25.45 % Favored : 71.18 % 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 aren not related in a simple way. whole: 2.76 (0.17), residues: 2704 helix: 2.74 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -0.42 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 105 TYR 0.010 0.001 TYR K 91 PHE 0.012 0.001 PHE D 60 HIS 0.005 0.001 HIS F 23 Details of bonding type rmsd covalent geometry : bond 0.00292 (22416) covalent geometry : angle 0.49444 (30096) hydrogen bonds : bond 0.04089 ( 1486) hydrogen bonds : angle 3.10193 ( 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 356 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 281 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8165 (ttp) cc_final: 0.7832 (mtm) REVERT: A 75 MET cc_start: 0.8160 (tpp) cc_final: 0.7691 (ttm) REVERT: A 167 PHE cc_start: 0.8382 (m-10) cc_final: 0.8179 (m-10) REVERT: B 14 GLU cc_start: 0.7789 (tm-30) cc_final: 0.6866 (tt0) REVERT: B 24 MET cc_start: 0.7850 (mmt) cc_final: 0.7588 (tpp) REVERT: B 71 GLU cc_start: 0.7706 (tp30) cc_final: 0.7102 (tm-30) REVERT: B 75 MET cc_start: 0.6851 (mtm) cc_final: 0.6633 (mtm) REVERT: C 155 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7855 (mm-30) REVERT: D 35 GLN cc_start: 0.6561 (mp10) cc_final: 0.6328 (mt0) REVERT: D 152 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7242 (mm-30) REVERT: E 1 MET cc_start: 0.3043 (ppp) cc_final: 0.2135 (ppp) REVERT: E 13 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7223 (mt-10) REVERT: E 36 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6634 (mt-10) REVERT: E 75 MET cc_start: 0.7374 (ttm) cc_final: 0.6955 (ttm) REVERT: E 88 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.8136 (m-10) REVERT: E 105 ARG cc_start: 0.7686 (ptm-80) cc_final: 0.7465 (ttp80) REVERT: E 127 LYS cc_start: 0.7606 (mmtm) cc_final: 0.7120 (tttp) REVERT: F 9 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8080 (mttp) REVERT: F 102 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: G 24 MET cc_start: 0.8772 (tpp) cc_final: 0.8549 (mmm) REVERT: H 98 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8354 (mt0) REVERT: H 127 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7789 (ttmt) REVERT: I 24 MET cc_start: 0.8846 (tpp) cc_final: 0.8605 (tpp) REVERT: J 75 MET cc_start: 0.8025 (ttm) cc_final: 0.7794 (mtp) REVERT: J 152 GLU cc_start: 0.7826 (pm20) cc_final: 0.7601 (mp0) REVERT: J 155 GLU cc_start: 0.7855 (tp30) cc_final: 0.7509 (mm-30) REVERT: K 1 MET cc_start: 0.4931 (pmm) cc_final: 0.3548 (mmm) REVERT: K 85 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: K 122 ARG cc_start: 0.6591 (ptp-110) cc_final: 0.6166 (mtm110) REVERT: K 140 TYR cc_start: 0.8339 (m-80) cc_final: 0.7924 (m-10) REVERT: K 165 GLU cc_start: 0.7813 (pp20) cc_final: 0.7437 (pp20) REVERT: N 40 ASN cc_start: 0.7921 (t0) cc_final: 0.7047 (t0) REVERT: N 152 GLU cc_start: 0.6020 (pm20) cc_final: 0.5746 (pm20) REVERT: O 1 MET cc_start: 0.7100 (pmm) cc_final: 0.6789 (pmm) REVERT: O 21 MET cc_start: 0.7964 (ttm) cc_final: 0.7716 (mtp) REVERT: O 34 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7607 (tt0) REVERT: O 71 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7701 (mp0) REVERT: P 63 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6624 (mp) REVERT: P 152 GLU cc_start: 0.7203 (pp20) cc_final: 0.6262 (mp0) outliers start: 75 outliers final: 58 residues processed: 339 average time/residue: 0.1414 time to fit residues: 76.3562 Evaluate side-chains 338 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 271 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 63 LEU Chi-restraints excluded: chain B residue 66 LEU 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 84 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 144 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 69 THR Chi-restraints excluded: chain E residue 88 TYR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 151 ASP 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 171 GLU 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 98 GLN 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 I residue 115 LYS Chi-restraints excluded: chain J residue 116 ILE Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 85 GLU 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 