Starting phenix.real_space_refine on Mon Jul 6 08:23:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xnn_38508/07_2026/8xnn_38508_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xnn_38508/07_2026/8xnn_38508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xnn_38508/07_2026/8xnn_38508_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xnn_38508/07_2026/8xnn_38508_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xnn_38508/07_2026/8xnn_38508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xnn_38508/07_2026/8xnn_38508.map" } resolution = 3.6 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= 0.002 sd= 0.081 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: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 12 5.49 5 S 245 5.16 5 C 22032 2.51 5 N 5856 2.21 5 O 6246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34420 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 743 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "B" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1258 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 10, 'TRANS': 146} Chain: "C" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1641 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 3056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3056 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 20, 'TRANS': 360} Chain breaks: 1 Chain: "E" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1635 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 21, 'TRANS': 188} Chain: "F" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3288 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 21, 'TRANS': 404} Chain: "G" Number of atoms: 5287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5287 Classifications: {'peptide': 687} Link IDs: {'PTRANS': 31, 'TRANS': 655} Chain: "H" Number of atoms: 2479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2479 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 22, 'TRANS': 287} Chain breaks: 2 Chain: "I" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1431 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 9, 'TRANS': 168} Chain: "P" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2720 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 19, 'TRANS': 319} Chain: "Q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 957 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "R" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 660 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "S" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 667 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "T" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "V" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1164 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "Z" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1152 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 9, 'TRANS': 129} Chain: "a" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 548 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "b" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 11, 'TRANS': 67} Chain: "q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1192 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "r" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 764 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 11, 'TRANS': 83} Chain breaks: 1 Chain: "s" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 189 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {'3PE': 1, 'UQ9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'UQ9:plan-2': 1, 'UQ9:plan-7': 1, 'UQ9:plan-8': 1, 'UQ9:plan-9': 1, 'UQ9:plan-10': 1} Unresolved non-hydrogen planarities: 23 Chain: "I" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "q" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 62 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1006 SG CYS B 99 85.937 58.942 103.282 1.00 29.52 S ATOM 1739 SG CYS B 194 88.994 55.674 106.695 1.00 29.28 S ATOM 1012 SG CYS B 100 84.137 54.611 102.008 1.00 30.11 S ATOM 1509 SG CYS B 164 83.444 55.265 108.098 1.00 28.96 S ATOM 7487 SG CYS E 134 148.215 49.424 145.829 1.00 56.01 S ATOM 7521 SG CYS E 139 151.153 50.961 144.742 1.00 56.50 S ATOM 7805 SG CYS E 175 146.295 53.072 148.466 1.00 54.42 S ATOM 7828 SG CYS E 179 149.233 54.737 149.118 1.00 57.95 S ATOM 11358 SG CYS F 425 129.905 59.009 149.613 1.00 45.60 S ATOM 11036 SG CYS F 385 129.560 56.587 143.807 1.00 39.95 S ATOM 11016 SG CYS F 382 125.453 57.765 146.347 1.00 40.29 S ATOM 10997 SG CYS F 379 127.554 53.655 149.046 1.00 43.09 S ATOM 12406 SG CYS G 131 108.528 46.787 133.848 1.00 31.31 S ATOM 12385 SG CYS G 128 110.282 50.623 129.144 1.00 30.26 S ATOM 12446 SG CYS G 137 108.325 52.690 135.299 1.00 33.13 S ATOM 13131 SG CYS G 226 110.578 46.763 142.327 1.00 34.31 S ATOM 12802 SG CYS G 182 114.055 45.054 147.875 1.00 36.31 S ATOM 12778 SG CYS G 179 113.321 50.644 145.387 1.00 35.62 S ATOM 12755 SG CYS G 176 116.578 46.358 142.705 1.00 34.05 S ATOM 11892 SG CYS G 64 114.892 56.668 147.324 1.00 35.53 S ATOM 11978 SG CYS G 75 115.531 58.710 145.621 1.00 36.47 S ATOM 12003 SG CYS G 78 114.774 62.933 147.612 1.00 36.76 S ATOM 12104 SG CYS G 92 114.136 60.904 150.863 1.00 39.04 S ATOM 20106 SG CYS I 123 93.111 50.164 115.972 1.00 27.30 S ATOM 20332 SG CYS I 152 92.513 49.012 110.886 1.00 27.39 S ATOM 20379 SG CYS I 158 98.301 49.082 112.617 1.00 26.60 S ATOM 20358 SG CYS I 155 95.250 53.548 112.506 1.00 27.04 S ATOM 20055 SG CYS I 116 103.355 45.953 122.692 1.00 29.24 S ATOM 20078 SG CYS I 119 98.773 45.698 119.630 1.00 28.85 S ATOM 20036 SG CYS I 113 101.917 40.840 119.504 1.00 28.61 S ATOM 20408 SG CYS I 162 104.737 45.403 117.222 1.00 28.07 S ATOM 24907 SG CYS R 79 118.341 38.669 120.501 1.00 32.60 S ATOM 25083 SG CYS R 104 115.789 39.157 123.228 1.00 32.49 S ATOM 25105 SG CYS R 107 115.310 37.953 119.078 1.00 30.78 S Time building chain proxies: 7.31, per 1000 atoms: 0.21 Number of scatterers: 34420 At special positions: 0 Unit cell: (177.1, 126.5, 199.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 245 16.00 P 12 15.00 O 6246 8.00 N 5856 7.00 C 22032 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 24 " - pdb=" SG CYS S 58 " distance=2.04 Simple disulfide: pdb=" SG CYS X 78 " - pdb=" SG CYS X 110 " distance=2.02 Simple disulfide: pdb=" SG CYS X 88 " - pdb=" SG CYS X 100 " distance=2.02 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: 3.17 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 134 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 139 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 175 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 179 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 78 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 75 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 64 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 92 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 164 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 100 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 194 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 99 " pdb=" SF4 F 502 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 379 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 382 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 425 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 385 " pdb=" SF4 G 801 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 131 " pdb="FE1 SF4 G 801 " - pdb=" NE2 HIS G 124 " pdb="FE3 SF4 G 801 " - pdb=" SG CYS G 128 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 137 " pdb=" SF4 G 802 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 176 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 226 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 179 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 182 " pdb=" SF4 I 302 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 123 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 152 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 155 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 158 " pdb="FE2 SF4 I 302 " - pdb=" NE2 HIS I 101 " pdb=" SF4 I 303 " pdb="FE3 SF4 I 303 " - pdb=" SG CYS I 113 " pdb="FE4 SF4 I 303 " - pdb=" SG CYS I 162 " pdb="FE2 SF4 I 303 " - pdb=" SG CYS I 119 " pdb="FE1 SF4 I 303 " - pdb=" SG CYS I 116 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 107 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 79 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 104 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 88 " Number of angles added : 3 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7948 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 32 sheets defined 49.3% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 Processing helix chain 'A' and resid 53 through 73 Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.311A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 108 Processing helix chain 'B' and resid 70 through 89 removed outlier: 3.637A pdb=" N ASP B 79 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 removed outlier: 4.014A pdb=" N MET B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 141 through 152 removed outlier: 3.711A pdb=" N LYS B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 215 Processing helix chain 'B' and resid 216 through 223 Processing helix chain 'C' and resid 50 through 68 removed outlier: 4.014A pdb=" N HIS C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 58 " --> pdb=" O HIS C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 102 through 106 removed outlier: 4.321A pdb=" N GLN C 106 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.116A pdb=" N TYR C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 129 through 138 Proline residue: D 134 - end of helix Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.515A pdb=" N ALA D 150 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 195 Processing helix chain 'D' and resid 197 through 219 removed outlier: 3.830A pdb=" N PHE D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 206 " --> pdb=" O TRP D 202 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 263 removed outlier: 4.178A pdb=" N SER D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 273 Processing helix chain 'D' and resid 279 through 286 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.922A pdb=" N SER D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 325 through 350 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 428 through 434 Processing helix chain 'D' and resid 434 through 439 Processing helix chain 'D' and resid 444 through 453 removed outlier: 3.708A pdb=" N VAL D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 463 removed outlier: 3.620A pdb=" N ILE D 461 " --> pdb=" O VAL D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 removed outlier: 3.952A pdb=" N TYR E 69 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 76 Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 107 through 118 removed outlier: 3.680A pdb=" N VAL E 111 " --> pdb=" O PRO E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 142 Processing helix chain 'E' and resid 143 through 156 removed outlier: 4.163A pdb=" N ILE E 147 " --> pdb=" O ASP E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 209 removed outlier: 3.577A pdb=" N ILE E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 201 " --> pdb=" O PRO E 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 64 through 72 Processing helix chain 'F' and resid 72 through 84 Processing helix chain 'F' and resid 94 through 101 Processing helix chain 'F' and resid 125 through 134 removed outlier: 3.554A pdb=" N GLU F 129 " --> pdb=" O CYS F 125 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 150 removed outlier: 3.923A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA F 148 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 180 removed outlier: 3.514A pdb=" N ALA F 166 " --> pdb=" O PHE F 162 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 208 through 218 removed outlier: 3.832A pdb=" N ILE F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 Processing helix chain 'F' and resid 245 through 266 removed outlier: 3.602A pdb=" N SER F 251 " --> pdb=" O THR F 247 " (cutoff:3.500A) Proline residue: F 252 - end of helix removed outlier: 5.533A pdb=" N GLY F 259 " --> pdb=" O CYS F 255 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TRP F 261 " --> pdb=" O ARG F 257 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE F 265 " --> pdb=" O TRP F 261 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 303 removed outlier: 3.562A pdb=" N ILE F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 335 removed outlier: 4.185A pdb=" N THR F 334 " --> pdb=" O SER F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 345 Processing helix chain 'F' and resid 362 through 376 removed outlier: 3.548A pdb=" N LEU F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 402 removed outlier: 3.661A pdb=" N ASP F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.774A pdb=" N SER F 411 " --> pdb=" O ALA F 407 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 457 removed outlier: 4.350A pdb=" N ASP F 429 " --> pdb=" O CYS F 425 " (cutoff:3.500A) Proline residue: F 434 - end of helix removed outlier: 3.519A pdb=" N ARG F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) Proline residue: F 444 - end of helix Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.597A pdb=" N VAL G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 115 removed outlier: 3.725A pdb=" N ARG G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 123 removed outlier: 3.714A pdb=" N ASN G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 147 Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.933A pdb=" N ASP G 203 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET G 204 " --> pdb=" O GLY G 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 200 through 204' Processing helix chain 'G' and resid 220 through 226 removed outlier: 3.818A pdb=" N ASP G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 293 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 318 through 333 Processing helix chain 'G' and resid 347 through 360 Processing helix chain 'G' and resid 390 through 397 removed outlier: 3.669A pdb=" N GLU G 395 " --> pdb=" O ALA G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 411 Processing helix chain 'G' and resid 411 through 424 removed outlier: 4.026A pdb=" N ARG G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 