Starting phenix.real_space_refine on Tue May 5 23:44:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xnn_38508/05_2026/8xnn_38508_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xnn_38508/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xnn_38508/05_2026/8xnn_38508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xnn_38508/05_2026/8xnn_38508.map" model { file = "/net/cci-nas-00/data/ceres_data/8xnn_38508/05_2026/8xnn_38508_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xnn_38508/05_2026/8xnn_38508_neut.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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: 7.08, 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: 3.64 Conformation dependent library (CDL) restraints added in 1.5 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: 1.12 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: 7.02 Time building geometry restraints manager: 4.65 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=" CB7 CDL q 201 " pdb=" OB8 CDL q 201 " ideal model delta sigma weight residual 1.334 1.450 -0.116 1.10e-02 8.26e+03 1.12e+02 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=" CA7 CDL q 201 " pdb=" OA8 CDL q 201 " ideal model delta sigma weight residual 1.334 1.449 -0.115 1.10e-02 8.26e+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 ... (remaining 35243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.17: 46960 6.17 - 12.33: 609 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: 20645 28.38 - 56.76: 581 56.76 - 85.15: 69 85.15 - 113.53: 6 113.53 - 141.91: 4 Dihedral angle restraints: 21305 sinusoidal: 8979 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 21302 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: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 40.780 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 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= 1.008 Angle : 2.173 48.469 47853 Z= 1.440 Chirality : 0.125 0.910 5217 Planarity : 0.008 0.231 6066 Dihedral : 13.002 141.909 13348 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 covalent geometry : bond 0.01419 (35248) covalent geometry : angle 2.04944 (47763) SS BOND : bond 0.01000 ( 3) SS BOND : angle 2.44084 ( 6) hydrogen bonds : bond 0.23527 ( 1461) hydrogen bonds : angle 9.10821 ( 4197) metal coordination : bond 0.49977 ( 37) metal coordination : angle 17.37850 ( 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 : 0.988 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: 0.2397 time to fit residues: 600.3200 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 : 1.314 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN 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 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 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.087249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.074035 restraints weight = 128443.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.076250 restraints weight = 58757.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.077719 restraints weight = 34531.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.078641 restraints weight = 23751.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.079275 restraints weight = 18495.683| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 35288 Z= 0.237 Angle : 1.064 58.611 47853 Z= 0.447 Chirality : 0.051 0.310 5217 Planarity : 0.007 0.139 6066 Dihedral : 9.766 154.330 4974 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.05 % Favored : 96.92 % Rotamer: Outliers : 4.53 % Allowed : 16.61 % Favored : 78.86 % 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: -0.92 (0.12), residues: 4193 helix: 0.16 (0.12), residues: 1867 sheet: -1.00 (0.27), residues: 355 loop : -1.23 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Z 57 TYR 0.029 0.003 TYR V 44 PHE 0.034 0.003 PHE T 126 TRP 0.025 0.002 TRP Z 142 HIS 0.009 0.002 HIS F 281 Details of bonding type rmsd covalent geometry : bond 0.00545 (35248) covalent geometry : angle 0.86015 (47763) SS BOND : bond 0.00178 ( 3) SS BOND : angle 0.97253 ( 6) hydrogen bonds : bond 0.05874 ( 1461) hydrogen bonds : angle 6.11917 ( 4197) metal coordination : bond 0.02633 ( 37) metal coordination : angle 14.95970 ( 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 1149 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 982 time to evaluate : 1.340 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: 0.8296 (m-40) cc_final: 0.7716 (t0) REVERT: A 68 GLU cc_start: 0.8744 (tt0) cc_final: 0.8492 (tt0) REVERT: A 88 MET cc_start: 0.8804 (ptm) cc_final: 0.8472 (mtm) REVERT: B 91 TRP cc_start: 0.8887 (m-10) cc_final: 0.8613 (m-10) REVERT: B 131 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.7882 (ttm) REVERT: B 151 GLN cc_start: 0.9201 (mt0) cc_final: 0.8975 (mt0) REVERT: C 166 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7705 (mt-10) REVERT: C 227 