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 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 136 ILE Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 147 TYR 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 136 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 153 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 242 optimal weight: 1.9990 chunk 193 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 98 GLN J 40 ASN N 40 ASN N 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.152007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.124440 restraints weight = 30720.086| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.95 r_work: 0.3684 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.7746 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= 0.122 Angle : 0.505 12.924 30096 Z= 0.260 Chirality : 0.040 0.146 3152 Planarity : 0.004 0.053 3888 Dihedral : 4.271 54.872 2953 Min Nonbonded Distance : 1.207 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.14 % Favored : 96.82 % Rotamer: Outliers : 3.73 % Allowed : 25.31 % 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 aren not related in a simple way. whole: 2.76 (0.17), residues: 2704 helix: 2.73 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -0.40 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 122 TYR 0.017 0.001 TYR J 121 PHE 0.012 0.001 PHE F 97 HIS 0.005 0.001 HIS F 23 Details of bonding type rmsd covalent geometry : bond 0.00293 (22416) covalent geometry : angle 0.50452 (30096) hydrogen bonds : bond 0.04043 ( 1486) hydrogen bonds : angle 3.09427 ( 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 364 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 281 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8142 (ttp) cc_final: 0.7936 (mtm) REVERT: A 75 MET cc_start: 0.8150 (tpp) cc_final: 0.7648 (ttm) REVERT: A 167 PHE cc_start: 0.8410 (m-10) cc_final: 0.8203 (m-10) REVERT: B 14 GLU cc_start: 0.7805 (tm-30) cc_final: 0.6855 (tt0) REVERT: B 24 MET cc_start: 0.7873 (mmt) cc_final: 0.7610 (tpp) REVERT: B 71 GLU cc_start: 0.7788 (tp30) cc_final: 0.7087 (tm-30) REVERT: B 75 MET cc_start: 0.6800 (mtm) cc_final: 0.6589 (mtm) REVERT: D 151 ASP cc_start: 0.7535 (m-30) cc_final: 0.7307 (m-30) REVERT: D 152 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7264 (mm-30) REVERT: D 164 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6465 (tptm) REVERT: E 1 MET cc_start: 0.2962 (ppp) cc_final: 0.1974 (ppp) REVERT: E 13 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7147 (mt-10) REVERT: E 36 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6658 (mt-10) REVERT: E 75 MET cc_start: 0.7387 (ttm) cc_final: 0.6980 (ttm) REVERT: E 88 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.8071 (m-10) REVERT: E 105 ARG cc_start: 0.7695 (ptm-80) cc_final: 0.7480 (ttp80) REVERT: E 127 LYS cc_start: 0.7662 (mmtm) cc_final: 0.7180 (tttp) REVERT: F 1 MET cc_start: 0.5345 (tpp) cc_final: 0.4339 (ptt) REVERT: F 9 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8077 (mttp) REVERT: F 102 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.6520 (mp0) REVERT: G 24 MET cc_start: 0.8783 (tpp) cc_final: 0.8566 (mmm) REVERT: H 127 LYS cc_start: 0.8174 (mtpp) cc_final: 0.7808 (ttmt) REVERT: I 24 MET cc_start: 0.8813 (tpp) cc_final: 0.8608 (tpp) REVERT: J 152 GLU cc_start: 0.7794 (pm20) cc_final: 0.7574 (mp0) REVERT: J 155 GLU cc_start: 0.7885 (tp30) cc_final: 0.7550 (mm-30) REVERT: K 1 MET cc_start: 0.5104 (pmm) cc_final: 0.3705 (mmm) REVERT: K 85 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: K 122 ARG cc_start: 0.6593 (ptp-110) cc_final: 0.6166 (mtm110) REVERT: K 165 GLU cc_start: 0.7795 (pp20) cc_final: 0.7403 (pp20) REVERT: M 21 MET cc_start: 0.8200 (mtm) cc_final: 0.7896 (mtm) REVERT: M 126 GLU cc_start: 0.7762 (tp30) cc_final: 0.7038 (tm-30) REVERT: N 34 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7174 (tt0) REVERT: N 40 ASN cc_start: 0.8084 (t0) cc_final: 0.7084 (t0) REVERT: N 134 ILE cc_start: 0.6991 (OUTLIER) cc_final: 0.6725 (tp) REVERT: O 1 MET cc_start: 0.6993 (pmm) cc_final: 0.6685 (pmm) REVERT: O 21 MET cc_start: 0.7966 (ttm) cc_final: 0.7717 (mtp) REVERT: O 34 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7624 (tt0) REVERT: O 71 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7672 (mp0) REVERT: P 