458 Processing helix chain 'G' and resid 461 through 468 removed outlier: 4.007A pdb=" N VAL G 465 " --> pdb=" O SER G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 482 removed outlier: 3.638A pdb=" N LEU G 481 " --> pdb=" O GLY G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 505 Processing helix chain 'G' and resid 522 through 528 Processing helix chain 'G' and resid 534 through 540 Processing helix chain 'G' and resid 618 through 629 Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 651 through 655 Processing helix chain 'G' and resid 664 through 675 removed outlier: 3.523A pdb=" N ALA G 668 " --> pdb=" O TYR G 664 " (cutoff:3.500A) Processing helix chain 'G' and resid 690 through 696 removed outlier: 3.641A pdb=" N PHE G 694 " --> pdb=" O THR G 690 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET G 696 " --> pdb=" O LYS G 692 " (cutoff:3.500A) Processing helix chain 'G' and resid 698 through 703 Processing helix chain 'G' and resid 704 through 715 Processing helix chain 'H' and resid 2 through 32 Proline residue: H 12 - end of helix removed outlier: 3.511A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY H 29 " --> pdb=" O ARG H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 58 removed outlier: 3.595A pdb=" N ASP H 51 " --> pdb=" O GLN H 47 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA H 52 " --> pdb=" O PRO H 48 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET H 53 " --> pdb=" O PHE H 49 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS H 54 " --> pdb=" O ALA H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 85 removed outlier: 3.739A pdb=" N THR H 76 " --> pdb=" O ILE H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 124 removed outlier: 3.687A pdb=" N SER H 112 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 156 removed outlier: 3.762A pdb=" N ALA H 137 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLN H 138 " --> pdb=" O ARG H 134 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET H 146 " --> pdb=" O TYR H 142 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 164 through 169 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.735A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 277 Processing helix chain 'H' and resid 281 through 291 Processing helix chain 'H' and resid 293 through 311 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 49 through 62 Processing helix chain 'I' and resid 63 through 78 removed outlier: 3.529A pdb=" N THR I 73 " --> pdb=" O GLY I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 123 Processing helix chain 'I' and resid 156 through 162 Processing helix chain 'I' and resid 179 through 183 removed outlier: 3.867A pdb=" N LEU I 183 " --> pdb=" O THR I 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 179 through 183' Processing helix chain 'I' and resid 186 through 209 removed outlier: 5.143A pdb=" N ALA I 199 " --> pdb=" O ASP I 195 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLU I 200 " --> pdb=" O LYS I 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 77 removed outlier: 3.805A pdb=" N TYR P 68 " --> pdb=" O PHE P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 90 Processing helix chain 'P' and resid 91 through 96 removed outlier: 3.669A pdb=" N ARG P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU P 96 " --> pdb=" O MET P 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 91 through 96' Processing helix chain 'P' and resid 112 through 122 removed outlier: 4.105A pdb=" N ILE P 116 " --> pdb=" O ASP P 112 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N HIS P 122 " --> pdb=" O LYS P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 146 Processing helix chain 'P' and resid 146 through 160 removed outlier: 3.626A pdb=" N ALA P 153 " --> pdb=" O PRO P 149 " (cutoff:3.500A) Processing helix chain 'P' and resid 178 through 195 removed outlier: 3.754A pdb=" N ARG P 192 " --> pdb=" O GLU P 188 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER P 193 " --> pdb=" O LYS P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 219 removed outlier: 4.080A pdb=" N PHE P 217 " --> pdb=" O PHE P 213 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 222 No H-bonds generated for 'chain 'P' and resid 220 through 222' Processing helix chain 'P' and resid 229 through 232 Processing helix chain 'P' and resid 242 through 254 Processing helix chain 'P' and resid 272 through 285 Processing helix chain 'P' and resid 294 through 308 removed outlier: 3.881A pdb=" N TRP P 300 " --> pdb=" O PHE P 296 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER P 308 " --> pdb=" O LEU P 304 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 323 Processing helix chain 'P' and resid 344 through 354 removed outlier: 4.033A pdb=" N LYS P 348 " --> pdb=" O PRO P 344 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE P 350 " --> pdb=" O GLU P 346 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLU P 351 " --> pdb=" O LEU P 347 " (cutoff:3.500A) Processing helix chain 'P' and resid 355 through 357 No H-bonds generated for 'chain 'P' and resid 355 through 357' Processing helix chain 'P' and resid 358 through 363 removed outlier: 4.675A pdb=" N SER P 363 " --> pdb=" O TYR P 359 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 66 removed outlier: 4.415A pdb=" N GLY Q 66 " --> pdb=" O THR Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 74 Processing helix chain 'Q' and resid 130 through 142 Processing helix chain 'Q' and resid 159 through 165 Processing helix chain 'R' and resid 44 through 49 removed outlier: 3.726A pdb=" N PHE R 48 " --> pdb=" O ARG R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 67 removed outlier: 4.039A pdb=" N ALA R 65 " --> pdb=" O ILE R 61 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 87 Processing helix chain 'S' and resid 30 through 48 removed outlier: 5.951A pdb=" N VAL S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 77 through 90 Processing helix chain 'T' and resid 111 through 126 Processing helix chain 'T' and resid 131 through 138 removed outlier: 3.678A pdb=" N LYS T 137 " --> pdb=" O ILE T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 150 Processing helix chain 'V' and resid 19 through 36 Processing helix chain 'V' and resid 42 through 62 Processing helix chain 'V' and resid 64 through 72 Processing helix chain 'V' and resid 76 through 98 removed outlier: 3.678A pdb=" N VAL V 80 " --> pdb=" O GLU V 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 53 removed outlier: 3.588A pdb=" N ARG W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) Proline residue: W 47 - end of helix Processing helix chain 'W' and resid 58 through 73 removed outlier: 3.616A pdb=" N ASN W 73 " --> pdb=" O MET W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 98 Processing helix chain 'W' and resid 102 through 108 Processing helix chain 'W' and resid 109 through 111 No H-bonds generated for 'chain 'W' and resid 109 through 111' Processing helix chain 'W' and resid 120 through 128 Processing helix chain 'X' and resid 10 through 14 removed outlier: 3.509A pdb=" N LYS X 14 " --> pdb=" O GLU X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 36 removed outlier: 4.427A pdb=" N HIS X 30 " --> pdb=" O LYS X 26 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N HIS X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA X 34 " --> pdb=" O HIS X 30 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 50 Processing helix chain 'X' and resid 52 through 77 removed outlier: 3.574A pdb=" N CYS X 56 " --> pdb=" O ASP X 52 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LYS X 58 " --> pdb=" O ARG X 54 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLU X 59 " --> pdb=" O ARG X 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 92 removed outlier: 3.945A pdb=" N SER X 92 " --> pdb=" O CYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 111 Processing helix chain 'X' and resid 140 through 144 removed outlier: 3.993A pdb=" N SER X 144 " --> pdb=" O PRO X 141 " (cutoff:3.500A) Processing helix chain 'Z' and resid 31 through 99 removed outlier: 3.534A pdb=" N GLY Z 39 " --> pdb=" O MET Z 35 " (cutoff:3.500A) Proline residue: Z 73 - end of helix Processing helix chain 'Z' and resid 120 through 126 Processing helix chain 'Z' and resid 129 through 139 Processing helix chain 'a' and resid 1 through 3 No H-bonds generated for 'chain 'a' and resid 1 through 3' Processing helix chain 'a' and resid 4 through 31 removed outlier: 4.633A pdb=" N GLY a 8 " --> pdb=" O GLU a 4 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 4.599A pdb=" N LYS a 28 " --> pdb=" O ALA a 24 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR a 30 " --> pdb=" O ILE a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 55 Processing helix chain 'b' and resid 7 through 15 Processing helix chain 'b' and resid 18 through 32 Processing helix chain 'b' and resid 38 through 49 removed outlier: 3.760A pdb=" N ALA b 42 " --> pdb=" O TYR b 38 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER b 43 " --> pdb=" O THR b 39 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 17 removed outlier: 3.556A pdb=" N HIS q 17 " --> pdb=" O GLN q 13 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 31 Processing helix chain 'q' and resid 55 through 58 Processing helix chain 'q' and resid 78 through 82 Processing helix chain 'q' and resid 83 through 91 removed outlier: 4.127A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 17 Processing helix chain 'r' and resid 53 through 57 Processing helix chain 'r' and resid 58 through 63 removed outlier: 3.954A pdb=" N GLU r 62 " --> pdb=" O ASP r 58 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL r 63 " --> pdb=" O GLY r 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 58 through 63' Processing helix chain 's' and resid 43 through 54 removed outlier: 4.202A pdb=" N LYS s 54 " --> pdb=" O LEU s 50 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94 removed outlier: 6.135A pdb=" N MET B 131 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET B 161 " --> pdb=" O MET B 131 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL B 133 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL B 158 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL B 191 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER B 160 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 86 through 87 removed outlier: 3.506A pdb=" N GLN C 74 " --> pdb=" O CYS C 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 109 through 117 removed outlier: 5.889A pdb=" N LEU C 110 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU C 132 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL C 116 " --> pdb=" O GLU C 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 152 through 153 removed outlier: 7.148A pdb=" N ILE C 152 " --> pdb=" O PHE C 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 207 through 212 removed outlier: 3.563A pdb=" N ARG C 210 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 82 through 84 removed outlier: 4.240A pdb=" N ARG D 96 " --> pdb=" O HIS D 112 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 98 " --> pdb=" O ASP D 110 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS D 108 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N SER D 102 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N VAL D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS D 442 " --> pdb=" O VAL D 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 394 through 401 Processing sheet with id=AA8, first strand: chain 'E' and resid 171 through 173 removed outlier: 5.587A pdb=" N MET E 184 " --> pdb=" O CYS E 134 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 194 through 199 removed outlier: 6.441A pdb=" N ALA F 154 " --> pdb=" O PHE F 196 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL F 198 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE F 156 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR F 241 " --> pdb=" O TYR F 112 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 286 through 291 removed outlier: 3.514A pdb=" N GLU F 290 " --> pdb=" O LYS F 274 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 294 through 295 removed outlier: 3.548A pdb=" N VAL F 294 " --> pdb=" O MET F 337 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 32 through 34 Processing sheet with id=AB4, first strand: chain 'G' and resid 79 through 80 Processing sheet with id=AB5, first strand: chain 'G' and resid 169 through 171 Processing sheet with id=AB6, first strand: chain 'G' and resid 246 through 251 removed outlier: 6.313A pdb=" N ARG G 266 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL G 270 " --> pdb=" O ARG G 266 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 306 through 308 Processing sheet with id=AB8, first strand: chain 'G' and resid 531 through 532 removed outlier: 6.455A pdb=" N LEU G 366 " --> pdb=" O LYS G 531 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA G 339 " --> pdb=" O PHE G 546 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU G 545 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 442 through 446 removed outlier: 6.203A pdb=" N VAL G 400 " --> pdb=" O ALA G 430 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE G 432 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU G 402 " --> pdb=" O ILE G 432 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 595 through 597 Processing sheet with id=AC2, first strand: chain 'I' and resid 100 through 103 Processing sheet with id=AC3, first strand: chain 'I' and resid 128 through 134 removed outlier: 6.407A pdb=" N GLU I 133 " --> pdb=" O THR I 142 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N THR I 142 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 103 through 107 removed outlier: 6.360A pdb=" N THR P 57 " --> pdb=" O ILE P 127 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 206 through 207 Processing sheet with id=AC6, first strand: chain 'P' and resid 226 through 227 removed outlier: 6.119A pdb=" N VAL P 226 " --> pdb=" O TYR P 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'Q' and resid 125 through 128 Processing sheet with id=AC8, first strand: chain 'Q' and resid 106 through 108 Processing sheet with id=AC9, first strand: chain 'R' and resid 70 through 71 removed outlier: 5.820A pdb=" N ASN R 70 " --> pdb=" O LYS R 112 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'R' and resid 76 through 79 removed outlier: 3.589A pdb=" N VAL R 91 " --> pdb=" O CYS R 79 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 53 through 58 removed outlier: 3.576A pdb=" N LYS S 64 " --> pdb=" O HIS S 22 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN S 73 " --> pdb=" O TYR S 69 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 130 through 131 Processing sheet with id=AD4, first strand: chain 'q' and resid 37 through 41 removed outlier: 6.595A pdb=" N TYR q 48 " --> pdb=" O VAL q 39 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'q' and resid 67 through 68 1461 hydrogen bonds defined for protein. 