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7907 (tp40) REVERT: C 238 TRP cc_start: 0.9188 (m100) cc_final: 0.8924 (m100) REVERT: D 82 LEU cc_start: 0.8700 (tp) cc_final: 0.8246 (tt) REVERT: D 107 ARG cc_start: 0.7764 (tpp-160) cc_final: 0.7327 (tpp80) REVERT: D 261 MET cc_start: 0.8999 (tpp) cc_final: 0.8768 (tpp) REVERT: D 292 MET cc_start: 0.8932 (tpp) cc_final: 0.8143 (mmt) REVERT: D 390 GLN cc_start: 0.8456 (tt0) cc_final: 0.8056 (tm-30) REVERT: D 460 GLU cc_start: 0.8513 (pt0) cc_final: 0.8312 (pt0) REVERT: E 129 TYR cc_start: 0.6513 (m-80) cc_final: 0.6185 (m-80) REVERT: E 140 MET cc_start: 0.8928 (tmm) cc_final: 0.8712 (ppp) REVERT: E 186 GLN cc_start: 0.8048 (tt0) cc_final: 0.7798 (tt0) REVERT: F 113 LEU cc_start: 0.8601 (tp) cc_final: 0.8401 (tp) REVERT: F 155 TYR cc_start: 0.9270 (m-10) cc_final: 0.8926 (m-10) REVERT: F 337 MET cc_start: 0.8296 (mmm) cc_final: 0.8065 (mmm) REVERT: F 342 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9021 (mp) REVERT: F 357 MET cc_start: 0.8304 (mtm) cc_final: 0.8065 (mtm) REVERT: F 381 GLN cc_start: 0.8785 (tt0) cc_final: 0.8497 (mt0) REVERT: F 383 THR cc_start: 0.9395 (m) cc_final: 0.9182 (p) REVERT: F 396 MET cc_start: 0.9388 (mmm) cc_final: 0.8804 (mmm) REVERT: G 149 ASP cc_start: 0.7640 (m-30) cc_final: 0.5838 (m-30) REVERT: G 172 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.9038 (tt) REVERT: G 271 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8082 (mmt) REVERT: G 301 ARG cc_start: 0.8057 (ttt90) cc_final: 0.7159 (ttt-90) REVERT: G 329 MET cc_start: 0.8116 (mmm) cc_final: 0.7635 (mmm) REVERT: G 445 LEU cc_start: 0.9069 (mt) cc_final: 0.8828 (mp) REVERT: G 591 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7604 (mt-10) REVERT: G 596 TYR cc_start: 0.8856 (m-80) cc_final: 0.8634 (m-10) REVERT: H 27 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8816 (mt) REVERT: H 51 ASP cc_start: 0.8950 (p0) cc_final: 0.8697 (p0) REVERT: H 176 LEU cc_start: 0.8990 (mm) cc_final: 0.8719 (tp) REVERT: H 194 ASN cc_start: 0.8913 (m-40) cc_final: 0.8503 (t0) REVERT: H 247 TYR cc_start: 0.8468 (t80) cc_final: 0.8127 (t80) REVERT: H 253 GLU cc_start: 0.8188 (pp20) cc_final: 0.7657 (mp0) REVERT: I 40 ASN cc_start: 0.8466 (t0) cc_final: 0.7931 (t0) REVERT: I 66 LEU cc_start: 0.9126 (mt) cc_final: 0.8794 (mp) REVERT: I 208 ASP cc_start: 0.9036 (t0) cc_final: 0.8808 (t0) REVERT: P 121 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7333 (mm110) REVERT: P 154 GLN cc_start: 0.7993 (tp-100) cc_final: 0.7698 (tp-100) REVERT: P 217 PHE cc_start: 0.8597 (m-10) cc_final: 0.8245 (m-80) REVERT: P 244 ASP cc_start: 0.8252 (m-30) cc_final: 0.7889 (m-30) REVERT: P 276 LEU cc_start: 0.9181 (mt) cc_final: 0.8883 (mt) REVERT: P 317 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8340 (m-30) REVERT: P 351 GLU cc_start: 0.8464 (pt0) cc_final: 0.8053 (pm20) REVERT: Q 112 MET cc_start: 0.7939 (mmm) cc_final: 0.7716 (mmm) REVERT: Q 124 MET cc_start: 0.7989 (ttp) cc_final: 0.7668 (ttm) REVERT: Q 133 ASP cc_start: 0.8756 (m-30) cc_final: 0.8298 (p0) REVERT: Q 148 GLU cc_start: 0.7166 (mp0) cc_final: 0.6894 (mp0) REVERT: R 54 GLU cc_start: 0.7853 (tp30) cc_final: 0.7652 (tp30) REVERT: R 66 GLN cc_start: 0.7857 (mp10) cc_final: 0.7415 (mp10) REVERT: S 60 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7920 (tm-30) REVERT: S 62 GLN cc_start: 0.8117 (mt0) cc_final: 0.7481 (mt0) REVERT: S 80 ASN cc_start: 0.8420 (t0) cc_final: 0.7883 (t0) REVERT: T 120 MET cc_start: 0.8652 (mtp) cc_final: 0.8405 (mtm) REVERT: T 143 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8361 (mt-10) REVERT: W 37 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8468 (mt-10) REVERT: W 43 TYR cc_start: 0.8840 (t80) cc_final: 0.8571 (t80) REVERT: W 55 LEU cc_start: 0.9409 (mt) cc_final: 0.9122 (mp) REVERT: W 107 MET cc_start: 0.8397 (mmt) cc_final: 0.8131 (mmm) REVERT: X 7 LEU cc_start: 0.8702 (mt) cc_final: 0.8219 (mt) REVERT: X 129 THR cc_start: 0.6772 (p) cc_final: 0.6534 (t) REVERT: Z 72 MET cc_start: 0.8669 (mmt) cc_final: 0.8462 (mmt) REVERT: Z 76 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7796 (tm-30) REVERT: Z 79 LYS cc_start: 0.8118 (tptt) cc_final: 0.7724 (tppt) REVERT: a 15 CYS cc_start: 0.9086 (m) cc_final: 0.8513 (m) REVERT: b 9 LEU cc_start: 0.8684 (tp) cc_final: 0.8185 (mt) REVERT: q 49 TYR cc_start: 0.8892 (m-80) cc_final: 0.8660 (m-80) REVERT: q 51 ASP cc_start: 0.7819 (t0) cc_final: 0.7505 (t0) REVERT: q 133 LYS cc_start: 0.8452 (mmmt) cc_final: 0.8165 (mmmt) REVERT: q 136 GLU cc_start: 0.8221 (pm20) cc_final: 0.7966 (mt-10) REVERT: r 54 TYR cc_start: 0.7621 (t80) cc_final: 0.6676 (t80) REVERT: r 103 ARG cc_start: 0.8347 (tpp80) cc_final: 0.7924 (tpp80) REVERT: s 54 LYS cc_start: 0.9067 (ptmm) cc_final: 0.8626 (ptpt) outliers start: 167 outliers final: 81 residues processed: 1072 average time/residue: 0.2153 time to fit residues: 376.8791 Evaluate side-chains 869 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 780 