63 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6572 (mp) REVERT: P 152 GLU cc_start: 0.7200 (pp20) cc_final: 0.6299 (mp0) outliers start: 83 outliers final: 62 residues processed: 345 average time/residue: 0.1569 time to fit residues: 85.0802 Evaluate side-chains 345 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 274 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 63 LEU Chi-restraints excluded: chain B residue 66 LEU 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 81 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 164 LYS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 88 TYR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 165 GLU 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 171 GLU 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 165 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 85 GLU 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 150 VAL Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 136 ILE 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 134 ILE Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 147 TYR 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 136 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 124 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 240 optimal weight: 0.0980 chunk 35 optimal weight: 5.9990 chunk 196 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 159 optimal weight: 0.0040 chunk 122 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 98 GLN J 40 ASN K 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 = 0.4164 r_free = 0.4164 target = 0.155034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.127841 restraints weight = 30786.933| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.94 r_work: 0.3733 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.7839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 22416 Z= 0.098 Angle : 0.476 13.627 30096 Z= 0.243 Chirality : 0.039 0.145 3152 Planarity : 0.004 0.051 3888 Dihedral : 4.156 57.994 2953 Min Nonbonded Distance : 1.258 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.88 % Favored : 97.08 % Rotamer: Outliers : 2.56 % Allowed : 26.17 % 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 aren not related in a simple way. whole: 2.98 (0.17), residues: 2704 helix: 2.89 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -0.30 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 46 TYR 0.009 0.001 TYR P 26 PHE 0.014 0.001 PHE F 97 HIS 0.005 0.001 HIS F 23 Details of bonding type rmsd covalent geometry : bond 0.00221 (22416) covalent geometry : angle 0.47571 (30096) hydrogen bonds : bond 0.03361 ( 1486) hydrogen bonds : angle 2.96088 ( 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 345 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 288 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.8085 (tpp) cc_final: 0.7684 (ttm) REVERT: B 14 GLU cc_start: 0.7747 (tm-30) cc_final: 0.6786 (tt0) REVERT: B 24 MET cc_start: 0.7832 (mmt) cc_final: 0.7604 (tpp) REVERT: B 71 GLU cc_start: 0.7756 (tp30) cc_final: 0.7178 (tm-30) REVERT: D 151 ASP cc_start: 0.7592 (m-30) cc_final: 0.7369 (m-30) REVERT: E 1 MET cc_start: 0.3065 (ppp) cc_final: 0.2814 (ppp) REVERT: E 13 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7105 (mt-10) REVERT: E 36 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6508 (mt-10) REVERT: E 75 MET cc_start: 0.7335 (ttm) cc_final: 0.6946 (ttm) REVERT: E 88 TYR cc_start: 0.8892 (OUTLIER) cc_final: 0.8045 (m-10) REVERT: E 105 ARG cc_start: 0.7684 (ptm-80) cc_final: 0.7418 (ttp80) REVERT: F 1 MET cc_start: 0.5283 (tpp) cc_final: 0.4277 (ptt) REVERT: F 9 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7983 (mttp) REVERT: G 21 MET cc_start: 0.7977 (mmm) cc_final: 0.7750 (mtt) REVERT: G 24 MET cc_start: 0.8806 (tpp) cc_final: 0.8588 (mmm) REVERT: H 127 LYS cc_start: 0.8155 (mtpp) cc_final: 0.7878 (ttmt) REVERT: I 24 MET cc_start: 0.8840 (tpp) cc_final: 0.8600 (tpp) REVERT: I 75 MET cc_start: 0.6753 (ttt) cc_final: 0.6158 (mtt) REVERT: J 152 GLU cc_start: 0.7801 (pm20) cc_final: 0.7568 (mp0) REVERT: J 155 GLU cc_start: 0.7848 (tp30) cc_final: 0.7551 (mm-30) REVERT: K 1 MET cc_start: 0.5101 (pmm) cc_final: 0.3687 (mmm) REVERT: K 85 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: K 122 ARG cc_start: 0.6560 (ptp-110) cc_final: 0.6138 (mtm110) REVERT: K 140 TYR cc_start: 0.8157 (m-80) cc_final: 0.7867 (m-80) REVERT: K 165 GLU cc_start: 0.7806 (pp20) cc_final: 0.7427 (pp20) REVERT: M 21 MET cc_start: 0.8133 (mtm) cc_final: 0.7830 (mtm) REVERT: M 126 GLU cc_start: 0.7746 (tp30) cc_final: 0.7021 (tm-30) REVERT: N 34 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7136 (tt0) REVERT: N 63 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6587 (mt) REVERT: N 98 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8467 (mp10) REVERT: N 121 TYR cc_start: 0.8222 (m-80) cc_final: 0.7888 (m-10) REVERT: N 134 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6635 (tp) REVERT: N 152 GLU cc_start: 0.5884 (pm20) cc_final: 0.5630 (pm20) REVERT: O 1 MET cc_start: 0.7142 (pmm) cc_final: 0.6829 (pmm) REVERT: O 34 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7640 (tt0) REVERT: O 71 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7805 (mp0) REVERT: P 63 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6276 (mp) REVERT: P 152 GLU cc_start: 0.7188 (pp20) cc_final: 0.6386 (mp0) outliers start: 57 outliers final: 43 residues processed: 329 average time/residue: 0.1487 time to fit residues: 78.0062 Evaluate side-chains 326 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 275 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 63 LEU Chi-restraints excluded: chain B residue 66 LEU 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 144 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 88 TYR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain F residue 9 LYS 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 84 VAL Chi-restraints excluded: chain G residue 145 CYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 85 GLU 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 150 VAL Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 136 ILE 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 98 GLN Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain N residue 147 TYR Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain O residue 136 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 145 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 chunk 217 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 198 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 203 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 98 GLN E 72 ASN J 40 ASN K 40 ASN N 98 GLN O 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.151493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.123789 restraints weight = 30611.438| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.95 r_work: 0.3679 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.7943 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= 0.133 Angle : 0.519 13.690 30096 Z= 0.266 Chirality : 0.040 0.148 3152 Planarity : 0.004 0.052 3888 Dihedral : 4.254 58.999 2953 Min Nonbonded Distance : 1.187 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.29 % Favored : 96.67 % Rotamer: Outliers : 2.88 % Allowed : 26.08 % 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 aren not related in a simple way. whole: 2.85 (0.17), residues: 2704 helix: 2.79 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -0.35 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 46 TYR 0.021 0.001 TYR J 121 PHE 0.013 0.001 PHE H 60 HIS 0.007 0.001 HIS F 23 Details of bonding type rmsd covalent geometry : bond 0.00325 (22416) covalent geometry : angle 0.51855 (30096) hydrogen bonds : bond 0.04141 ( 1486) hydrogen bonds : angle 3.10965 ( 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 346 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 282 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8267 (tpp) cc_final: 0.7880 (ttm) REVERT: A 140 TYR cc_start: 0.7668 (m-80) cc_final: 0.7352 (m-80) REVERT: B 14 GLU cc_start: 0.7790 (tm-30) cc_final: 0.6815 (tt0) REVERT: B 24 MET cc_start: 0.7817 (mmt) cc_final: 0.7587 (tpp) REVERT: B 71 GLU cc_start: 0.7720 (tp30) cc_final: 0.7162 (tm-30) REVERT: B 88 TYR cc_start: 0.8702 (m-80) cc_final: 0.8476 (m-80) REVERT: D 151 ASP cc_start: 0.7604 (m-30) cc_final: 0.7357 (m-30) REVERT: D 152 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7298 (mm-30) REVERT: E 13 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7191 (mt-10) REVERT: E 36 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6619 (mt-10) REVERT: E 75 MET cc_start: 0.7396 (ttm) cc_final: 0.6994 (ttm) REVERT: E 88 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.8032 (m-10) REVERT: E 105 ARG cc_start: 0.7700 (ptm-80) cc_final: 0.7485 (ttp80) REVERT: E 127 LYS cc_start: 0.7594 (mmtm) cc_final: 0.6975 (tttp) REVERT: F 1 MET cc_start: 0.5328 (tpp) cc_final: 0.4299 (ptt) REVERT: F 9 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8112 (mttp) REVERT: F 102 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6265 (mp0) REVERT: G 24 MET cc_start: 0.8777 (tpp) cc_final: 0.8569 (mmm) REVERT: H 127 LYS cc_start: 0.8196 (mtpp) cc_final: 0.7915 (ttmt) REVERT: I 24 MET cc_start: 0.8874 (tpp) cc_final: 0.8638 (tpp) REVERT: J 152 GLU cc_start: 0.7849 (pm20) cc_final: 0.7607 (mp0) REVERT: J 155 GLU cc_start: 0.7885 (tp30) cc_final: 0.7543 (mm-30) REVERT: K 1 MET cc_start: 0.5298 (pmm) cc_final: 0.3818 (mmm) REVERT: K 85 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: K 122 ARG cc_start: 0.6479 (ptp-110) cc_final: 0.5979 (mtm110) REVERT: K 140 TYR cc_start: 0.8256 (m-80) cc_final: 0.7951 (m-80) REVERT: K 165 GLU cc_start: 0.7825 (pp20) cc_final: 0.7455 (pp20) REVERT: M 21 MET cc_start: 0.8173 (mtm) cc_final: 0.7879 (mtm) REVERT: M 126 GLU cc_start: 0.7859 (tp30) cc_final: 0.7109 (tm-30) REVERT: N 34 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7121 (tt0) REVERT: N 134 ILE cc_start: 0.6959 (OUTLIER) cc_final: 0.6684 (tp) REVERT: N 152 GLU cc_start: 0.5924 (pm20) cc_final: 0.5679 (pm20) REVERT: O 1 MET cc_start: 0.7091 (pmm) cc_final: 0.6683 (pmm) REVERT: O 34 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7598 (tt0) REVERT: O 71 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7748 (mp0) REVERT: P 63 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6585 (mp) REVERT: P 152 GLU cc_start: 0.7186 (pp20) cc_final: 0.6302 (mp0) outliers start: 64 outliers final: 49 residues processed: 331 average time/residue: 0.1529 time to fit residues: 80.4406 Evaluate side-chains 336 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 279 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 63 LEU 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 144 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 87 MET Chi-restraints excluded: chain E residue 88 TYR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 165 GLU 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 171 GLU 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 H residue 165 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 136 ILE 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 134 ILE Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 147 TYR Chi-restraints excluded: chain O residue 20 SER Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain O residue 136 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: 4.9990 chunk 164 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 240 optimal weight: 0.0020 chunk 103 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN E 72 ASN F 58 ASN J 40 ASN K 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 = 0.4148 r_free = 0.4148 target = 0.153679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.126320 restraints weight = 30626.197| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.93 r_work: 0.3713 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.8015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 22416 Z= 0.106 Angle : 0.489 13.792 30096 Z= 0.249 Chirality : 0.039 0.144 3152 Planarity : 0.004 0.051 3888 Dihedral : 4.138 56.006 2951 Min Nonbonded Distance : 1.237 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.56 % Allowed : 26.21 % 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 aren not related in a simple way. whole: 2.95 (0.17), residues: 2704 helix: 2.86 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -0.29 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 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 covalent geometry : bond 0.00250 (22416) covalent geometry : angle 0.48914 (30096) hydrogen bonds : bond 0.03636 ( 1486) hydrogen bonds : angle 3.02921 ( 4296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6038.40 seconds wall clock time: 104 minutes 7.80 seconds (6247.80 seconds total)