4197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.37 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.36: 11177 1.36 - 1.58: 23596 1.58 - 1.79: 189 1.79 - 2.01: 206 2.01 - 2.23: 80 Bond restraints: 35248 Sorted by residual: bond pdb=" O6 EHZ W 201 " pdb=" P1 EHZ W 201 " ideal model delta sigma weight residual 2.378 1.649 0.729 2.00e-02 2.50e+03 1.33e+03 bond pdb=" C20 EHZ W 201 " pdb=" O6 EHZ W 201 " ideal model delta sigma weight residual 1.191 1.399 -0.208 2.00e-02 2.50e+03 1.09e+02 bond pdb=" CA GLY F 234 " pdb=" C GLY F 234 " ideal model delta sigma weight residual 1.521 1.404 0.117 1.13e-02 7.83e+03 1.08e+02 bond pdb=" N PRO F 227 " pdb=" CD PRO F 227 " ideal model delta sigma weight residual 1.473 1.615 -0.142 1.40e-02 5.10e+03 1.03e+02 bond pdb=" N VAL F 235 " pdb=" CA VAL F 235 " ideal model delta sigma weight residual 1.457 1.342 0.115 1.19e-02 7.06e+03 9.39e+01 ... (remaining 35243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.17: 46956 6.17 - 12.33: 613 12.33 - 18.50: 184 18.50 - 24.66: 7 24.66 - 30.83: 3 Bond angle restraints: 47763 Sorted by residual: angle pdb=" N THR G 174 " pdb=" CA THR G 174 " pdb=" C THR G 174 " ideal model delta sigma weight residual 114.39 89.01 25.38 1.45e+00 4.76e-01 3.06e+02 angle pdb=" S1 FES E 301 " pdb="FE2 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 87.61 16.72 1.14e+00 7.69e-01 2.15e+02 angle pdb=" S1 FES E 301 " pdb="FE1 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 87.46 16.87 1.20e+00 6.94e-01 1.98e+02 angle pdb=" N ILE G 632 " pdb=" CA ILE G 632 " pdb=" C ILE G 632 " ideal model delta sigma weight residual 107.80 88.01 19.79 1.45e+00 4.76e-01 1.86e+02 angle pdb=" N ILE G 251 " pdb=" CA ILE G 251 " pdb=" C ILE G 251 " ideal model delta sigma weight residual 108.17 126.79 -18.62 1.40e+00 5.10e-01 1.77e+02 ... (remaining 47758 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.38: 20675 28.38 - 56.76: 573 56.76 - 85.15: 63 85.15 - 113.53: 6 113.53 - 141.91: 4 Dihedral angle restraints: 21321 sinusoidal: 8995 harmonic: 12326 Sorted by residual: dihedral pdb=" CB CYS X 88 " pdb=" SG CYS X 88 " pdb=" SG CYS X 100 " pdb=" CB CYS X 100 " ideal model delta sinusoidal sigma weight residual 93.00 161.58 -68.58 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" C TYR D 214 " pdb=" N TYR D 214 " pdb=" CA TYR D 214 " pdb=" CB TYR D 214 " ideal model delta harmonic sigma weight residual -122.60 -104.94 -17.66 0 2.50e+00 1.60e-01 4.99e+01 dihedral pdb=" C LEU G 387 " pdb=" N LEU G 387 " pdb=" CA LEU G 387 " pdb=" CB LEU G 387 " ideal model delta harmonic sigma weight residual -122.60 -105.64 -16.96 0 2.50e+00 1.60e-01 4.60e+01 ... (remaining 21318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 4688 0.182 - 0.364: 459 0.364 - 0.546: 42 0.546 - 0.728: 4 0.728 - 0.910: 24 Chirality restraints: 5217 Sorted by residual: chirality pdb="FE1 SF4 B 301 " pdb=" S2 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False -10.55 -9.64 -0.91 2.00e-01 2.50e+01 2.07e+01 chirality pdb="FE4 SF4 G 801 " pdb=" S1 SF4 G 801 " pdb=" S2 SF4 G 801 " pdb=" S3 SF4 G 801 " both_signs ideal model delta sigma weight residual False 10.55 9.65 0.91 2.00e-01 2.50e+01 2.06e+01 chirality pdb="FE4 SF4 G 802 " pdb=" S1 SF4 G 802 " pdb=" S2 SF4 G 802 " pdb=" S3 SF4 G 802 " both_signs ideal model delta sigma weight residual False 10.55 9.65 0.90 2.00e-01 2.50e+01 2.04e+01 ... (remaining 5214 not shown) Planarity restraints: 6066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 H 401 " -0.076 2.00e-02 2.50e+03 2.31e-01 1.60e+03 pdb=" C1M UQ9 H 401 " -0.261 2.00e-02 2.50e+03 pdb=" C2 UQ9 H 401 " -0.050 2.00e-02 2.50e+03 pdb=" C3 UQ9 H 401 " 0.090 2.00e-02 2.50e+03 pdb=" C4 UQ9 H 401 " -0.034 2.00e-02 2.50e+03 pdb=" C5 UQ9 H 401 " -0.104 2.00e-02 2.50e+03 pdb=" C6 UQ9 H 401 " 0.093 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 401 " 0.535 2.00e-02 2.50e+03 pdb=" O2 UQ9 H 401 " -0.136 2.00e-02 2.50e+03 pdb=" O3 UQ9 H 401 " 0.350 2.00e-02 2.50e+03 pdb=" O4 UQ9 H 401 " -0.089 2.00e-02 2.50e+03 pdb=" O5 UQ9 H 401 " -0.319 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 UQ9 H 401 " 0.129 2.00e-02 2.50e+03 1.08e-01 1.45e+02 pdb=" C23 UQ9 H 401 " -0.173 2.00e-02 2.50e+03 pdb=" C24 UQ9 H 401 " -0.040 2.00e-02 2.50e+03 pdb=" C25 UQ9 H 401 " -0.014 2.00e-02 2.50e+03 pdb=" C26 UQ9 H 401 " 0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET H 91 " -0.106 5.00e-02 4.00e+02 1.63e-01 4.27e+01 pdb=" N PRO H 92 " 0.283 5.00e-02 4.00e+02 pdb=" CA PRO H 92 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO H 92 " -0.086 5.00e-02 4.00e+02 ... (remaining 6063 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.38: 78 2.38 - 3.01: 23576 3.01 - 3.64: 54308 3.64 - 4.27: 86466 4.27 - 4.90: 139371 Nonbonded interactions: 303799 Sorted by model distance: nonbonded pdb=" O ASP I 208 " pdb=" OD1 ASP I 208 " model vdw 1.756 3.040 nonbonded pdb=" O ASP Q 146 " pdb=" OD1 ASP Q 146 " model vdw 1.969 3.040 nonbonded pdb=" O ASN H 97 " pdb=" OD1 ASN H 97 " model vdw 1.984 3.040 nonbonded pdb=" O PHE G 63 " pdb=" SG CYS G 64 " model vdw 2.009 3.400 nonbonded pdb=" N THR G 174 " pdb=" N ARG G 175 " model vdw 2.081 2.560 ... (remaining 303794 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.620 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 38.050 Find NCS groups from input model: 0.230 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 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 : 0.022 1.048 35288 Z= 1.005 Angle : 2.174 48.469 47853 Z= 1.438 Chirality : 0.125 0.910 5217 Planarity : 0.008 0.231 6066 Dihedral : 12.872 141.909 13364 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 42.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.01 % Favored : 94.87 % Rotamer: Outliers : 0.33 % Allowed : 7.44 % Favored : 92.24 % Cbeta Deviations : 1.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.12), residues: 4193 helix: -0.67 (0.12), residues: 1796 sheet: -1.11 (0.28), residues: 352 loop : -1.98 (0.12), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 333 TYR 0.033 0.002 TYR D 214 PHE 0.029 0.002 PHE D 200 TRP 0.031 0.002 TRP V 114 HIS 0.011 0.001 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.01419 / 0.90 (35248) covalent geometry : angle 2.05025 / 1.44 (47763) SS BOND : bond 0.01000 / 0.51 ( 3) SS BOND : angle 2.44084 / 1.22 ( 6) hydrogen bonds : bond 0.23527 / 15.50 ( 1461) hydrogen bonds : angle 9.10821 / 6.48 ( 4197) metal coordination : bond 0.49977 / 32.76 ( 37) metal coordination : angle 17.37850 / 13.24 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1596 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1584 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.8963 (mm) cc_final: 0.8610 (mt) REVERT: B 76 THR cc_start: 0.7625 (p) cc_final: 0.6708 (t) REVERT: B 112 TYR cc_start: 0.6757 (m-80) cc_final: 0.6265 (m-80) REVERT: C 132 LEU cc_start: 0.8356 (tp) cc_final: 0.8119 (tp) REVERT: C 238 TRP cc_start: 0.8392 (m100) cc_final: 0.7990 (m100) REVERT: D 375 MET cc_start: 0.8152 (tpp) cc_final: 0.7848 (tpp) REVERT: E 121 TYR cc_start: 0.6752 (m-80) cc_final: 0.6335 (m-10) REVERT: G 271 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7322 (mmt) REVERT: G 440 TYR cc_start: 0.7278 (p90) cc_final: 0.6940 (p90) REVERT: G 654 VAL cc_start: 0.8762 (p) cc_final: 0.8560 (t) REVERT: H 51 ASP cc_start: 0.7420 (p0) cc_final: 0.7142 (p0) REVERT: H 183 MET cc_start: 0.7616 (mtt) cc_final: 0.7398 (mtt) REVERT: H 276 SER cc_start: 0.7502 (m) cc_final: 0.6813 (t) REVERT: I 66 LEU cc_start: 0.8347 (mt) cc_final: 0.7702 (mt) REVERT: I 177 THR cc_start: 0.7959 (p) cc_final: 0.7669 (t) REVERT: P 269 ASN cc_start: 0.6468 (p0) cc_final: 0.5917 (p0) REVERT: Q 79 ILE cc_start: 0.8904 (mt) cc_final: 0.8034 (mt) REVERT: Q 124 MET cc_start: 0.6999 (ttp) cc_final: 0.6770 (ttm) REVERT: S 80 ASN cc_start: 0.7736 (t0) cc_final: 0.7068 (t0) REVERT: T 84 LEU cc_start: 0.8732 (mt) cc_final: 0.8521 (mt) REVERT: W 27 ASP cc_start: 0.6987 (p0) cc_final: 0.5912 (p0) REVERT: W 43 TYR cc_start: 0.7749 (t80) cc_final: 0.7543 (t80) REVERT: a 12 MET cc_start: 0.8072 (mtp) cc_final: 0.7776 (ttm) REVERT: q 51 ASP cc_start: 0.6277 (t0) cc_final: 0.5913 (t0) REVERT: q 78 ASP cc_start: 0.6265 (p0) cc_final: 0.5894 (p0) outliers start: 12 outliers final: 1 residues processed: 1591 average time/residue: 0.2136 time to fit residues: 539.2154 Evaluate side-chains 886 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 884 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain P residue 242 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 HIS C 73 GLN C 74 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN C 195 HIS C 227 GLN D 92 HIS D 117 HIS ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 HIS ** E 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN F 170 GLN F 220 GLN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 HIS F 376 HIS G 74 ASN G 140 GLN G 142 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 495 ASN ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 571 HIS H 47 GLN ** H 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 HIS ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 ASN P 71 ASN P 72 HIS P 251 ASN P 323 HIS P 356 HIS ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 163 ASN Q 167 ASN R 33 HIS ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 73 GLN V 21 HIS V 41 HIS V 50 GLN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 ASN W 61 GLN W 73 ASN X 64 ASN X 140 ASN Z 135 ASN a 27 HIS ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 42 GLN q 54 GLN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 123 GLN r 21 GLN r 36 GLN ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 110 GLN s 49 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.087242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.074057 restraints weight = 128504.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.076307 restraints weight = 58937.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.077793 restraints weight = 34466.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.078709 restraints weight = 23683.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.079321 restraints weight = 18378.840| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 35288 Z= 0.246 Angle : 1.054 57.789 47853 Z= 0.445 Chirality : 0.050 0.361 5217 Planarity : 0.006 0.136 6066 Dihedral : 9.370 154.097 4990 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 22.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.01 % Favored : 96.97 % Rotamer: Outliers : 4.23 % Allowed : 16.88 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.12), residues: 4193 helix: 0.21 (0.12), residues: 1866 sheet: -0.96 (0.27), residues: 357 loop : -1.24 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Z 57 TYR 0.027 0.003 TYR V 44 PHE 0.034 0.003 PHE T 126 TRP 0.026 0.002 TRP Z 142 HIS 0.011 0.002 HIS D 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (35248) covalent geometry : angle 0.85586 / 0.44 (47763) SS BOND : bond 0.00197 / 0.10 ( 3) SS BOND : angle 1.15323 / 0.55 ( 6) hydrogen bonds : bond 0.05937 / 3.88 ( 1461) hydrogen bonds : angle 6.12818 / 4.26 ( 4197) metal coordination : bond 0.02736 / 1.56 ( 37) metal coordination : angle 14.68614 / 10.00 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 961 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.8320 (m-40) cc_final: 0.7855 (t0) REVERT: A 68 GLU cc_start: 0.8725 (tt0) cc_final: 0.8456 (tt0) REVERT: A 88 MET cc_start: 0.8795 (ptm) cc_final: 0.8474 (mtm) REVERT: B 131 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.7969 (ttm) REVERT: B 151 GLN cc_start: 0.9190 (mt0) cc_final: 0.8959 (mt0) REVERT: C 166 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7730 (mt-10) REVERT: C 227 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7919 (tp40) REVERT: C 238 TRP cc_start: 0.9192 (m100) cc_final: 0.8968 (m100) REVERT: D 82 LEU cc_start: 0.8685 (tp) cc_final: 0.8232 (tt) REVERT: D 107 ARG cc_start: 0.7733 (tpp-160) cc_final: 0.7295 (tpp80) REVERT: D 261 MET cc_start: 0.8922 (tpp) cc_final: 0.8651 (tpp) REVERT: D 292 MET cc_start: 0.8884 (tpp) cc_final: 0.8348 (mmt) REVERT: D 387 GLU cc_start: 0.8625 (tt0) cc_final: 0.8276 (tt0) REVERT: D 390 GLN cc_start: 0.8463 (tt0) cc_final: 0.8073 (tm-30) REVERT: D 460 GLU cc_start: 0.8511 (pt0) cc_final: 0.8305 (pt0) REVERT: E 129 TYR cc_start: 0.6468 (m-80) cc_final: 0.6149 (m-80) REVERT: E 140 MET cc_start: 0.8975 (tmm) cc_final: 0.8740 (ppp) REVERT: F 155 TYR cc_start: 0.9280 (m-10) cc_final: 0.8984 (m-10) REVERT: F 337 MET cc_start: 0.8375 (mmm) cc_final: 0.8148 (mmm) REVERT: F 342 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9011 (mp) REVERT: F 357 MET cc_start: 0.8329 (mtm) cc_final: 0.7788 (mpp) REVERT: F 381 GLN cc_start: 0.8773 (tt0) cc_final: 0.8482 (mt0) REVERT: F 396 MET cc_start: 0.9396 (mmm) cc_final: 0.8801 (mmm) REVERT: G 144 MET cc_start: 0.8828 (tpp) cc_final: 0.8622 (mmm) REVERT: G 149 ASP cc_start: 0.7595 (m-30) cc_final: 0.5730 (m-30) REVERT: G 271 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8092 (mmt) REVERT: G 301 ARG cc_start: 0.8052 (ttt90) cc_final: 0.7157 (ttt-90) REVERT: G 329 MET cc_start: 0.8100 (mmm) cc_final: 0.7597 (mmm) REVERT: G 445 LEU cc_start: 0.9077 (mt) cc_final: 0.8773 (mp) REVERT: G 591 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7590 (mt-10) REVERT: G 596 TYR cc_start: 0.8857 (m-80) cc_final: 0.8597 (m-10) REVERT: H 27 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8782 (mt) REVERT: H 51 ASP cc_start: 0.8924 (p0) cc_final: 0.8673 (p0) REVERT: H 176 LEU cc_start: 0.8984 (mm) cc_final: 0.8772 (tp) REVERT: H 194 ASN cc_start: 0.8908 (m-40) cc_final: 0.8520 (t0) REVERT: H 225 MET cc_start: 0.9396 (mtm) cc_final: 0.8796 (mtm) REVERT: H 247 TYR cc_start: 0.8450 (t80) cc_final: 0.8189 (t80) REVERT: H 253 GLU cc_start: 0.8181 (pp20) cc_final: 0.7596 (mp0) REVERT: I 40 ASN cc_start: 0.8511 (t0) cc_final: 0.7848 (t0) REVERT: I 63 TRP cc_start: 0.8998 (OUTLIER) cc_final: 0.8789 (m-90) REVERT: I 159 GLN cc_start: 0.8695 (tt0) cc_final: 0.8422 (mt0) REVERT: I 