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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 71 LEU Chi-restraints excluded: chain A residue 79 ILE 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 182 ASN Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 322 SER 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 172 ILE Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 281 ILE 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 205 SER 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 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 128 ILE 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 165 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 94 VAL Chi-restraints excluded: chain S residue 95 LEU 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 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 a residue 47 LEU 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 21 GLN Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 46 LEU 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: 5.9990 chunk 50 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 174 optimal weight: 8.9990 chunk 312 optimal weight: 0.9990 chunk 336 optimal weight: 1.9990 chunk 220 optimal weight: 0.0570 chunk 404 optimal weight: 6.9990 chunk 324 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 GLN ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** P 356 HIS Q 51 GLN Q 71 HIS Q 92 ASN Q 167 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 111 GLN W 73 ASN X 77 HIS ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 71 GLN q 54 GLN ** 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** ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 49 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.087311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.074176 restraints weight = 128093.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.076409 restraints weight = 58625.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.077880 restraints weight = 34481.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.078822 restraints weight = 23734.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.079363 restraints weight = 18343.997| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 35288 Z= 0.170 Angle : 0.944 62.400 47853 Z= 0.384 Chirality : 0.046 0.227 5217 Planarity : 0.006 0.130 6066 Dihedral : 9.528 154.566 4973 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.29 % Favored : 96.68 % Rotamer: Outliers : 4.31 % Allowed : 19.05 % Favored : 76.64 % 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: -0.54 (0.13), residues: 4193 helix: 0.48 (0.12), residues: 1870 sheet: -0.97 (0.26), residues: 376 loop : -1.00 (0.14), residues: 1947 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 0.026 0.002 PHE F 442 TRP 0.035 0.002 TRP Z 142 HIS 0.016 0.001 HIS P 323 Details of bonding type rmsd covalent geometry : bond 0.00385 (35248) covalent geometry : angle 0.75109 (47763) SS BOND : bond 0.00176 ( 3) SS BOND : angle 0.89887 ( 6) hydrogen bonds : bond 0.04904 ( 1461) hydrogen bonds : angle 5.67316 ( 4197) metal coordination : bond 0.01903 ( 37) metal coordination : angle 13.64941 ( 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 1048 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 889 time to evaluate : 1.317 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: A 10 ASN cc_start: 0.8168 (m-40) cc_final: 0.7807 (t0) REVERT: A 22 PHE cc_start: 0.7647 (t80) cc_final: 0.7152 (t80) REVERT: A 23 TRP cc_start: 0.7488 (OUTLIER) cc_final: 0.7276 (m-10) REVERT: A 68 GLU cc_start: 0.8758 (tt0) cc_final: 0.8489 (tt0) REVERT: B 145 LEU cc_start: 0.9440 (tp) cc_final: 0.9147 (tp) REVERT: B 150 ASP cc_start: 0.8903 (m-30) cc_final: 0.8353 (m-30) REVERT: B 151 GLN cc_start: 0.9191 (mt0) cc_final: 0.8979 (mt0) REVERT: B 215 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7661 (tm-30) REVERT: B 216 GLN cc_start: 0.8387 (pm20) cc_final: 0.7824 (pm20) REVERT: C 166 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7614 (mt-10) REVERT: C 211 TYR cc_start: 0.8903 (t80) cc_final: 0.8327 (t80) REVERT: C 227 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7800 (tp40) REVERT: D 259 GLU cc_start: 0.8818 (tp30) cc_final: 0.8445 (tp30) REVERT: D 261 MET cc_start: 0.8993 (tpp) cc_final: 0.8760 (tpp) REVERT: D 292 MET cc_start: 0.8404 (tpp) cc_final: 0.8031 (mpp) REVERT: D 351 MET cc_start: 0.8629 (tpp) cc_final: 0.8324 (tpp) REVERT: D 390 GLN cc_start: 0.8362 (tt0) cc_final: 0.7889 (tm-30) REVERT: D 410 TYR cc_start: 0.8991 (t80) cc_final: 0.8691 (t80) REVERT: E 140 MET cc_start: 0.8943 (tmm) cc_final: 0.8667 (ppp) REVERT: E 181 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7508 (t0) REVERT: F 147 ARG cc_start: 0.8522 (tpp80) cc_final: 0.8274 (tpt-90) REVERT: F 155 TYR cc_start: 0.9252 (m-10) cc_final: 0.8865 (m-10) REVERT: F 222 LYS cc_start: 0.8857 (mttm) cc_final: 0.8494 (mttm) REVERT: F 292 