208 ASP cc_start: 0.9055 (t0) cc_final: 0.8819 (t0) REVERT: P 121 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7148 (mm110) REVERT: P 154 GLN cc_start: 0.7971 (tp-100) cc_final: 0.7667 (tp-100) REVERT: P 217 PHE cc_start: 0.8575 (m-10) cc_final: 0.8181 (m-80) REVERT: P 316 LYS cc_start: 0.8858 (mttp) cc_final: 0.8571 (tmmt) REVERT: P 317 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8084 (m-30) REVERT: P 351 GLU cc_start: 0.8443 (pt0) cc_final: 0.8055 (pm20) REVERT: Q 112 MET cc_start: 0.7878 (mmm) cc_final: 0.7664 (mmm) REVERT: Q 124 MET cc_start: 0.7977 (ttp) cc_final: 0.7695 (ttm) REVERT: Q 133 ASP cc_start: 0.8775 (m-30) cc_final: 0.8343 (p0) REVERT: Q 148 GLU cc_start: 0.7138 (mp0) cc_final: 0.6850 (mp0) REVERT: R 38 TYR cc_start: 0.6930 (m-10) cc_final: 0.6481 (m-10) REVERT: R 66 GLN cc_start: 0.7822 (mp10) cc_final: 0.7552 (mp10) REVERT: S 60 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7914 (tm-30) REVERT: S 80 ASN cc_start: 0.8394 (t0) cc_final: 0.8162 (t0) REVERT: T 93 ILE cc_start: 0.8877 (mm) cc_final: 0.8641 (mm) REVERT: T 96 GLU cc_start: 0.7682 (mp0) cc_final: 0.7481 (mp0) REVERT: T 143 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8336 (mt-10) REVERT: W 55 LEU cc_start: 0.9435 (mt) cc_final: 0.9126 (mp) REVERT: W 107 MET cc_start: 0.8352 (mmt) cc_final: 0.8090 (mmm) REVERT: X 7 LEU cc_start: 0.8701 (mt) cc_final: 0.8219 (mt) REVERT: Z 76 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7790 (tm-30) REVERT: Z 79 LYS cc_start: 0.8117 (tptt) cc_final: 0.7728 (tppt) REVERT: b 9 LEU cc_start: 0.8699 (tp) cc_final: 0.8191 (mt) REVERT: q 49 TYR cc_start: 0.8868 (m-80) cc_final: 0.8594 (m-80) REVERT: q 51 ASP cc_start: 0.7808 (t0) cc_final: 0.7496 (t0) REVERT: q 69 ASN cc_start: 0.7905 (t0) cc_final: 0.7566 (t0) REVERT: q 133 LYS cc_start: 0.8465 (mmmt) cc_final: 0.8190 (mmmt) REVERT: q 136 GLU cc_start: 0.8239 (pm20) cc_final: 0.7972 (mt-10) REVERT: r 54 TYR cc_start: 0.7614 (t80) cc_final: 0.6656 (t80) REVERT: s 54 LYS cc_start: 0.9062 (ptmm) cc_final: 0.8615 (ptpt) outliers start: 156 outliers final: 78 residues processed: 1047 average time/residue: 0.1944 time to fit residues: 332.6961 Evaluate side-chains 859 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 773 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 368 THR Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 279 ARG Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 63 TRP Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 204 ASN Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 317 ASP Chi-restraints excluded: chain P residue 324 ILE Chi-restraints excluded: chain P residue 327 VAL Chi-restraints excluded: chain P residue 330 THR Chi-restraints excluded: chain Q residue 54 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 89 SER Chi-restraints excluded: chain Q residue 167 ASN Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain T residue 91 ASP Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain T residue 143 GLU Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain a residue 42 GLN Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 54 GLN Chi-restraints excluded: chain r residue 36 GLN Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 49 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 371 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 174 optimal weight: 0.0060 chunk 312 optimal weight: 7.9990 chunk 336 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 404 optimal weight: 0.8980 chunk 324 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN C 88 HIS ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 HIS ** E 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN E 132 GLN F 170 GLN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN H 99 ASN H 138 GLN H 163 GLN ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 ASN P 356 HIS Q 71 HIS Q 92 ASN Q 167 ASN S 73 GLN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 111 GLN W 73 ASN X 77 HIS X 124 GLN Z 135 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 71 GLN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 21 GLN r 36 GLN ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 49 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.088150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.075130 restraints weight = 127790.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.077370 restraints weight = 58124.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.078841 restraints weight = 34082.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.079764 restraints weight = 23410.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.080377 restraints weight = 18067.965| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 35288 Z= 0.164 Angle : 0.931 62.267 47853 Z= 0.382 Chirality : 0.046 0.225 5217 Planarity : 0.006 0.126 6066 Dihedral : 9.118 155.854 4989 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.36 % Favored : 96.61 % Rotamer: Outliers : 4.26 % Allowed : 18.62 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.13), residues: 4193 helix: 0.48 (0.12), residues: 1865 sheet: -0.92 (0.26), residues: 369 loop : -0.99 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 146 TYR 0.027 0.002 TYR C 211 PHE 0.027 0.002 PHE H 280 TRP 0.033 0.002 TRP Z 142 HIS 0.015 0.001 HIS P 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (35248) covalent geometry : angle 0.74661 / 0.38 (47763) SS BOND : bond 0.00193 / 0.09 ( 3) SS BOND : angle 0.97908 / 0.46 ( 6) hydrogen bonds : bond 0.04804 / 3.12 ( 1461) hydrogen bonds : angle 5.64003 / 3.93 ( 4197) metal coordination : bond 0.01878 / 1.21 ( 37) metal coordination : angle 13.27720 / 8.87 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 909 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.8185 (m-40) cc_final: 0.7807 (t0) REVERT: A 22 PHE cc_start: 0.7688 (t80) cc_final: 0.7206 (t80) REVERT: A 23 TRP cc_start: 0.7464 (OUTLIER) cc_final: 0.7229 (m-10) REVERT: A 62 PHE cc_start: 0.8748 (t80) cc_final: 0.8497 (t80) REVERT: A 68 GLU cc_start: 0.8747 (tt0) cc_final: 0.8517 (tt0) REVERT: A 88 MET cc_start: 0.8678 (ptm) cc_final: 0.8304 (mtm) REVERT: B 145 LEU cc_start: 0.9418 (tp) cc_final: 0.9066 (tp) REVERT: B 150 ASP cc_start: 0.8954 (m-30) cc_final: 0.8485 (m-30) REVERT: B 216 GLN cc_start: 0.8281 (pm20) cc_final: 0.7810 (pm20) REVERT: C 166 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7595 (mt-10) REVERT: D 82 LEU cc_start: 0.8781 (tp) cc_final: 0.8343 (tt) REVERT: D 107 ARG cc_start: 0.7728 (tpp-160) cc_final: 0.7275 (tpp80) REVERT: D 145 MET cc_start: 0.8711 (mtp) cc_final: 0.8306 (mmm) REVERT: D 328 ASP cc_start: 0.7933 (t0) cc_final: 0.7697 (t0) REVERT: D 351 MET cc_start: 0.8660 (tpp) cc_final: 0.8368 (tpp) REVERT: D 376 GLU cc_start: 0.8443 (mp0) cc_final: 0.7965 (mp0) REVERT: D 387 GLU cc_start: 0.8701 (tt0) cc_final: 0.8465 (tt0) REVERT: D 390 GLN cc_start: 0.8363 (tt0) cc_final: 0.7891 (tm-30) REVERT: D 410 TYR cc_start: 0.8956 (t80) cc_final: 0.8688 (t80) REVERT: E 140 MET cc_start: 0.8953 (tmm) cc_final: 0.8665 (ppp) REVERT: E 181 ASN cc_start: 0.7861 (OUTLIER) cc_final: 0.7595 (t0) REVERT: F 102 MET cc_start: 0.7823 (ptm) cc_final: 0.7190 (ptm) REVERT: F 155 TYR cc_start: 0.9224 (m-10) cc_final: 0.8841 (m-10) REVERT: F 292 MET cc_start: 0.8203 (mtm) cc_final: 0.7885 (mtm) REVERT: F 337 MET cc_start: 0.8405 (mmm) cc_final: 0.8037 (mmm) REVERT: F 342 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9042 (mp) REVERT: F 381 GLN cc_start: 0.8685 (tt0) cc_final: 0.8365 (tt0) REVERT: F 396 MET cc_start: 0.9335 (mmm) cc_final: 0.9093 (mmm) REVERT: G 126 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8280 (pp) REVERT: G 329 MET cc_start: 0.8075 (mmm) cc_final: 0.7552 (mmm) REVERT: G 591 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7677 (mt-10) REVERT: G 596 TYR cc_start: 0.8889 (m-80) cc_final: 0.8617 (m-10) REVERT: H 78 SER cc_start: 0.9176 (m) cc_final: 0.8875 (p) REVERT: H 214 GLU cc_start: 0.6997 (pm20) cc_final: 0.5912 (pm20) REVERT: H 215 TYR cc_start: 0.7238 (m-80) cc_final: 0.6899 (m-80) REVERT: H 225 MET cc_start: 0.9284 (mtm) cc_final: 0.8896 (mtm) REVERT: H 234 MET cc_start: 0.8544 (mmm) cc_final: 0.8270 (mmt) REVERT: H 253 GLU cc_start: 0.8131 (pp20) cc_final: 0.7635 (mp0) REVERT: I 40 ASN cc_start: 0.8430 (t0) cc_final: 0.7912 (t0) REVERT: I 72 MET cc_start: 0.9012 (tpp) cc_final: 0.8769 (tpp) REVERT: I 76 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7729 (t80) REVERT: I 106 TYR cc_start: 0.7539 (m-80) cc_final: 0.7332 (m-80) REVERT: I 122 ILE cc_start: 0.9446 (tp) cc_final: 0.9210 (tp) REVERT: I 208 ASP cc_start: 0.9192 (t0) cc_final: 0.8667 (t0) REVERT: P 121 GLN cc_start: 0.7663 (mm-40) cc_final: 0.7159 (mm110) REVERT: P 154 GLN cc_start: 0.7986 (tp-100) cc_final: 0.7531 (tp-100) REVERT: P 175 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7418 (mtmm) REVERT: P 244 ASP cc_start: 0.8289 (m-30) cc_final: 0.7983 (m-30) REVERT: P 316 LYS cc_start: 0.8840 (mttp) cc_final: 0.8614 (tmmt) REVERT: P 317 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.7985 (m-30) REVERT: Q 112 MET cc_start: 0.7804 (mmm) cc_final: 0.7581 (mmm) REVERT: Q 133 ASP cc_start: 0.8746 (m-30) cc_final: 0.8494 (p0) REVERT: Q 148 GLU cc_start: 0.7333 (mp0) cc_final: 0.6945 (mp0) REVERT: R 42 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.6851 (t0) REVERT: R 45 ARG cc_start: 0.8017 (mtp180) cc_final: 0.7719 (mtp85) REVERT: S 60 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7755 (tm-30) REVERT: S 80 ASN cc_start: 0.8466 (t0) cc_final: 0.8257 (t0) REVERT: T 124 ASP cc_start: 0.8439 (m-30) cc_final: 0.7951 (t70) REVERT: W 95 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8113 (mt-10) REVERT: X 7 LEU cc_start: 0.7950 (mt) cc_final: 0.7397 (mm) REVERT: X 135 ARG cc_start: 0.5592 (ptm160) cc_final: 0.5186 (ptm160) REVERT: Z 10 MET cc_start: 0.9068 (tpp) cc_final: 0.8780 (mmm) REVERT: Z 51 MET cc_start: 0.8976 (ttp) cc_final: 0.8547 (ptm) REVERT: Z 69 ILE cc_start: 0.8704 (mm) cc_final: 0.8274 (mm) REVERT: Z 79 LYS cc_start: 0.8164 (tptt) cc_final: 0.7638 (tppt) REVERT: Z 87 LEU cc_start: 0.8882 (mt) cc_final: 0.8658 (pp) REVERT: b 9 LEU cc_start: 0.8668 (tp) cc_final: 0.8188 (mt) REVERT: q 41 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7610 (tm-30) REVERT: q 49 TYR cc_start: 0.8905 (m-80) cc_final: 0.8687 (m-80) REVERT: q 51 ASP cc_start: 0.8056 (t0) cc_final: 0.6587 (t0) REVERT: r 62 GLU cc_start: 0.5035 (tm-30) cc_final: 0.4749 (tm-30) REVERT: r 70 MET cc_start: 0.7464 (mmt) cc_final: 0.7240 (tpt) REVERT: s 43 TYR cc_start: 0.8688 (m-80) cc_final: 0.8354 (m-10) REVERT: s 44 THR cc_start: 0.8842 (m) cc_final: 0.8605 (p) REVERT: s 54 LYS cc_start: 0.9056 (ptmm) cc_final: 0.8696 (ptpp) outliers start: 157 outliers final: 59 residues processed: 994 average time/residue: 0.1924 time to fit residues: 315.5930 Evaluate side-chains 845 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 778 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 23 TRP Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 279 ARG Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 317 ASP Chi-restraints excluded: chain P residue 324 ILE Chi-restraints excluded: chain P residue 330 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 111 THR Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 46 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 132 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 148 optimal weight: 8.9990 chunk 371 optimal weight: 10.0000 chunk 254 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 HIS ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 GLN D 182 ASN ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN G 74 ASN G 142 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN H 169 GLN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN P 93 HIS P 166 HIS P 238 GLN ** P 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 ASN Z 135 ASN a 31 ASN ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.086180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.072962 restraints weight = 127618.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.075182 restraints weight = 59300.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.076646 restraints weight = 35227.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.077574 restraints weight = 24397.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.078141 restraints weight = 18988.075| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 35288 Z= 0.171 Angle : 0.913 68.065 47853 Z= 0.364 Chirality : 0.045 0.207 5217 Planarity : 0.005 0.123 6066 Dihedral : 8.955 159.155 4986 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.67 % Favored : 96.30 % Rotamer: Outliers : 4.12 % Allowed : 19.76 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.13), residues: 4193 helix: 0.60 (0.12), residues: 1864 sheet: -0.92 (0.26), residues: 381 loop : -0.84 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 48 TYR 0.034 0.002 TYR I 211 PHE 0.026 0.002 PHE A 56 TRP 0.021 0.001 TRP X 86 HIS 0.011 0.001 HIS P 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (35248) covalent geometry : angle 0.72217 / 0.36 (47763) SS BOND : bond 0.00249 / 0.12 ( 3) SS BOND : angle 0.95590 / 0.43 ( 6) hydrogen bonds : bond 0.04345 / 2.82 ( 1461) hydrogen bonds : angle 5.42122 / 3.77 ( 4197) metal coordination : bond 0.02024 / 1.18 ( 37) metal coordination : angle 13.35311 / 8.58 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 829 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.7686 (t80) cc_final: 0.6947 (t80) REVERT: A 23 TRP cc_start: 0.7324 (OUTLIER) cc_final: 0.7026 (m-10) REVERT: A 62 PHE cc_start: 0.8900 (t80) cc_final: 0.8643 (t80) REVERT: A 88 MET cc_start: 0.8663 (ptm) cc_final: 0.8383 (ptt) REVERT: B 80 ASP cc_start: 0.8709 (m-30) cc_final: 0.8310 (t70) REVERT: B 93 MET cc_start: 0.8476 (ptm) cc_final: 0.8221 (ptm) REVERT: B 150 ASP cc_start: 0.8989 (m-30) cc_final: 0.8482 (m-30) REVERT: B 199 GLU cc_start: 0.8316 (mp0) cc_final: 0.7987 (mp0) REVERT: C 166 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7590 (mt-10) REVERT: C 190 TYR cc_start: 0.7988 (m-80) cc_final: 0.7786 (m-10) REVERT: C 227 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7904 (tp40) REVERT: D 82 LEU cc_start: 0.8801 (tp) cc_final: 0.8309 (tt) REVERT: D 107 ARG cc_start: 0.7761 (tpp-160) cc_final: 0.7287 (tpp80) REVERT: D 145 MET cc_start: 0.8623 (mtp) cc_final: 0.8229 (mmm) REVERT: D 203 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8275 (mmm) REVERT: D 328 ASP cc_start: 0.7969 (t0) cc_final: 