MET cc_start: 0.8166 (mtm) cc_final: 0.7837 (mtm) REVERT: F 337 MET cc_start: 0.8359 (mmm) cc_final: 0.8001 (mmm) REVERT: F 342 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9043 (mp) REVERT: F 381 GLN cc_start: 0.8719 (tt0) cc_final: 0.8121 (tt0) REVERT: F 396 MET cc_start: 0.9358 (mmm) cc_final: 0.9094 (mmm) REVERT: G 74 ASN cc_start: 0.8552 (m110) cc_final: 0.8337 (m-40) REVERT: G 126 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8144 (pp) REVERT: G 172 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.9053 (tt) REVERT: G 329 MET cc_start: 0.8065 (mmm) cc_final: 0.7635 (mmm) REVERT: G 591 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7690 (mt-10) REVERT: G 596 TYR cc_start: 0.8893 (m-80) cc_final: 0.8656 (m-10) REVERT: H 78 SER cc_start: 0.9162 (m) cc_final: 0.8860 (p) REVERT: H 91 MET cc_start: 0.8588 (ptp) cc_final: 0.8339 (ptp) REVERT: H 194 ASN cc_start: 0.8638 (m-40) cc_final: 0.8329 (t0) REVERT: H 225 MET cc_start: 0.9311 (mtm) cc_final: 0.8944 (mtm) REVERT: H 234 MET cc_start: 0.8547 (mmm) cc_final: 0.8268 (mmt) REVERT: H 253 GLU cc_start: 0.8146 (pp20) cc_final: 0.7632 (mp0) REVERT: I 40 ASN cc_start: 0.8440 (t0) cc_final: 0.7906 (t0) REVERT: I 63 TRP cc_start: 0.9007 (OUTLIER) cc_final: 0.8694 (m-90) REVERT: I 66 LEU cc_start: 0.9115 (mt) cc_final: 0.8448 (mt) REVERT: I 72 MET cc_start: 0.8967 (tpp) cc_final: 0.8730 (tpp) REVERT: I 76 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7851 (t80) REVERT: I 208 ASP cc_start: 0.9185 (t0) cc_final: 0.8728 (t0) REVERT: P 121 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7201 (mm110) REVERT: P 154 GLN cc_start: 0.8002 (tp-100) cc_final: 0.7516 (tp-100) REVERT: P 175 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7493 (mtmm) REVERT: P 244 ASP cc_start: 0.8356 (m-30) cc_final: 0.8058 (m-30) REVERT: P 271 TYR cc_start: 0.8389 (m-80) cc_final: 0.8133 (m-80) REVERT: P 276 LEU cc_start: 0.9254 (mt) cc_final: 0.9045 (mt) REVERT: P 317 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8298 (m-30) REVERT: P 351 GLU cc_start: 0.8301 (pt0) cc_final: 0.7820 (pm20) REVERT: Q 133 ASP cc_start: 0.8748 (m-30) cc_final: 0.8508 (p0) REVERT: Q 148 GLU cc_start: 0.7355 (mp0) cc_final: 0.6969 (mp0) REVERT: R 45 ARG cc_start: 0.8020 (mtp180) cc_final: 0.7533 (mtp85) REVERT: S 60 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7771 (tm-30) REVERT: S 80 ASN cc_start: 0.8440 (t0) cc_final: 0.8063 (t0) REVERT: T 97 LYS cc_start: 0.8768 (tttm) cc_final: 0.8350 (tttm) REVERT: W 55 LEU cc_start: 0.9376 (mt) cc_final: 0.9087 (mp) REVERT: X 7 LEU cc_start: 0.7970 (mt) cc_final: 0.7415 (mm) REVERT: Z 10 MET cc_start: 0.8971 (tpp) cc_final: 0.8763 (mmm) REVERT: Z 51 MET cc_start: 0.9017 (ttp) cc_final: 0.8601 (ptm) REVERT: Z 69 ILE cc_start: 0.8768 (mm) cc_final: 0.8441 (mm) REVERT: Z 79 LYS cc_start: 0.8222 (tptt) cc_final: 0.7708 (tppt) REVERT: b 9 LEU cc_start: 0.8688 (tp) cc_final: 0.8193 (mt) REVERT: q 51 ASP cc_start: 0.7980 (t0) cc_final: 0.7669 (t0) REVERT: q 93 MET cc_start: 0.8883 (tpp) cc_final: 0.8524 (mtp) REVERT: r 62 GLU cc_start: 0.5108 (tm-30) cc_final: 0.4839 (tm-30) REVERT: s 43 TYR cc_start: 0.8691 (m-80) cc_final: 0.8376 (m-10) REVERT: s 44 THR cc_start: 0.8817 (m) cc_final: 0.8550 (p) REVERT: s 54 LYS cc_start: 0.9051 (ptmm) cc_final: 0.8747 (ptpt) REVERT: s 55 PHE cc_start: 0.8709 (m-80) cc_final: 0.8441 (m-80) outliers start: 159 outliers final: 65 residues processed: 979 average time/residue: 0.2095 time to fit residues: 337.7036 Evaluate side-chains 845 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 769 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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 78 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 188 ASP Chi-restraints excluded: chain B residue 215 GLU 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 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 181 ASN Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 274 LEU 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 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 63 TRP Chi-restraints excluded: chain I residue 76 TYR 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 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 63 THR Chi-restraints excluded: chain Q residue 152 VAL 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 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 Z residue 36 PHE Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 121 ILE 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 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 54 GLN 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: 2.9990 chunk 118 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 371 optimal weight: 3.9990 chunk 254 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 HIS ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN D 265 ASN ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 GLN F 270 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** 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 166 HIS P 238 GLN ** P 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 356 HIS Q 51 GLN Q 92 ASN Q 123 ASN R 66 GLN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 ASN a 31 ASN ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 123 GLN ** r 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 49 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.084030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.070913 restraints weight = 127992.