0.7561 (t0) REVERT: D 356 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9084 (pp) REVERT: D 376 GLU cc_start: 0.8498 (mp0) cc_final: 0.8019 (mp0) REVERT: D 387 GLU cc_start: 0.8599 (tt0) cc_final: 0.8241 (tt0) REVERT: D 390 GLN cc_start: 0.8357 (tt0) cc_final: 0.7593 (tm-30) REVERT: D 410 TYR cc_start: 0.8986 (t80) cc_final: 0.8660 (t80) REVERT: E 132 GLN cc_start: 0.7818 (mt0) cc_final: 0.7564 (mt0) REVERT: E 140 MET cc_start: 0.8939 (tmm) cc_final: 0.8725 (ppp) REVERT: E 181 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7586 (t0) REVERT: F 126 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8302 (ptmt) REVERT: F 155 TYR cc_start: 0.9248 (m-10) cc_final: 0.8837 (m-10) REVERT: F 337 MET cc_start: 0.8350 (mmm) cc_final: 0.7952 (mmm) REVERT: F 396 MET cc_start: 0.9265 (mmm) cc_final: 0.8990 (mmm) REVERT: G 42 MET cc_start: 0.8360 (mmm) cc_final: 0.8093 (mmm) REVERT: G 97 MET cc_start: 0.7555 (tpp) cc_final: 0.7294 (mpp) REVERT: G 591 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7459 (mt-10) REVERT: G 596 TYR cc_start: 0.8931 (m-80) cc_final: 0.8669 (m-10) REVERT: G 605 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7862 (tt0) REVERT: H 78 SER cc_start: 0.9255 (m) cc_final: 0.8961 (p) REVERT: H 114 TYR cc_start: 0.7740 (m-80) cc_final: 0.7432 (m-10) REVERT: H 118 TRP cc_start: 0.9036 (m-10) cc_final: 0.8438 (m-90) REVERT: H 129 LEU cc_start: 0.8649 (mm) cc_final: 0.8416 (mm) REVERT: H 134 ARG cc_start: 0.8436 (mmm-85) cc_final: 0.7466 (mmm-85) REVERT: H 138 GLN cc_start: 0.9360 (tt0) cc_final: 0.8834 (tm-30) REVERT: H 214 GLU cc_start: 0.6855 (pm20) cc_final: 0.6129 (pm20) REVERT: H 225 MET cc_start: 0.9238 (mtm) cc_final: 0.8974 (mtm) REVERT: H 253 GLU cc_start: 0.8053 (pp20) cc_final: 0.7684 (mp0) REVERT: H 274 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8837 (ttt180) REVERT: H 290 TRP cc_start: 0.8708 (m100) cc_final: 0.8506 (m100) REVERT: I 40 ASN cc_start: 0.8506 (t0) cc_final: 0.7871 (t0) REVERT: I 72 MET cc_start: 0.9050 (tpp) cc_final: 0.8599 (tpp) REVERT: I 106 TYR cc_start: 0.7774 (m-80) cc_final: 0.7509 (m-80) REVERT: I 144 ARG cc_start: 0.8203 (ttm170) cc_final: 0.7704 (ttm-80) REVERT: I 208 ASP cc_start: 0.9199 (t0) cc_final: 0.8654 (t0) REVERT: I 211 TYR cc_start: 0.8344 (m-10) cc_final: 0.8029 (m-10) REVERT: P 121 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7404 (mm110) REVERT: P 154 GLN cc_start: 0.8028 (tp-100) cc_final: 0.7643 (tp-100) REVERT: P 175 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7448 (mtmm) REVERT: P 217 PHE cc_start: 0.8423 (m-10) cc_final: 0.8136 (m-80) REVERT: P 244 ASP cc_start: 0.8363 (m-30) cc_final: 0.8078 (m-30) REVERT: P 269 ASN cc_start: 0.7063 (p0) cc_final: 0.6615 (p0) REVERT: P 316 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8665 (tmmt) REVERT: P 351 GLU cc_start: 0.8248 (pt0) cc_final: 0.7904 (pm20) REVERT: Q 133 ASP cc_start: 0.8793 (m-30) cc_final: 0.8524 (p0) REVERT: Q 148 GLU cc_start: 0.7680 (mp0) cc_final: 0.7258 (mp0) REVERT: R 42 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7094 (t0) REVERT: R 45 ARG cc_start: 0.7952 (mtp180) cc_final: 0.7730 (mtp85) REVERT: R 106 TYR cc_start: 0.9176 (m-80) cc_final: 0.8873 (m-80) REVERT: S 60 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7770 (tm-30) REVERT: T 105 MET cc_start: 0.8246 (mtp) cc_final: 0.8018 (mtm) REVERT: T 139 MET cc_start: 0.6802 (ppp) cc_final: 0.6492 (ppp) REVERT: V 73 GLN cc_start: 0.8041 (pp30) cc_final: 0.7698 (pp30) REVERT: W 27 ASP cc_start: 0.8306 (t0) cc_final: 0.7992 (p0) REVERT: W 28 LEU cc_start: 0.8833 (tp) cc_final: 0.8565 (tp) REVERT: W 100 TRP cc_start: 0.8715 (m-10) cc_final: 0.7789 (m-10) REVERT: Z 10 MET cc_start: 0.9115 (tpp) cc_final: 0.8849 (mmm) REVERT: Z 51 MET cc_start: 0.9030 (ttp) cc_final: 0.8702 (ptm) REVERT: Z 69 ILE cc_start: 0.8664 (mm) cc_final: 0.8163 (mm) REVERT: Z 72 MET cc_start: 0.7920 (mmt) cc_final: 0.7643 (mmt) REVERT: Z 79 LYS cc_start: 0.8237 (tptt) cc_final: 0.7746 (tppt) REVERT: a 59 ARG cc_start: 0.8590 (ptt-90) cc_final: 0.8081 (ptp90) REVERT: b 9 LEU cc_start: 0.8661 (tp) cc_final: 0.8175 (mt) REVERT: q 51 ASP cc_start: 0.7942 (t0) cc_final: 0.7404 (t0) REVERT: q 67 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7564 (tp30) REVERT: q 68 MET cc_start: 0.6753 (ttp) cc_final: 0.6325 (ttp) REVERT: q 93 MET cc_start: 0.8424 (mmm) cc_final: 0.8132 (mmm) REVERT: s 44 THR cc_start: 0.8748 (m) cc_final: 0.8528 (p) REVERT: s 55 PHE cc_start: 0.8513 (m-80) cc_final: 0.8283 (m-80) outliers start: 152 outliers final: 82 residues processed: 915 average time/residue: 0.1913 time to fit residues: 290.4962 Evaluate side-chains 847 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 754 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 23 TRP Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 605 GLN Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 301 CYS Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain I residue 63 TRP Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 316 LYS Chi-restraints excluded: chain P residue 324 ILE Chi-restraints excluded: chain P residue 330 THR Chi-restraints excluded: chain Q residue 54 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 167 ASN Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 125 GLU Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 20 optimal weight: 0.9980 chunk 253 optimal weight: 10.0000 chunk 282 optimal weight: 10.0000 chunk 170 optimal weight: 0.9980 chunk 292 optimal weight: 6.9990 chunk 240 optimal weight: 1.9990 chunk 334 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 397 optimal weight: 8.9990 chunk 220 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN E 152 GLN G 30 ASN G 142 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN H 99 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN P 93 HIS ** P 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN Q 92 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 21 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.083615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.070258 restraints weight = 129426.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.072406 restraints weight = 60366.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.073849 restraints weight = 36131.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.074764 restraints weight = 25109.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.075377 restraints weight = 19615.451| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 35288 Z= 0.205 Angle : 0.932 73.311 47853 Z= 0.370 Chirality : 0.046 0.274 5217 Planarity : 0.005 0.123 6066 Dihedral : 8.955 158.470 4986 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.96 % Favored : 96.02 % Rotamer: Outliers : 4.21 % Allowed : 20.57 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 4193 helix: 0.62 (0.12), residues: 1879 sheet: -1.00 (0.26), residues: 390 loop : -0.76 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 266 TYR 0.034 0.002 TYR H 215 PHE 0.023 0.002 PHE X 70 TRP 0.022 0.002 TRP a 45 HIS 0.011 0.001 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (35248) covalent geometry : angle 0.72945 / 0.37 (47763) SS BOND : bond 0.00301 / 0.15 ( 3) SS BOND : angle 1.04348 / 0.47 ( 6) hydrogen bonds : bond 0.04300 / 2.77 ( 1461) hydrogen bonds : angle 5.37207 / 3.73 ( 4197) metal coordination : bond 0.02478 / 1.45 ( 37) metal coordination : angle 13.85202 / 8.68 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 794 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.7652 (t80) cc_final: 0.6840 (t80) REVERT: A 23 TRP cc_start: 0.7312 (OUTLIER) cc_final: 0.7037 (m-10) REVERT: A 88 MET cc_start: 0.8720 (ptm) cc_final: 0.8416 (ptt) REVERT: A 109 LYS cc_start: 0.8539 (mmmm) cc_final: 0.7934 (pttt) REVERT: B 147 LYS cc_start: 0.8282 (tptm) cc_final: 0.7813 (tptm) REVERT: B 150 ASP cc_start: 0.9034 (m-30) cc_final: 0.8547 (m-30) REVERT: B 151 GLN cc_start: 0.9001 (mt0) cc_final: 0.8377 (mt0) REVERT: B 175 TYR cc_start: 0.9064 (p90) cc_final: 0.8658 (p90) REVERT: C 68 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9205 (mm) REVERT: D 82 LEU cc_start: 0.8863 (tp) cc_final: 0.8372 (tt) REVERT: D 145 MET cc_start: 0.8656 (mtp) cc_final: 0.8019 (mmm) REVERT: D 203 MET cc_start: 0.8755 (mmm) cc_final: 0.8517 (mmm) REVERT: D 207 ARG cc_start: 0.8398 (mtp180) cc_final: 0.8137 (ttt-90) REVERT: D 328 ASP cc_start: 0.8250 (t0) cc_final: 0.8041 (t0) REVERT: D 356 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9110 (pp) REVERT: D 371 MET cc_start: 0.9266 (ttp) cc_final: 0.8918 (ttp) REVERT: D 387 GLU cc_start: 0.8485 (tt0) cc_final: 0.8018 (tt0) REVERT: E 181 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7546 (t0) REVERT: F 126 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8457 (ptmt) REVERT: F 155 TYR cc_start: 0.9287 (m-10) cc_final: 0.8875 (m-10) REVERT: F 222 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8744 (ttmt) REVERT: F 337 MET cc_start: 0.8270 (mmm) cc_final: 0.7861 (mmm) REVERT: F 396 MET cc_start: 0.9353 (mmm) cc_final: 0.8623 (mmm) REVERT: G 42 MET cc_start: 0.8476 (mmm) cc_final: 0.8270 (mmm) REVERT: G 97 MET cc_start: 0.7722 (tpp) cc_final: 0.7462 (mpp) REVERT: G 605 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: H 47 GLN cc_start: 0.9373 (tp40) cc_final: 0.9031 (tp40) REVERT: H 78 SER cc_start: 0.9358 (m) cc_final: 0.9138 (p) REVERT: H 114 TYR cc_start: 0.7572 (m-80) cc_final: 0.7178 (m-10) REVERT: H 118 TRP cc_start: 0.9110 (m-10) cc_final: 0.8401 (m-90) REVERT: H 134 ARG cc_start: 0.8511 (mmm-85) cc_final: 0.7517 (mmm-85) REVERT: H 138 GLN cc_start: 0.9294 (tt0) cc_final: 0.8937 (tm-30) REVERT: H 225 MET cc_start: 0.9276 (mtm) cc_final: 0.9047 (mtm) REVERT: H 247 TYR cc_start: 0.8355 (t80) cc_final: 0.8023 (t80) REVERT: H 253 GLU cc_start: 0.8151 (pp20) cc_final: 0.7773 (mp0) REVERT: H 271 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8408 (mt) REVERT: H 274 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8798 (ttt180) REVERT: H 281 ARG cc_start: 0.7354 (ttm110) cc_final: 0.6550 (ttp-170) REVERT: H 282 TYR cc_start: 0.8062 (t80) cc_final: 0.7344 (t80) REVERT: I 40 ASN cc_start: 0.8649 (t0) cc_final: 0.7993 (t0) REVERT: I 86 TYR cc_start: 0.8388 (t80) cc_final: 0.8177 (t80) REVERT: I 106 TYR cc_start: 0.7978 (m-80) cc_final: 0.7708 (m-80) REVERT: I 208 ASP cc_start: 0.9187 (t0) cc_final: 0.8664 (t0) REVERT: I 211 TYR cc_start: 0.8444 (m-10) cc_final: 0.8091 (m-10) REVERT: P 45 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7862 (tptp) REVERT: P 121 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7608 (mm110) REVERT: P 154 GLN cc_start: 0.8029 (tp-100) cc_final: 0.7670 (tp-100) REVERT: P 175 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7542 (mtmm) REVERT: P 217 PHE cc_start: 0.8467 (m-10) cc_final: 0.8083 (m-80) REVERT: P 269 ASN cc_start: 0.7270 (p0) cc_final: 0.6786 (p0) REVERT: P 316 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8681 (ttpt) REVERT: P 351 GLU cc_start: 0.8319 (pt0) cc_final: 0.7935 (pm20) REVERT: Q 52 LEU cc_start: 0.9065 (mp) cc_final: 0.8827 (mp) REVERT: Q 148 GLU cc_start: 0.7864 (mp0) cc_final: 0.7469 (mp0) REVERT: R 42 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7222 (t0) REVERT: R 45 ARG cc_start: 0.8103 (mtp180) cc_final: 0.7622 (mtp85) REVERT: S 60 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7897 (tm-30) REVERT: S 62 GLN cc_start: 0.8299 (mt0) cc_final: 0.8085 (mt0) REVERT: S 68 ARG cc_start: 0.8321 (ttm170) cc_final: 0.7989 (ttm170) REVERT: T 120 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7948 (ptp) REVERT: W 27 ASP cc_start: 0.8374 (t0) cc_final: 0.8006 (p0) REVERT: W 45 GLU cc_start: 0.8635 (tp30) cc_final: 0.8053 (tp30) REVERT: W 100 TRP cc_start: 0.8790 (m-10) cc_final: 0.8000 (m-10) REVERT: X 7 LEU cc_start: 0.5883 (pt) cc_final: 0.5471 (tt) REVERT: Z 10 MET cc_start: 0.9111 (tpp) cc_final: 0.8729 (mmm) REVERT: Z 51 MET cc_start: 0.9045 (ttp) cc_final: 0.8758 (ptm) REVERT: Z 69 ILE cc_start: 0.8844 (mm) cc_final: 0.8387 (mm) REVERT: Z 72 MET cc_start: 0.8255 (mmt) cc_final: 0.7942 (mmt) REVERT: Z 79 LYS cc_start: 0.8251 (tptt) cc_final: 0.7870 (tppt) REVERT: Z 124 MET cc_start: 0.7839 (mpp) cc_final: 0.7489 (mpp) REVERT: Z 137 ASN cc_start: 0.8968 (m-40) cc_final: 0.8506 (m-40) REVERT: a 57 VAL cc_start: 0.7553 (p) cc_final: 0.7311 (m) REVERT: a 59 ARG cc_start: 0.8605 (ptt-90) cc_final: 0.8318 (ptp90) REVERT: a 61 TYR cc_start: 0.6713 (m-80) cc_final: 0.6353 (m-80) REVERT: q 67 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7604 (tp30) outliers start: 155 outliers final: 93 residues processed: 879 average time/residue: 0.1931 time to fit residues: 281.2346 Evaluate side-chains 820 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 713 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 23 TRP Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 222 LYS Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 605 GLN Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 186 PHE Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 301 CYS Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 63 TRP Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 316 LYS Chi-restraints excluded: chain P residue 324 ILE Chi-restraints excluded: chain P residue 330 THR Chi-restraints excluded: chain Q residue 54 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 167 ASN Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 58 ASN Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 120 MET Chi-restraints excluded: chain T residue 125 GLU Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain X residue 94 MET Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain q residue 2 GLU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 111 THR Chi-restraints excluded: chain q residue 135 HIS Chi-restraints excluded: chain r residue 5 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 369 optimal weight: 0.9980 chunk 349 optimal weight: 3.9990 chunk 174 optimal weight: 0.3980 chunk 137 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 242 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN F 381 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 HIS ** P 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN Q 92 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 ASN ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 116 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.085036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.071812 restraints weight = 127229.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.073984 restraints weight = 58825.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.075421 restraints weight = 34891.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.076340 restraints weight = 24202.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.076926 restraints weight = 18871.634| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.6151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 35288 Z= 0.144 Angle : 0.900 71.880 47853 Z= 0.357 Chirality : 0.045 0.229 5217 Planarity : 0.005 0.120 6066 Dihedral : 8.808 159.597 4986 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.70 % Favored : 96.28 % Rotamer: Outliers : 3.83 % Allowed : 21.55 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.13), residues: 4193 helix: 0.71 (0.12), residues: 1866 sheet: -0.99 (0.26), residues: 383 loop : -0.71 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 333 TYR 0.032 0.002 TYR W 43 PHE 0.037 0.002 PHE Z 138 TRP 0.037 0.001 TRP a 45 HIS 0.010 0.001 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (35248) covalent geometry : angle 0.71356 / 0.35 (47763) SS BOND : bond 0.00360 / 0.17 ( 3) SS BOND : angle 1.10777 / 0.48 ( 6) hydrogen bonds : bond 0.04106 / 2.64 ( 1461) hydrogen bonds : angle 5.19957 / 3.61 ( 4197) metal coordination : bond 0.01486 / 0.95 ( 37) metal coordination : angle 13.12546 / 8.14 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 815 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.7717 (t80) cc_final: 0.6880 (t80) REVERT: A 63 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8532 (mp) REVERT: A 68 GLU cc_start: 0.8892 (tt0) cc_final: 0.8614 (tt0) REVERT: A 88 MET cc_start: 0.8733 (ptm) cc_final: 0.8405 (ptt) REVERT: A 90 MET cc_start: 0.5297 (ptt) cc_final: 0.4674 (ttt) REVERT: A 109 LYS cc_start: 0.8582 (mmmm) cc_final: 0.7973 (pttt) REVERT: B 147 LYS cc_start: 0.8213 (tptm) cc_final: 0.7721 (tptm) REVERT: B 150 ASP cc_start: 0.9045 (m-30) cc_final: 0.8555 (m-30) REVERT: B 151 GLN cc_start: 0.9004 (mt0) cc_final: 0.8341 (mt0) REVERT: B 199 GLU cc_start: 0.8288 (mp0) cc_final: 0.7951 (mp0) REVERT: C 68 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9139 (mm) REVERT: C 224 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7112 (mt-10) REVERT: C 241 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.7214 (t80) REVERT: D 82 LEU cc_start: 0.8834 (tp) cc_final: 0.8333 (tt) REVERT: D 328 ASP cc_start: 0.8182 (t0) cc_final: 0.7697 (t0) REVERT: D 356 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9068 (pp) REVERT: D 371 MET cc_start: 0.9246 (ttp) cc_final: 0.8844 (ttp) REVERT: D 410 TYR cc_start: 0.8949 (t80) cc_final: 0.8604 (t80) REVERT: E 181 ASN cc_start: 0.7797 (OUTLIER) cc_final: 0.7367 (t0) REVERT: F 155 TYR cc_start: 0.9267 (m-10) cc_final: 0.8847 (m-10) REVERT: F 292 MET cc_start: 0.8236 (mtm) cc_final: 0.8008 (mpp) REVERT: F 337 MET cc_start: 0.8415 (mmm) cc_final: 0.7940 (mmm) REVERT: F 396 MET cc_start: 0.9336 (mmm) cc_final: 0.8522 (mmm) REVERT: G 42 MET cc_start: 0.8507 (mmm) cc_final: 0.8292 (mmm) REVERT: G 271 MET cc_start: 0.7809 (mmt) cc_final: 0.7246 (mmm) REVERT: G 345 LEU cc_start: 0.8982 (mp) cc_final: 0.8407 (mt) REVERT: H 35 LYS cc_start: 0.8625 (mtmt) cc_final: 0.8386 (mtpt) REVERT: H 47 GLN cc_start: 0.9313 (tp40) cc_final: 0.8973 (tp40) REVERT: H 78 SER cc_start: 0.9370 (m) cc_final: 0.9141 (p) REVERT: H 138 GLN cc_start: 0.9319 (tt0) cc_final: 0.8949 (tm-30) REVERT: H 194 ASN cc_start: 0.8561 (m-40) cc_final: 0.7925 (t0) REVERT: H 247 TYR cc_start: 0.8362 (t80) cc_final: 0.7959 (t80) REVERT: H 253 GLU cc_start: 0.7994 (pp20) cc_final: 0.7678 (mp0) REVERT: H 274 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8781 (ttt180) REVERT: H 290 TRP cc_start: 0.8662 (m100) cc_final: 0.8397 (m100) REVERT: I 40 ASN cc_start: 0.8594 (t0) cc_final: 0.8088 (t0) REVERT: I 72 MET cc_start: 0.8939 (tpp) cc_final: 0.7986 (tpp) REVERT: I 93 LEU cc_start: 0.8557 (mt) cc_final: 0.8345 (mp) REVERT: I 106 TYR cc_start: 0.8021 (m-80) cc_final: 0.7721 (m-80) REVERT: I 122 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9196 (tp) REVERT: I 149 MET cc_start: 0.8873 (mmm) cc_final: 0.8566 (mmm) REVERT: I 185 TYR cc_start: 0.8141 (m-10) cc_final: 0.7899 (m-80) REVERT: I 206 GLN cc_start: 0.8985 (tp-100) cc_final: 0.8740 (tp40) REVERT: I 208 ASP cc_start: 0.9070 (t0) cc_final: 0.8466 (t0) REVERT: I 211 TYR cc_start: 0.8378 (m-10) cc_final: 0.8056 (m-10) REVERT: P 121 GLN cc_start: 0.8116 (mm-40) cc_final: 0.7670 (mm110) REVERT: P 154 GLN cc_start: 0.7974 (tp-100) cc_final: 0.7575 (tp-100) REVERT: P 169 HIS cc_start: 0.8442 (t70) cc_final: 0.8229 (t-90) REVERT: P 175 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7522 (mtmm) REVERT: P 214 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8695 (tt) REVERT: P 217 PHE cc_start: 0.8501 (m-10) cc_final: 0.8065 (m-80) REVERT: P 269 ASN cc_start: 0.7341 (p0) cc_final: 0.6872 (p0) REVERT: P 281 PHE cc_start: 0.9009 (m-80) cc_final: 0.8749 (m-80) REVERT: Q 133 ASP cc_start: 0.8815 (m-30) cc_final: 0.8588 (p0) REVERT: Q 148 GLU cc_start: 0.7876 (mp0) cc_final: 0.7486 (mp0) REVERT: R 42 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.6928 (t0) REVERT: R 45 ARG cc_start: 0.8054 (mtp180) cc_final: 0.7815 (mtp85) REVERT: R 49 VAL cc_start: 0.8671 (t) cc_final: 0.8410 (m) REVERT: R 50 ASP cc_start: 0.8402 (t0) cc_final: 0.8149 (t0) REVERT: S 41 TYR cc_start: 0.8227 (t80) cc_final: 0.7998 (t80) REVERT: S 59 SER cc_start: 0.8694 (t) cc_final: 0.8435 (p) REVERT: S 60 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7754 (tm-30) REVERT: S 68 ARG cc_start: 0.8224 (ttm170) cc_final: 0.7928 (ttm170) REVERT: S 89 ARG cc_start: 0.8200 (ptp-170) cc_final: 0.7879 (ptp-170) REVERT: W 27 ASP cc_start: 0.8342 (t0) cc_final: 0.7988 (p0) REVERT: W 45 GLU cc_start: 0.8557 (tp30) cc_final: 0.7744 (tp30) REVERT: W 100 TRP cc_start: 0.8722 (m-10) cc_final: 0.7914 (m-10) REVERT: X 7 LEU cc_start: 0.6248 (pt) cc_final: 0.5856 (tt) REVERT: X 82 PHE cc_start: 0.8692 (t80) cc_final: 0.8471 (t80) REVERT: Z 10 MET cc_start: 0.9144 (tpp) cc_final: 0.8882 (mmm) REVERT: Z 24 ASN cc_start: 0.8115 (t0) cc_final: 0.7702 (t0) REVERT: Z 51 MET cc_start: 0.9043 (ttp) cc_final: 0.8770 (ptm) REVERT: Z 69 ILE cc_start: 0.8928 (mm) cc_final: 0.8679 (mt) REVERT: Z 79 LYS cc_start: 0.8299 (tptt) cc_final: 0.7890 (tppt) REVERT: a 57 VAL cc_start: 0.7457 (p) cc_final: 0.7199 (m) REVERT: a 59 ARG cc_start: 0.8538 (ptt-90) cc_final: 0.7950 (ptp90) REVERT: a 61 TYR cc_start: 0.6537 (m-80) cc_final: 0.6210 (m-80) REVERT: b 9 LEU cc_start: 0.8648 (tp) cc_final: 0.8101 (mt) REVERT: b 44 MET cc_start: 0.8222 (ptp) cc_final: 0.7667 (ptp) REVERT: q 51 ASP cc_start: 0.7622 (t0) cc_final: 0.7344 (t0) REVERT: q 53 LYS cc_start: 0.8964 (mtmm) cc_final: 0.8763 (mtmm) REVERT: q 67 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7633 (tp30) REVERT: q 93 MET cc_start: 0.8494 (tpt) cc_final: 0.7715 (tpt) outliers start: 141 outliers final: 79 residues processed: 887 average time/residue: 0.1842 time to fit residues: 273.0362 Evaluate side-chains 825 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 735 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 63 TRP Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 324 ILE Chi-restraints excluded: chain P residue 330 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 167 ASN Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 58 ASN Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 125 GLU Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 111 THR Chi-restraints excluded: chain r residue 41 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 230 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 chunk 171 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 363 optimal weight: 9.9990 chunk 399 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 240 optimal weight: 2.9990 chunk 304 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 354 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN P 93 HIS ** P 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN Q 92 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 123 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.082968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.069720 restraints weight = 129139.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.071876 restraints weight = 60363.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.073279 restraints weight = 35826.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.074136 restraints weight = 24992.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.074753 restraints weight = 19666.816| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.6347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 35288 Z= 0.194 Angle : 0.926 75.683 47853 Z= 0.370 Chirality : 0.046 0.211 5217 Planarity : 0.005 0.120 6066 Dihedral : 8.768 158.743 4986 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.96 % Favored : 96.02 % Rotamer: Outliers : 3.66 % Allowed : 22.66 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.13), residues: 4193 helix: 0.74 (0.12), residues: 1864 sheet: -0.85 (0.27), residues: 374 loop : -0.66 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 333 TYR 0.033 0.002 TYR W 43 PHE 0.030 0.002 PHE Z 138 TRP 0.033 0.002 TRP a 45 HIS 0.012 0.001 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (35248) covalent geometry : angle 0.73206 / 0.37 (47763) SS BOND : bond 0.00328 / 0.16 ( 3) SS BOND : angle 1.00134 / 0.44 ( 6) hydrogen bonds : bond 0.04086 / 2.62 ( 1461) hydrogen bonds : angle 5.25661 / 3.65 ( 4197) metal coordination : bond 0.02300 / 1.40 ( 37) metal coordination : angle 13.56254 / 8.23 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 759 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8530 (mp) REVERT: A 68 GLU cc_start: 0.8857 (tt0) cc_final: 0.8467 (tt0) REVERT: A 88 MET cc_start: 0.8720 (ptm) cc_final: 0.8400 (ptt) REVERT: A 109 LYS cc_start: 0.8619 (mmmm) cc_final: 0.7998 (pttt) REVERT: B 147 LYS cc_start: 0.8281 (tptm) cc_final: 0.7736 (tptm) REVERT: B 150 ASP cc_start: 0.9071 (m-30) cc_final: 0.8597 (m-30) REVERT: B 151 GLN cc_start: 0.9039 (mt0) cc_final: 0.8349 (mt0) REVERT: B 199 GLU cc_start: 0.8341 (mp0) cc_final: 0.7994 (mp0) REVERT: C 68 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9188 (mm) REVERT: C 149 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8613 (pp) REVERT: C 227 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: C 241 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7304 (t80) REVERT: D 82 LEU cc_start: 0.8871 (tp) cc_final: 0.8359 (tt) REVERT: D 145 MET cc_start: 0.8655 (mtp) cc_final: 0.8105 (mmm) REVERT: D 328 ASP cc_start: 0.8381 (t0) cc_final: 0.7908 (t0) REVERT: D 356 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.9086 (pp) REVERT: D 371 MET cc_start: 0.9286 (ttp) cc_final: 0.8780 (ttp) REVERT: D 387 GLU cc_start: 0.8463 (tt0) cc_final: 0.7875 (tt0) REVERT: E 181 ASN cc_start: 0.7891 (OUTLIER) cc_final: 0.7472 (t0) REVERT: E 205 ASP cc_start: 0.8937 (m-30) cc_final: 0.8703 (m-30) REVERT: F 149 MET cc_start: 0.8510 (mmt) cc_final: 0.7890 (mmt) REVERT: F 155 TYR cc_start: 0.9280 (m-10) cc_final: 0.8868 (m-10) REVERT: F 220 GLN cc_start: 0.8900 (tt0) cc_final: 0.8602 (pt0) REVERT: F 337 MET cc_start: 0.8409 (mmm) cc_final: 0.7932 (mmm) REVERT: G 97 MET cc_start: 0.7789 (tpp) cc_final: 0.7507 (mpp) REVERT: G 266 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8292 (ttp-110) REVERT: H 35 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8538 (mtpt) REVERT: H 78 SER cc_start: 0.9393 (m) cc_final: 0.9178 (p) REVERT: H 118 TRP cc_start: 0.9139 (m-10) cc_final: 0.8416 (m-90) REVERT: H 138 GLN cc_start: 0.9260 (tt0) cc_final: 0.9024 (tm-30) REVERT: H 194 ASN cc_start: 0.8662 (m-40) cc_final: 0.8114 (t0) REVERT: H 225 MET cc_start: 0.9338 (mtm) cc_final: 0.9045 (mtm) REVERT: H 227 GLU cc_start: 0.9076 (tp30) cc_final: 0.8648 (tp30) REVERT: H 247 TYR cc_start: 0.8431 (t80) cc_final: 0.8107 (t80) REVERT: H 253 GLU cc_start: 0.8048 (pp20) cc_final: 0.7787 (mp0) REVERT: H 274 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8840 (ttt180) REVERT: I 40 ASN cc_start: 0.8541 (t0) cc_final: 0.8144 (t0) REVERT: I 72 MET cc_start: 0.8710 (tpp) cc_final: 0.8065 (tpp) REVERT: I 122 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9163 (tp) REVERT: I 208 ASP cc_start: 0.9129 (t0) cc_final: 0.8617 (t0) REVERT: I 211 TYR cc_start: 0.8490 (m-10) cc_final: 0.7832 (m-10) REVERT: P 45 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8106 (tptp) REVERT: P 121 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7762 (mm110) REVERT: P 154 GLN cc_start: 0.7885 (tp-100) cc_final: 0.7476 (tp-100) REVERT: P 175 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7546 (mtmm) REVERT: P 214 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8735 (tt) REVERT: P 217 PHE cc_start: 0.8550 (m-10) cc_final: 0.8145 (m-80) REVERT: P 269 ASN cc_start: 0.7440 (p0) cc_final: 0.6877 (p0) REVERT: P 351 GLU cc_start: 0.8369 (pt0) cc_final: 0.7928 (pm20) REVERT: Q 148 GLU cc_start: 0.8037 (mp0) cc_final: 0.7647 (mp0) REVERT: R 42 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.6924 (t0) REVERT: R 45 ARG cc_start: 0.8171 (mtp180) cc_final: 0.7708 (mtp85) REVERT: R 49 VAL cc_start: 0.8717 (t) cc_final: 0.8447 (m) REVERT: R 50 ASP cc_start: 0.8367 (t0) cc_final: 0.8059 (t0) REVERT: S 59 SER cc_start: 0.8767 (t) cc_final: 0.8486 (p) REVERT: S 60 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7665 (tm-30) REVERT: T 115 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8431 (tt0) REVERT: W 27 ASP cc_start: 0.8332 (t0) cc_final: 0.7963 (p0) REVERT: W 45 GLU cc_start: 0.8522 (tp30) cc_final: 0.7943 (tp30) REVERT: W 100 TRP cc_start: 0.8665 (m-10) cc_final: 0.8277 (m-10) REVERT: X 7 LEU cc_start: 0.6401 (pt) cc_final: 0.6109 (tt) REVERT: X 82 PHE cc_start: 0.8762 (t80) cc_final: 0.8556 (t80) REVERT: Z 10 MET cc_start: 0.9144 (tpp) cc_final: 0.8879 (mmm) REVERT: Z 24 ASN cc_start: 0.8404 (t0) cc_final: 0.7951 (t0) REVERT: Z 51 MET cc_start: 0.9043 (ttp) cc_final: 0.8781 (ptm) REVERT: Z 69 ILE cc_start: 0.8950 (mm) cc_final: 0.8596 (mm) REVERT: Z 72 MET cc_start: 0.8112 (mmt) cc_final: 0.7779 (mmt) REVERT: Z 79 LYS cc_start: 0.8316 (tptt) cc_final: 0.7903 (tppt) REVERT: a 59 ARG cc_start: 0.8569 (ptt-90) cc_final: 0.7965 (ptp90) REVERT: b 9 LEU cc_start: 0.8658 (tp) cc_final: 0.8096 (mt) REVERT: q 51 ASP cc_start: 0.7633 (t0) cc_final: 0.7277 (t0) REVERT: q 53 LYS cc_start: 0.8963 (mtmm) cc_final: 0.8750 (mtmm) REVERT: s 55 PHE cc_start: 0.8300 (m-10) cc_final: 0.8028 (m-10) outliers start: 135 outliers final: 93 residues processed: 831 average time/residue: 0.1932 time to fit residues: 267.3132 Evaluate side-chains 815 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 708 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 266 ARG Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 605 GLN Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 31 MET Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 63 TRP Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 324 ILE Chi-restraints excluded: chain P residue 330 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 167 ASN Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 58 ASN Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 125 GLU Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain X residue 94 MET Chi-restraints excluded: chain X residue 135 ARG Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain q residue 2 GLU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 111 THR Chi-restraints excluded: chain q residue 116 ASN Chi-restraints excluded: chain q residue 135 HIS Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 41 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 308 optimal weight: 5.9990 chunk 294 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 chunk 298 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 401 optimal weight: 4.9990 chunk 235 optimal weight: 0.9980 chunk 202 optimal weight: 0.9990 chunk 281 optimal weight: 7.9990 chunk 302 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 GLN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN P 93 HIS Q 51 GLN Q 92 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.084235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.071265 restraints weight = 126617.