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.073091 restraints weight = 59481.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.074504 restraints weight = 35313.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.075381 restraints weight = 24550.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.075916 restraints weight = 19294.480| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 35288 Z= 0.199 Angle : 0.943 70.843 47853 Z= 0.375 Chirality : 0.046 0.231 5217 Planarity : 0.006 0.129 6066 Dihedral : 9.300 158.589 4970 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.89 % Favored : 96.09 % Rotamer: Outliers : 4.53 % Allowed : 19.54 % Favored : 75.93 % 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: -0.39 (0.13), residues: 4193 helix: 0.53 (0.12), residues: 1889 sheet: -0.94 (0.27), residues: 366 loop : -0.85 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 48 TYR 0.036 0.002 TYR R 43 PHE 0.027 0.002 PHE H 224 TRP 0.029 0.002 TRP B 91 HIS 0.013 0.001 HIS H 304 Details of bonding type rmsd covalent geometry : bond 0.00459 (35248) covalent geometry : angle 0.73635 (47763) SS BOND : bond 0.00280 ( 3) SS BOND : angle 1.08794 ( 6) hydrogen bonds : bond 0.04474 ( 1461) hydrogen bonds : angle 5.49479 ( 4197) metal coordination : bond 0.02494 ( 37) metal coordination : angle 14.08677 ( 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 984 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 817 time to evaluate : 1.363 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: 0.7692 (t80) cc_final: 0.6952 (t80) REVERT: A 23 TRP cc_start: 0.7345 (OUTLIER) cc_final: 0.7001 (m-10) REVERT: A 89 ILE cc_start: 0.8912 (mt) cc_final: 0.8657 (mm) REVERT: B 150 ASP cc_start: 0.8944 (m-30) cc_final: 0.8603 (m-30) REVERT: B 151 GLN cc_start: 0.9137 (mt0) cc_final: 0.8847 (mt0) REVERT: B 216 GLN cc_start: 0.8309 (pm20) cc_final: 0.8043 (pm20) REVERT: D 84 PHE cc_start: 0.7793 (t80) cc_final: 0.7540 (t80) REVERT: D 144 MET cc_start: 0.8783 (mpp) cc_final: 0.8340 (mpp) REVERT: D 203 MET cc_start: 0.8616 (mmm) cc_final: 0.8388 (mmm) REVERT: D 261 MET cc_start: 0.9033 (tpp) cc_final: 0.8674 (tpp) REVERT: D 356 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9143 (pp) REVERT: E 140 MET cc_start: 0.8969 (tmm) cc_final: 0.8731 (ppp) REVERT: E 181 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7596 (t0) REVERT: F 155 TYR cc_start: 0.9298 (m-10) cc_final: 0.8810 (m-10) REVERT: F 241 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.8879 (m) REVERT: F 292 MET cc_start: 0.8114 (mtm) cc_final: 0.7877 (mtm) REVERT: F 337 MET cc_start: 0.8405 (mmm) cc_final: 0.8080 (mmm) REVERT: F 342 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9137 (mp) REVERT: F 381 GLN cc_start: 0.8825 (tt0) cc_final: 0.8590 (tt0) REVERT: F 396 MET cc_start: 0.9357 (mmm) cc_final: 0.9086 (mmm) REVERT: G 42 MET cc_start: 0.8600 (mmt) cc_final: 0.8297 (mmm) REVERT: G 97 MET cc_start: 0.7732 (tpp) cc_final: 0.7458 (mpp) REVERT: G 172 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9004 (tp) REVERT: G 271 MET cc_start: 0.8452 (mmt) cc_final: 0.8243 (mmt) REVERT: G 329 MET cc_start: 0.8113 (mmm) cc_final: 0.7666 (mmm) REVERT: G 591 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7632 (mt-10) REVERT: H 78 SER cc_start: 0.9289 (m) cc_final: 0.9064 (p) REVERT: H 129 LEU cc_start: 0.8706 (mm) cc_final: 0.8467 (mm) REVERT: H 134 ARG cc_start: 0.8490 (mmm-85) cc_final: 0.7466 (mmm-85) REVERT: H 138 GLN cc_start: 0.9235 (tt0) cc_final: 0.8864 (tm-30) REVERT: H 214 GLU cc_start: 0.6976 (pm20) cc_final: 0.5994 (pm20) REVERT: H 215 TYR cc_start: 0.7145 (m-80) cc_final: 0.6878 (m-80) REVERT: H 225 MET cc_start: 0.9286 (mtm) cc_final: 0.9037 (mtm) REVERT: H 253 GLU cc_start: 0.8147 (pp20) cc_final: 0.7729 (mp0) REVERT: H 274 ARG cc_start: 0.9195 (ttt180) cc_final: 0.8900 (ttt180) REVERT: H 279 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7161 (ttm-80) REVERT: H 281 ARG cc_start: 0.7382 (ttm110) cc_final: 0.6604 (ttp-170) REVERT: I 40 ASN cc_start: 0.8540 (t0) cc_final: 0.7989 (t0) REVERT: I 72 MET cc_start: 0.9118 (tpp) cc_final: 0.8708 (tpp) REVERT: I 76 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.7900 (t80) REVERT: I 208 ASP cc_start: 0.9240 (t0) cc_final: 0.8759 (t0) REVERT: P 121 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7372 (mm110) REVERT: P 154 GLN cc_start: 