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.073417 restraints weight = 58699.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.074837 restraints weight = 34818.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.075751 restraints weight = 24057.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.076296 restraints weight = 18720.056| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.6566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 35288 Z= 0.146 Angle : 0.909 73.605 47853 Z= 0.364 Chirality : 0.045 0.345 5217 Planarity : 0.005 0.117 6066 Dihedral : 8.635 159.444 4986 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.82 % Favored : 96.16 % Rotamer: Outliers : 3.34 % Allowed : 23.66 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.13), residues: 4193 helix: 0.78 (0.12), residues: 1859 sheet: -0.83 (0.26), residues: 373 loop : -0.66 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 333 TYR 0.033 0.002 TYR C 129 PHE 0.027 0.002 PHE A 22 TRP 0.044 0.002 TRP a 45 HIS 0.010 0.001 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (35248) covalent geometry : angle 0.72573 / 0.36 (47763) SS BOND : bond 0.00350 / 0.17 ( 3) SS BOND : angle 0.95061 / 0.41 ( 6) hydrogen bonds : bond 0.03926 / 2.51 ( 1461) hydrogen bonds : angle 5.17611 / 3.61 ( 4197) metal coordination : bond 0.01427 / 0.95 ( 37) metal coordination : angle 13.08834 / 7.95 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 799 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8571 (mp) REVERT: A 68 GLU cc_start: 0.8799 (tt0) cc_final: 0.8569 (tt0) REVERT: A 88 MET cc_start: 0.8659 (ptm) cc_final: 0.8355 (ptt) REVERT: A 90 MET cc_start: 0.5653 (ptt) cc_final: 0.4934 (ttt) REVERT: A 109 LYS cc_start: 0.8655 (mmmm) cc_final: 0.7999 (pttt) REVERT: B 147 LYS cc_start: 0.8282 (tptm) cc_final: 0.7713 (tptm) REVERT: B 150 ASP cc_start: 0.9077 (m-30) cc_final: 0.8603 (m-30) REVERT: B 151 GLN cc_start: 0.9040 (mt0) cc_final: 0.8434 (mt0) REVERT: B 199 GLU cc_start: 0.8379 (mp0) cc_final: 0.8075 (mp0) REVERT: C 241 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7184 (t80) REVERT: D 82 LEU cc_start: 0.8784 (tp) cc_final: 0.8295 (tt) REVERT: D 145 MET cc_start: 0.8581 (mtp) cc_final: 0.8137 (mmm) REVERT: D 328 ASP cc_start: 0.8210 (t0) cc_final: 0.7757 (t0) REVERT: D 356 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9075 (pp) REVERT: D 371 MET cc_start: 0.9252 (ttp) cc_final: 0.8749 (ttt) REVERT: D 410 TYR cc_start: 0.8930 (t80) cc_final: 0.8549 (t80) REVERT: E 105 GLN cc_start: 0.8940 (mp10) cc_final: 0.8726 (mp10) REVERT: E 181 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7485 (t0) REVERT: E 184 MET cc_start: 0.9085 (tmm) cc_final: 0.8752 (tmm) REVERT: E 205 ASP cc_start: 0.8923 (m-30) cc_final: 0.8692 (m-30) REVERT: F 155 TYR cc_start: 0.9271 (m-10) cc_final: 0.8900 (m-10) REVERT: F 220 GLN cc_start: 0.8801 (tt0) cc_final: 0.8353 (pt0) REVERT: F 337 MET cc_start: 0.8334 (mmm) cc_final: 0.7925 (mmm) REVERT: F 357 MET cc_start: 0.8409 (mtm) cc_final: 0.8195 (mpp) REVERT: G 39 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8233 (mp10) REVERT: G 42 MET cc_start: 0.8322 (mmm) cc_final: 0.7859 (mmm) REVERT: G 97 MET cc_start: 0.7764 (tpp) cc_final: 0.7479 (mpp) REVERT: H 78 SER cc_start: 0.9381 (m) cc_final: 0.9149 (p) REVERT: H 118 TRP cc_start: 0.9158 (m-10) cc_final: 0.8400 (m-90) REVERT: H 121 TRP cc_start: 0.5959 (t60) cc_final: 0.5734 (t-100) REVERT: H 194 ASN cc_start: 0.8619 (m-40) cc_final: 0.8097 (t0) REVERT: H 227 GLU cc_start: 0.9056 (tp30) cc_final: 0.8650 (tp30) REVERT: H 247 TYR cc_start: 0.8363 (t80) cc_final: 0.8031 (t80) REVERT: H 274 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8823 (ttt180) REVERT: H 301 CYS cc_start: 0.9396 (t) cc_final: 0.9143 (p) REVERT: H 302 MET cc_start: 0.8324 (ttm) cc_final: 0.7474 (tmm) REVERT: I 40 ASN cc_start: 0.8466 (t0) cc_final: 0.8095 (t0) REVERT: I 72 MET cc_start: 0.8701 (tpp) cc_final: 0.8202 (tpp) REVERT: I 122 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9129 (tp) REVERT: I 206 GLN cc_start: 0.9044 (tp-100) cc_final: 0.8805 (tp40) REVERT: I 208 ASP cc_start: 0.8981 (t0) cc_final: 0.8562 (t0) REVERT: P 45 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8109 (tptp) REVERT: P 54 VAL cc_start: 0.9057 (t) cc_final: 0.8805 (t) REVERT: P 102 GLN cc_start: 0.8353 (tp-100) cc_final: 0.7979 (tp-100) REVERT: P 121 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7762 (mm110) REVERT: P 154 GLN cc_start: 0.7855 (tp-100) cc_final: 0.7421 (tp-100) REVERT: P 175 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7567 (mtmm) REVERT: P 214 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8773 (tt) REVERT: P 217 PHE cc_start: 0.8528 (m-10) cc_final: 0.8133 (m-80) REVERT: P 269 ASN cc_start: 0.7450 (p0) cc_final: 0.6937 (p0) REVERT: P 355 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6631 (mmt-90) REVERT: Q 52 LEU cc_start: 0.9203 (mp) cc_final: 0.8933 (mp) REVERT: Q 76 LYS cc_start: 0.9055 (tptm) cc_final: 0.8724 (tptp) REVERT: Q 133 ASP cc_start: 0.8788 (m-30) cc_final: 0.8566 (p0) REVERT: Q 148 GLU cc_start: 0.8091 (mp0) cc_final: 0.7757 (mp0) REVERT: R 42 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7010 (t0) REVERT: R 45 ARG cc_start: 0.8113 (mtp180) cc_final: 0.7870 (mtp85) REVERT: R 49 VAL cc_start: 0.8860 (t) cc_final: 0.8646 (m) REVERT: R 50 ASP cc_start: 0.8372 (t0) cc_final: 0.8048 (t0) REVERT: S 59 SER cc_start: 0.8705 (t) cc_final: 0.8444 (p) REVERT: S 60 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7617 (tm-30) REVERT: S 68 ARG cc_start: 0.8251 (ttm170) cc_final: 0.7973 (ttm170) REVERT: W 27 ASP cc_start: 0.8340 (t0) cc_final: 0.8023 (p0) REVERT: W 45 GLU cc_start: 0.8387 (tp30) cc_final: 0.7773 (tp30) REVERT: Z 10 MET cc_start: 0.9131 (tpp) cc_final: 0.8885 (mmm) REVERT: Z 24 ASN cc_start: 0.8388 (t0) cc_final: 0.7804 (t0) REVERT: Z 69 ILE cc_start: 0.8904 (mm) cc_final: 0.8625 (mt) REVERT: Z 72 MET cc_start: 0.7873 (mmt) cc_final: 0.7477 (mmt) REVERT: Z 79 LYS cc_start: 0.8299 (tptt) cc_final: 0.7866 (tppt) REVERT: a 52 ARG cc_start: 0.8301 (ttp80) cc_final: 0.8094 (ptt180) REVERT: a 59 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7571 (ptp90) REVERT: a 61 TYR cc_start: 0.6600 (m-80) cc_final: 0.6042 (m-80) REVERT: b 9 LEU cc_start: 0.8653 (tp) cc_final: 0.8131 (mt) REVERT: q 51 ASP cc_start: 0.7592 (t0) cc_final: 0.7199 (t0) REVERT: q 53 LYS cc_start: 0.8967 (mtmm) cc_final: 0.8756 (mtmm) REVERT: q 67 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7984 (tm-30) REVERT: r 21 GLN cc_start: 0.8158 (tp40) cc_final: 0.7958 (tp40) outliers start: 123 outliers final: 81 residues processed: 869 average time/residue: 0.1895 time to fit residues: 274.1722 Evaluate side-chains 829 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 736 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain H residue 31 MET Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 63 TRP Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 76 MET Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 324 ILE Chi-restraints excluded: chain P residue 330 THR Chi-restraints excluded: chain P residue 355 ARG Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 167 ASN Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 125 GLU Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 109 PHE Chi-restraints excluded: chain X residue 94 MET Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain a residue 59 ARG Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain q residue 2 GLU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 111 THR Chi-restraints excluded: chain q residue 116 ASN Chi-restraints excluded: chain q residue 135 HIS Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 41 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 244 optimal weight: 4.9990 chunk 315 optimal weight: 0.0370 chunk 271 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 301 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 390 optimal weight: 10.0000 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN C 159 HIS ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 381 GLN G 51 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN P 93 HIS Q 51 GLN Q 92 ASN S 62 GLN ** V 83 GLN ** 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 = 0.3587 r_free = 0.3587 target = 0.083643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.070705 restraints weight = 126824.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.072832 restraints weight = 58902.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.074212 restraints weight = 34899.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.075127 restraints weight = 24245.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.075718 restraints weight = 18848.319| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.6695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 35288 Z= 0.164 Angle : 0.927 74.862 47853 Z= 0.376 Chirality : 0.046 0.316 5217 Planarity : 0.005 0.117 6066 Dihedral : 8.673 158.464 4986 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.05 % Favored : 95.92 % Rotamer: Outliers : 2.99 % Allowed : 24.86 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.13), residues: 4193 helix: 0.78 (0.12), residues: 1857 sheet: -0.71 (0.26), residues: 391 loop : -0.66 (0.15), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 333 TYR 0.033 0.002 TYR W 43 PHE 0.029 0.002 PHE X 82 TRP 0.045 0.002 TRP a 45 HIS 0.010 0.001 HIS H 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (35248) covalent geometry : angle 0.74568 / 0.37 (47763) SS BOND : bond 0.00481 / 0.23 ( 3) SS BOND : angle 1.41779 / 0.57 ( 6) hydrogen bonds : bond 0.03944 / 2.54 ( 1461) hydrogen bonds : angle 5.18012 / 3.60 ( 4197) metal coordination : bond 0.01710 / 1.08 ( 37) metal coordination : angle 13.18071 / 7.90 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 753 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8554 (mp) REVERT: A 68 GLU cc_start: 0.8821 (tt0) cc_final: 0.8591 (tt0) REVERT: A 88 MET cc_start: 0.8605 (ptm) cc_final: 0.8326 (ptt) REVERT: A 90 MET cc_start: 0.5706 (ptt) cc_final: 0.4863 (ttt) REVERT: A 109 LYS cc_start: 0.8704 (mmmm) cc_final: 0.7994 (pttt) REVERT: B 141 MET cc_start: 0.8559 (mmm) cc_final: 0.8335 (tpp) REVERT: B 147 LYS cc_start: 0.8272 (tptm) cc_final: 0.7699 (tptm) REVERT: B 150 ASP cc_start: 0.9088 (m-30) cc_final: 0.8630 (m-30) REVERT: B 151 GLN cc_start: 0.9060 (mt0) cc_final: 0.8458 (mt0) REVERT: C 227 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8097 (tt0) REVERT: C 241 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7143 (t80) REVERT: D 82 LEU cc_start: 0.8751 (tp) cc_final: 0.8289 (tt) REVERT: D 145 MET cc_start: 0.8598 (mtp) cc_final: 0.8185 (mmm) REVERT: D 202 TRP cc_start: 0.8219 (m-10) cc_final: 0.7192 (m-10) REVERT: D 328 ASP cc_start: 0.8246 (t0) cc_final: 0.7806 (t0) REVERT: D 356 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9076 (pp) REVERT: D 371 MET cc_start: 0.9271 (ttp) cc_final: 0.8742 (ttt) REVERT: D 387 GLU cc_start: 0.8433 (tt0) cc_final: 0.7828 (tt0) REVERT: E 105 GLN cc_start: 0.8946 (mp10) cc_final: 0.8710 (mp10) REVERT: E 181 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7607 (t0) REVERT: E 184 MET cc_start: 0.9074 (tmm) cc_final: 0.8774 (tmm) REVERT: E 205 ASP cc_start: 0.8922 (m-30) cc_final: 0.8692 (m-30) REVERT: F 155 TYR cc_start: 0.9276 (m-10) cc_final: 0.8848 (m-10) REVERT: F 220 GLN cc_start: 0.8754 (tt0) cc_final: 0.8338 (pt0) REVERT: F 337 MET cc_start: 0.8254 (mmm) cc_final: 0.7878 (mmm) REVERT: F 381 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8058 (mt0) REVERT: G 42 MET cc_start: 0.8321 (mmm) cc_final: 0.7896 (mmm) REVERT: G 97 MET cc_start: 0.7771 (tpp) cc_final: 0.7516 (mpp) REVERT: H 78 SER cc_start: 0.9392 (m) cc_final: 0.9168 (p) REVERT: H 118 TRP cc_start: 0.9175 (m-10) cc_final: 0.8400 (m-90) REVERT: H 121 TRP cc_start: 0.6035 (t60) cc_final: 0.5772 (t-100) REVERT: H 179 TRP cc_start: 0.8529 (p-90) cc_final: 0.8291 (p-90) REVERT: H 185 TRP cc_start: 0.9047 (t-100) cc_final: 0.8787 (t-100) REVERT: H 194 ASN cc_start: 0.8622 (m-40) cc_final: 0.8178 (t0) REVERT: H 227 GLU cc_start: 0.9040 (tp30) cc_final: 0.8599 (tp30) REVERT: H 234 MET cc_start: 0.8519 (mmm) cc_final: 0.8296 (mmt) REVERT: H 274 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8861 (ttt180) REVERT: H 301 CYS cc_start: 0.9384 (t) cc_final: 0.9166 (p) REVERT: H 302 MET cc_start: 0.8296 (ttm) cc_final: 0.7586 (tmm) REVERT: I 40 ASN cc_start: 0.8461 (t0) cc_final: 0.7984 (t0) REVERT: I 72 MET cc_start: 0.8525 (tpp) cc_final: 0.7879 (tpp) REVERT: I 122 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.9141 (tp) REVERT: I 208 ASP cc_start: 0.8996 (t0) cc_final: 0.8551 (t0) REVERT: I 211 TYR cc_start: 0.8226 (m-10) cc_final: 