0.8082 (tp-100) cc_final: 0.7664 (tp-100) REVERT: P 175 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7537 (mtmm) REVERT: P 244 ASP cc_start: 0.8434 (m-30) cc_final: 0.8121 (m-30) REVERT: P 269 ASN cc_start: 0.7112 (p0) cc_final: 0.6610 (p0) REVERT: P 316 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8654 (ttpt) REVERT: P 351 GLU cc_start: 0.8385 (pt0) cc_final: 0.7855 (pm20) REVERT: Q 148 GLU cc_start: 0.7732 (mp0) cc_final: 0.7341 (mp0) REVERT: R 42 ASP cc_start: 0.7826 (m-30) cc_final: 0.7507 (m-30) REVERT: R 47 ARG cc_start: 0.9001 (ptp-170) cc_final: 0.8743 (ptt180) REVERT: R 56 ASN cc_start: 0.8080 (t0) cc_final: 0.7875 (t0) REVERT: R 106 TYR cc_start: 0.9243 (m-80) cc_final: 0.8821 (m-80) REVERT: S 41 TYR cc_start: 0.8312 (t80) cc_final: 0.8105 (t80) REVERT: S 60 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7940 (tm-30) REVERT: S 89 ARG cc_start: 0.8235 (ptp-170) cc_final: 0.7925 (ptp-170) REVERT: T 105 MET cc_start: 0.8275 (mtp) cc_final: 0.8044 (mtm) REVERT: T 139 MET cc_start: 0.6964 (ppp) cc_final: 0.6580 (ppp) REVERT: V 73 GLN cc_start: 0.8167 (pp30) cc_final: 0.7780 (pp30) REVERT: W 27 ASP cc_start: 0.8380 (t0) cc_final: 0.7988 (p0) REVERT: W 45 GLU cc_start: 0.8680 (tp30) cc_final: 0.8127 (tp30) REVERT: W 100 TRP cc_start: 0.8796 (m-10) cc_final: 0.7904 (m-10) REVERT: Z 10 MET cc_start: 0.9082 (tpp) cc_final: 0.8811 (mmm) REVERT: Z 24 ASN cc_start: 0.8277 (t0) cc_final: 0.7806 (t0) REVERT: Z 51 MET cc_start: 0.9046 (ttp) cc_final: 0.8714 (ptm) REVERT: Z 69 ILE cc_start: 0.8763 (mm) cc_final: 0.8119 (mm) REVERT: Z 72 MET cc_start: 0.8244 (mmt) cc_final: 0.7858 (mmt) REVERT: Z 79 LYS cc_start: 0.8276 (tptt) cc_final: 0.7799 (tppt) REVERT: Z 124 MET cc_start: 0.8151 (mpp) cc_final: 0.7844 (mpp) REVERT: a 57 VAL cc_start: 0.7531 (p) cc_final: 0.7331 (m) REVERT: a 61 TYR cc_start: 0.6735 (m-80) cc_final: 0.6522 (m-80) REVERT: b 9 LEU cc_start: 0.8680 (tp) cc_final: 0.8186 (mt) REVERT: q 41 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7774 (tm-30) REVERT: q 51 ASP cc_start: 0.7957 (t0) cc_final: 0.7576 (t0) REVERT: q 67 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7644 (tp30) REVERT: q 68 MET cc_start: 0.6808 (ttp) cc_final: 0.6425 (ttp) REVERT: s 54 LYS cc_start: 0.9136 (ptmm) cc_final: 0.8806 (ptpt) outliers start: 167 outliers final: 91 residues processed: 914 average time/residue: 0.2140 time to fit residues: 325.2366 Evaluate side-chains 841 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 740 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 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 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 128 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 223 VAL 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 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 E residue 222 PHE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 220 GLN Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 383 THR 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 172 ILE Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 244 GLU Chi-restraints excluded: chain G residue 249 GLU 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 11 VAL Chi-restraints excluded: chain H residue 17 MET 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 279 ARG Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 76 TYR 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 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 99 MET Chi-restraints excluded: chain Q residue 152 VAL 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 133 ILE Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain W residue 48 ASN 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 96 THR Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain Z residue 36 PHE Chi-restraints excluded: chain Z residue 87 LEU 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 39 THR Chi-restraints excluded: chain b residue 78 LEU 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 q residue 135 HIS Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 64 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 20 optimal weight: 2.9990 chunk 253 optimal weight: 9.9990 chunk 282 optimal weight: 6.9990 chunk 170 optimal weight: 0.6980 chunk 292 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 334 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 397 optimal weight: 0.8980 chunk 220 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS ** 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 ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN 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** H 284 GLN ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 HIS ** 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** ** r 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 49 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.085362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.071966 restraints weight = 127672.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.074183 restraints weight = 59084.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.075636 restraints weight = 35053.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.076575 restraints weight = 24244.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.077198 restraints weight = 18896.763| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 35288 Z= 0.147 Angle : 0.904 70.539 47853 Z= 0.357 Chirality : 0.045 0.271 5217 Planarity : 0.005 0.125 6066 Dihedral : 9.145 157.319 4970 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 3.72 % Allowed : 21.22 % Favored : 75.06 % 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: -0.27 (0.13), residues: 4193 helix: 0.61 (0.12), residues: 1887 sheet: -0.87 (0.27), residues: 378 loop : -0.74 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 147 TYR 0.026 0.002 TYR Q 160 PHE 0.027 0.002 PHE X 107 TRP 0.031 0.001 TRP a 45 HIS 0.010 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00340 (35248) covalent geometry : angle 0.70890 (47763) SS BOND : bond 0.00274 ( 3) SS BOND : angle 1.04213 ( 6) hydrogen bonds : bond 0.04236 ( 1461) hydrogen bonds : angle 5.26739 ( 4197) metal coordination : bond 0.01442 ( 37) metal coordination : angle 13.38835 ( 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 983 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 846 time to evaluate : 1.256 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: A 22 PHE cc_start: 0.7644 (t80) cc_final: 0.6851 (t80) REVERT: A 63 LEU cc_start: 0.8645 (mm) cc_final: 0.8388 (mm) REVERT: A 109 LYS cc_start: 0.8539 (mmmm) cc_final: 0.7930 (pttt) REVERT: B 147 LYS cc_start: 0.8217 (tptm) cc_final: 0.7722 (tptm) REVERT: B 150 ASP cc_start: 0.9030 (m-30) cc_final: 0.8526 (m-30) REVERT: B 151 GLN cc_start: 0.9126 (mt0) cc_final: 0.8641 (mt0) REVERT: B 199 GLU cc_start: 0.8298 (mp0) cc_final: 0.7938 (mp0) REVERT: D 84 PHE cc_start: 0.7840 (t80) cc_final: 0.7599 (t80) REVERT: D 261 MET cc_start: 0.9055 (tpp) cc_final: 0.8711 (tpp) REVERT: D 328 ASP cc_start: 0.7958 (t0) cc_final: 0.7738 (t0) REVERT: D 356 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9085 (pp) REVERT: D 371 MET cc_start: 0.9231 (ttp) cc_final: 0.8832 (ttp) REVERT: D 410 TYR cc_start: 0.8958 (t80) cc_final: 0.8613 (t80) REVERT: E 132 GLN cc_start: 0.7632 (mt0) cc_final: 0.7370 (mt0) REVERT: E 140 MET cc_start: 0.8885 (tmm) cc_final: 0.8661 (ppp) REVERT: E 181 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7503 (t0) REVERT: F 155 TYR cc_start: 0.9288 (m-10) cc_final: 0.8912 (m-10) REVERT: F 292 MET cc_start: 0.8094 (mtm) cc_final: 0.7892 (mtm) REVERT: F 337 MET cc_start: 0.8398 (mmm) cc_final: 0.8003 (mmm) REVERT: F 396 MET cc_start: 0.9346 (mmm) cc_final: 0.8601 (mmm) REVERT: F 420 GLU cc_start: 0.8717 (tt0) cc_final: 0.8484 (tt0) REVERT: G 42 MET cc_start: 0.8584 (mmt) cc_final: 0.8110 (mmm) REVERT: G 97 MET cc_start: 0.7646 (tpp) cc_final: 0.7341 (mpp) REVERT: G 172 ILE cc_start: 0.9325 (mt) cc_final: 0.8960 (tp) REVERT: G 213 MET cc_start: 0.6632 (ppp) cc_final: 0.6421 (ppp) REVERT: G 329 MET cc_start: 0.8114 (mmm) cc_final: 0.7891 (tpp) REVERT: G 591 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7747 (mt-10) REVERT: G 596 TYR cc_start: 0.8976 (m-80) cc_final: 0.8720 (m-10) REVERT: H 47 GLN cc_start: 0.9399 (tp40) cc_final: 0.9069 (tp40) REVERT: H 78 SER cc_start: 0.9306 (m) cc_final: 0.9084 (p) REVERT: H 118 TRP cc_start: 0.9080 (m-10) cc_final: 0.8393 (m-90) REVERT: H 134 ARG cc_start: 0.8480 (mmm-85) cc_final: 0.7510 (mmm-85) REVERT: H 138 GLN cc_start: 0.9227 (tt0) cc_final: 0.8931 (tm-30) REVERT: H 214 GLU cc_start: 0.6783 (pm20) cc_final: 0.6157 (pm20) REVERT: H 225 MET cc_start: 0.9329 (mtm) cc_final: 0.9073 (mtm) REVERT: H 227 GLU cc_start: 0.9058 (tp30) cc_final: 0.8734 (tp30) REVERT: H 247 TYR cc_start: 0.8194 (t80) cc_final: 0.7815 (t80) REVERT: H 253 GLU cc_start: 0.8135 (pp20) cc_final: 0.7766 (mp0) REVERT: H 271 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8416 (mt) REVERT: H 274 ARG cc_start: 0.9169 (ttt180) cc_final: 0.8780 (ttt180) REVERT: H 277 TYR cc_start: 0.7714 (m-10) cc_final: 0.7508 (m-80) REVERT: H 282 TYR cc_start: 0.8055 (t80) cc_final: 0.7611 (t80) REVERT: I 35 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.8961 (p) REVERT: I 40 ASN cc_start: 0.8585 (t0) cc_final: 0.8101 (t0) REVERT: I 72 MET cc_start: 0.9149 (tpp) cc_final: 0.8792 (tpp) REVERT: I 122 ILE cc_start: 0.9405 (tp) cc_final: 0.9156 (tp) REVERT: I 149 MET cc_start: 0.8915 (mmm) cc_final: 0.8583 (mmm) REVERT: I 174 GLU cc_start: 0.8411 (mp0) cc_final: 0.8102 (mp0) REVERT: I 185 TYR cc_start: 0.8391 (m-10) cc_final: 0.8144 (m-80) REVERT: I 208 ASP cc_start: 0.9154 (t0) cc_final: 0.8684 (t0) REVERT: P 45 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7805 (tptp) REVERT: P 54 VAL cc_start: 0.9027 (t) cc_final: 0.8755 (t) REVERT: P 121 