0.8004 (m-10) REVERT: P 45 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8177 (tptp) REVERT: P 54 VAL cc_start: 0.9046 (t) cc_final: 0.8817 (t) REVERT: P 121 GLN cc_start: 0.8299 (mm-40) cc_final: 0.7828 (mm110) REVERT: P 154 GLN cc_start: 0.7776 (tp-100) cc_final: 0.7360 (tp-100) REVERT: P 175 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7538 (mtmm) REVERT: P 213 PHE cc_start: 0.8542 (t80) cc_final: 0.8288 (t80) REVERT: P 214 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8890 (tt) REVERT: P 217 PHE cc_start: 0.8619 (m-10) cc_final: 0.8278 (m-80) REVERT: P 269 ASN cc_start: 0.7591 (p0) cc_final: 0.6987 (p0) REVERT: P 355 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6642 (mmt-90) REVERT: Q 52 LEU cc_start: 0.9186 (mp) cc_final: 0.8887 (mp) REVERT: Q 148 GLU cc_start: 0.8164 (mp0) cc_final: 0.7824 (mp0) REVERT: R 42 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.6931 (t0) REVERT: R 45 ARG cc_start: 0.8172 (mtp180) cc_final: 0.7749 (mtp85) REVERT: R 49 VAL cc_start: 0.8871 (t) cc_final: 0.8661 (m) REVERT: R 50 ASP cc_start: 0.8364 (t0) cc_final: 0.8049 (t0) REVERT: S 59 SER cc_start: 0.8790 (t) cc_final: 0.8553 (p) REVERT: S 60 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7650 (tm-30) REVERT: S 89 ARG cc_start: 0.8301 (ptp-170) cc_final: 0.8041 (ptp-170) REVERT: W 27 ASP cc_start: 0.8334 (t0) cc_final: 0.8015 (p0) REVERT: W 45 GLU cc_start: 0.8431 (tp30) cc_final: 0.7797 (tp30) REVERT: W 48 ASN cc_start: 0.9380 (m-40) cc_final: 0.9175 (m110) REVERT: Z 10 MET cc_start: 0.9137 (tpp) cc_final: 0.8917 (mmm) REVERT: Z 51 MET cc_start: 0.9027 (ttp) cc_final: 0.8618 (ptm) REVERT: Z 69 ILE cc_start: 0.8900 (mm) cc_final: 0.8664 (mm) REVERT: Z 79 LYS cc_start: 0.8267 (tptt) cc_final: 0.7847 (tppt) REVERT: a 61 TYR cc_start: 0.6423 (m-80) cc_final: 0.6097 (m-80) REVERT: b 9 LEU cc_start: 0.8633 (tp) cc_final: 0.8112 (mt) REVERT: q 51 ASP cc_start: 0.7624 (t0) cc_final: 0.7204 (t0) REVERT: q 53 LYS cc_start: 0.8968 (mtmm) cc_final: 0.8748 (mtmm) REVERT: q 67 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8008 (tm-30) REVERT: q 68 MET cc_start: 0.7715 (ttp) cc_final: 0.7428 (ttp) outliers start: 110 outliers final: 79 residues processed: 815 average time/residue: 0.1894 time to fit residues: 257.3444 Evaluate side-chains 816 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 724 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 381 GLN Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 63 TRP Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 76 MET Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 324 ILE Chi-restraints excluded: chain P residue 330 THR Chi-restraints excluded: chain P residue 355 ARG Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 167 ASN Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain X residue 94 MET Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain q residue 2 GLU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 111 THR Chi-restraints excluded: chain q residue 116 ASN Chi-restraints excluded: chain q residue 135 HIS Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 41 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 152 optimal weight: 2.9990 chunk 305 optimal weight: 0.3980 chunk 300 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 243 optimal weight: 5.9990 chunk 342 optimal weight: 8.9990 chunk 287 optimal weight: 5.9990 chunk 220 optimal weight: 0.2980 chunk 205 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 101 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN F 381 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 GLN P 93 HIS Q 51 GLN Q 92 ASN S 62 GLN V 83 GLN ** r 36 GLN ** 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 = 0.3617 r_free = 0.3617 target = 0.085087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.072131 restraints weight = 126446.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.074324 restraints weight = 58732.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.075751 restraints weight = 34624.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.076685 restraints weight = 23839.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.077305 restraints weight = 18487.197| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.6859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 35288 Z= 0.147 Angle : 0.939 73.512 47853 Z= 0.384 Chirality : 0.046 0.310 5217 Planarity : 0.005 0.116 6066 Dihedral : 8.556 158.228 4986 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.89 % Favored : 96.09 % Rotamer: Outliers : 2.52 % Allowed : 25.37 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.13), residues: 4193 helix: 0.70 (0.12), residues: 1860 sheet: -0.69 (0.26), residues: 392 loop : -0.70 (0.15), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 147 TYR 0.034 0.002 TYR B 190 PHE 0.050 0.002 PHE A 62 TRP 0.051 0.002 TRP a 45 HIS 0.009 0.001 HIS H 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (35248) covalent geometry : angle 0.76521 / 0.38 (47763) SS BOND : bond 0.00653 / 0.31 ( 3) SS BOND : angle 1.80790 / 0.69 ( 6) hydrogen bonds : bond 0.03979 / 2.57 ( 1461) hydrogen bonds : angle 5.16755 / 3.60 ( 4197) metal coordination : bond 0.01256 / 0.85 ( 37) metal coordination : angle 12.99518 / 7.80 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 794 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7766 (mm) REVERT: A 68 GLU cc_start: 0.8791 (tt0) cc_final: 0.8479 (tt0) REVERT: A 75 LEU cc_start: 0.9300 (tp) cc_final: 0.8974 (tt) REVERT: A 88 MET cc_start: 0.8453 (ptm) cc_final: 0.8213 (ptt) REVERT: A 90 MET cc_start: 0.5848 (ptt) cc_final: 0.5010 (ttt) REVERT: A 109 LYS cc_start: 0.8698 (mmmm) cc_final: 0.7986 (pttt) REVERT: B 80 ASP cc_start: 0.8646 (m-30) cc_final: 0.8273 (t70) REVERT: B 147 LYS cc_start: 0.8238 (tptm) cc_final: 0.7655 (tptm) REVERT: B 150 ASP cc_start: 0.9055 (m-30) cc_final: 0.8601 (m-30) REVERT: B 151 GLN cc_start: 0.9044 (mt0) cc_final: 0.8455 (mt0) REVERT: B 161 MET cc_start: 0.8364 (mtp) cc_final: 0.8122 (mtp) REVERT: C 241 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7087 (t80) REVERT: D 98 VAL cc_start: 0.9268 (t) cc_final: 0.9049 (p) REVERT: D 145 MET cc_start: 0.8574 (mtp) cc_final: 0.8189 (mmm) REVERT: D 328 ASP cc_start: 0.8077 (t0) cc_final: 0.7659 (t0) REVERT: D 356 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9054 (pp) REVERT: D 387 GLU cc_start: 0.8442 (tt0) cc_final: 0.7862 (tt0) REVERT: E 105 GLN cc_start: 0.8935 (mp10) cc_final: 0.8674 (mp10) REVERT: E 143 ASP cc_start: 0.8987 (t0) cc_final: 0.8767 (t0) REVERT: E 181 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.7543 (t0) REVERT: E 184 MET cc_start: 0.9049 (tmm) cc_final: 0.8768 (tmm) REVERT: E 205 ASP cc_start: 0.8894 (m-30) cc_final: 0.8657 (m-30) REVERT: F 155 TYR cc_start: 0.9258 (m-10) cc_final: 0.8871 (m-10) REVERT: F 337 MET cc_start: 0.8192 (mmm) cc_final: 0.7861 (mmm) REVERT: F 381 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8164 (mt0) REVERT: G 39 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8327 (mp10) REVERT: G 42 MET cc_start: 0.8292 (mmm) cc_final: 0.7903 (mmm) REVERT: G 97 MET cc_start: 0.7778 (tpp) cc_final: 0.7518 (mpp) REVERT: H 31 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8813 (mtm) REVERT: H 78 SER cc_start: 0.9397 (m) cc_final: 0.9189 (p) REVERT: H 118 TRP cc_start: 0.9165 (m-10) cc_final: 0.8380 (m-90) REVERT: H 121 TRP cc_start: 0.6023 (t60) cc_final: 0.5809 (t-100) REVERT: H 179 TRP cc_start: 0.8495 (p-90) cc_final: 0.8292 (p-90) REVERT: H 185 TRP cc_start: 0.8901 (t-100) cc_final: 0.8622 (t-100) REVERT: H 194 ASN cc_start: 0.8585 (m-40) cc_final: 0.8157 (t0) REVERT: H 227 GLU cc_start: 0.9055 (tp30) cc_final: 0.8622 (tp30) REVERT: H 234 MET cc_start: 0.8523 (mmm) cc_final: 0.8252 (mmt) REVERT: H 274 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8889 (ttt180) REVERT: H 301 CYS cc_start: 0.9335 (t) cc_final: 0.9108 (p) REVERT: H 302 MET cc_start: 0.8387 (ttm) cc_final: 0.7462 (tmm) REVERT: H 318 MET cc_start: 0.5830 (ptp) cc_final: 0.5341 (ppp) REVERT: I 40 ASN cc_start: 0.8392 (t0) cc_final: 0.7917 (t0) REVERT: I 50 MET cc_start: 0.8204 (tpp) cc_final: 0.6855 (mpp) REVERT: I 72 MET cc_start: 0.8391 (tpp) cc_final: 0.7946 (tpp) REVERT: I 122 ILE cc_start: 0.9376 (tp) cc_final: 0.9117 (tp) REVERT: I 149 MET cc_start: 0.8703 (mmm) cc_final: 0.7824 (mmm) REVERT: I 154 TYR cc_start: 0.9043 (m-80) cc_final: 0.8814 (m-80) REVERT: I 185 TYR cc_start: 0.7645 (m-80) cc_final: 0.7269 (m-80) REVERT: I 206 GLN cc_start: 0.9031 (tp-100) cc_final: 0.8819 (tp40) REVERT: I 208 ASP cc_start: 0.8885 (t0) cc_final: 0.8562 (t0) REVERT: P 54 VAL cc_start: 0.9007 (t) cc_final: 0.8795 (t) REVERT: P 121 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7830 (mm110) REVERT: P 154 GLN cc_start: 0.7660 (tp-100) cc_final: 0.7154 (tp-100) REVERT: P 175 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7159 (mmmt) REVERT: P 213 PHE cc_start: 0.8580 (t80) cc_final: 0.8331 (t80) REVERT: P 214 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8821 (tt) REVERT: P 217 PHE cc_start: 0.8617 (m-10) cc_final: 0.8240 (m-80) REVERT: P 269 ASN cc_start: 0.7588 (p0) cc_final: 0.6985 (p0) REVERT: P 336 GLU cc_start: 0.8852 (tt0) cc_final: 0.8232 (mm-30) REVERT: P 355 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6666 (mmt-90) REVERT: Q 52 LEU cc_start: 0.9107 (mp) cc_final: 0.8860 (mp) REVERT: Q 76 LYS cc_start: 0.9119 (tptm) cc_final: 0.8711 (tptp) REVERT: Q 148 GLU cc_start: 0.8193 (mp0) cc_final: 0.7942 (mp0) REVERT: R 42 ASP cc_start: 0.7602 (m-30) cc_final: 0.6947 (t0) REVERT: R 45 ARG cc_start: 0.8118 (mtp180) cc_final: 0.7722 (mtp85) REVERT: R 50 ASP cc_start: 0.8355 (t0) cc_final: 0.8059 (t0) REVERT: S 59 SER cc_start: 0.8764 (t) cc_final: 0.8483 (p) REVERT: S 60 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7676 (tm-30) REVERT: S 89 ARG cc_start: 0.8343 (ptp-170) cc_final: 0.7852 (mtm180) REVERT: T 115 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8026 (tt0) REVERT: W 27 ASP cc_start: 0.8319 (t0) cc_final: 0.7938 (p0) REVERT: W 43 TYR cc_start: 0.8996 (t80) cc_final: 0.8705 (t80) REVERT: W 45 GLU cc_start: 0.8378 (tp30) cc_final: 0.7699 (tp30) REVERT: W 48 ASN cc_start: 0.9372 (m-40) cc_final: 0.9168 (m110) REVERT: W 114 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8185 (tm-30) REVERT: X 40 ASN cc_start: 0.8604 (t0) cc_final: 0.7857 (t0) REVERT: X 44 MET cc_start: 0.7998 (mmm) cc_final: 0.7325 (mpp) REVERT: Z 10 MET cc_start: 0.9156 (tpp) cc_final: 0.8940 (mmm) REVERT: Z 24 ASN cc_start: 0.8304 (t0) cc_final: 0.7873 (t0) REVERT: Z 51 MET cc_start: 0.9027 (ttp) cc_final: 0.8630 (ptm) REVERT: Z 79 LYS cc_start: 0.8287 (tptt) cc_final: 0.7888 (tppt) REVERT: a 51 ASP cc_start: 0.8037 (p0) cc_final: 0.7639 (p0) REVERT: a 61 TYR cc_start: 0.6429 (m-80) cc_final: 0.6223 (m-80) REVERT: b 9 LEU cc_start: 0.8602 (tp) cc_final: 0.8094 (mt) REVERT: q 51 ASP cc_start: 0.7420 (t0) cc_final: 0.6982 (t0) REVERT: q 53 LYS cc_start: 0.8994 (mtmm) cc_final: 0.8749 (mtmm) REVERT: q 67 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7999 (tm-30) REVERT: q 68 MET cc_start: 0.7620 (ttp) cc_final: 0.7390 (ttp) REVERT: r 54 TYR cc_start: 0.7746 (t80) cc_final: 0.7405 (t80) outliers start: 93 outliers final: 72 residues processed: 847 average time/residue: 0.1818 time to fit residues: 258.1236 Evaluate side-chains 819 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 737 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 381 GLN Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain H residue 31 MET Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 63 TRP Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 76 MET Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 324 ILE Chi-restraints excluded: chain P residue 330 THR Chi-restraints excluded: chain P residue 355 ARG Chi-restraints excluded: chain Q residue 54 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 167 ASN Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain q residue 2 GLU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 116 ASN Chi-restraints excluded: chain q residue 135 HIS Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 41 LEU Chi-restraints excluded: chain r residue 68 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 324 optimal weight: 3.9990 chunk 339 optimal weight: 6.9990 chunk 200 optimal weight: 8.9990 chunk 262 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 230 optimal weight: 7.9990 chunk 252 optimal weight: 2.9990 chunk 371 optimal weight: 9.9990 chunk 291 optimal weight: 0.2980 chunk 43 optimal weight: 9.9990 chunk 393 optimal weight: 8.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN C 227 GLN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 381 GLN G 140 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN H 287 HIS P 93 HIS Q 51 GLN Q 88 GLN Q 92 ASN a 27 HIS q 116 ASN ** r 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.083127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.069972 restraints weight = 128297.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.072109 restraints weight = 60313.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.073485 restraints weight = 36216.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.074339 restraints weight = 25486.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.074985 restraints weight = 20101.524| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.6959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 35288 Z= 0.217 Angle : 1.004 78.354 47853 Z= 0.403 Chirality : 0.048 0.275 5217 Planarity : 0.006 0.207 6066 Dihedral : 8.635 156.538 4986 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.46 % Favored : 95.52 % Rotamer: Outliers : 2.74 % Allowed : 25.73 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.13), residues: 4193 helix: 0.65 (0.12), residues: 1866 sheet: -0.83 (0.26), residues: 401 loop : -0.68 (0.15), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 333 TYR 0.029 0.002 TYR B 190 PHE 0.056 0.002 PHE X 107 TRP 0.038 0.002 TRP a 45 HIS 0.005 0.001 HIS C 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 (35248) covalent geometry : angle 0.80954 / 0.40 (47763) SS BOND : bond 0.00662 / 0.32 ( 3) SS BOND : angle 1.92643 / 0.81 ( 6) hydrogen bonds : bond 0.04086 / 2.64 ( 1461) hydrogen bonds : angle 5.32499 / 3.70 ( 4197) metal coordination : bond 0.02675 / 1.59 ( 37) metal coordination : angle 14.19248 / 8.60 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6929.79 seconds wall clock time: 120 minutes 30.41 seconds (7230.41 seconds total)