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7549 (mm110) REVERT: P 154 GLN cc_start: 0.8031 (tp-100) cc_final: 0.7636 (tp-100) REVERT: P 175 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7623 (mtmm) REVERT: P 244 ASP cc_start: 0.8462 (m-30) cc_final: 0.8139 (m-30) REVERT: P 269 ASN cc_start: 0.7129 (p0) cc_final: 0.6694 (p0) REVERT: P 281 PHE cc_start: 0.8990 (m-80) cc_final: 0.8729 (m-80) REVERT: P 316 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8671 (ttpt) REVERT: P 351 GLU cc_start: 0.8307 (pt0) cc_final: 0.7839 (pm20) REVERT: Q 133 ASP cc_start: 0.8831 (m-30) cc_final: 0.8595 (p0) REVERT: Q 148 GLU cc_start: 0.7801 (mp0) cc_final: 0.7391 (mp0) REVERT: R 42 ASP cc_start: 0.8035 (m-30) cc_final: 0.7717 (m-30) REVERT: R 47 ARG cc_start: 0.8957 (ptp-170) cc_final: 0.8736 (ptt180) REVERT: R 106 TYR cc_start: 0.9222 (m-80) cc_final: 0.8872 (m-80) REVERT: S 41 TYR cc_start: 0.8244 (t80) cc_final: 0.8006 (t80) REVERT: S 59 SER cc_start: 0.8698 (t) cc_final: 0.8453 (p) REVERT: S 60 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7860 (tm-30) REVERT: S 62 GLN cc_start: 0.8391 (mt0) cc_final: 0.8167 (mt0) REVERT: S 68 ARG cc_start: 0.8333 (ttm170) cc_final: 0.8010 (ttm170) REVERT: S 80 ASN cc_start: 0.8581 (t0) cc_final: 0.8148 (t0) REVERT: T 81 ASP cc_start: 0.9429 (t0) cc_final: 0.9185 (m-30) REVERT: T 120 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8260 (ptp) REVERT: W 27 ASP cc_start: 0.8389 (t0) cc_final: 0.8044 (p0) REVERT: W 43 TYR cc_start: 0.9035 (t80) cc_final: 0.8371 (t80) REVERT: W 45 GLU cc_start: 0.8603 (tp30) cc_final: 0.7997 (tp30) REVERT: W 73 ASN cc_start: 0.9303 (m-40) cc_final: 0.9029 (m110) REVERT: Z 10 MET cc_start: 0.9137 (tpp) cc_final: 0.8933 (mmm) REVERT: Z 24 ASN cc_start: 0.8314 (t0) cc_final: 0.7719 (t0) REVERT: Z 51 MET cc_start: 0.9021 (ttp) cc_final: 0.8714 (ptm) REVERT: Z 69 ILE cc_start: 0.8772 (mm) cc_final: 0.8517 (mt) REVERT: Z 79 LYS cc_start: 0.8246 (tptt) cc_final: 0.7846 (tppt) REVERT: a 4 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8187 (mm-30) REVERT: a 61 TYR cc_start: 0.6513 (m-80) cc_final: 0.6273 (m-80) REVERT: b 32 MET cc_start: 0.8593 (mmm) cc_final: 0.8389 (mmm) REVERT: b 44 MET cc_start: 0.8262 (ptp) cc_final: 0.7458 (ptp) REVERT: q 51 ASP cc_start: 0.7919 (t0) cc_final: 0.7113 (t0) REVERT: q 67 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7597 (tp30) REVERT: r 62 GLU cc_start: 0.4940 (tm-30) cc_final: 0.4672 (tm-30) REVERT: s 55 PHE cc_start: 0.8570 (m-80) cc_final: 0.8318 (m-10) outliers start: 137 outliers final: 78 residues processed: 926 average time/residue: 0.2180 time to fit residues: 334.4375 Evaluate side-chains 838 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 752 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 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 93 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain C residue 82 GLU 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 D residue 130 LEU Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 265 ASN 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 78 VAL 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 53 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 261 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 17 MET 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 271 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 301 CYS Chi-restraints excluded: chain I residue 35 THR 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 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 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 63 THR Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 152 VAL 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 94 VAL Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 120 MET 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 X residue 50 GLU Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 121 ILE 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 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 104 THR Chi-restraints excluded: chain q residue 111 THR 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: 5.9990 chunk 68 optimal weight: 1.9990 chunk 369 optimal weight: 4.9990 chunk 349 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 242 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** 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 132 GLN ** 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 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN P 93 HIS ** 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 116 ASN q 123 GLN s 41 ASN s 49 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.084248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.071034 restraints weight = 127972.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.073196 restraints weight = 59517.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.074633 restraints weight = 35322.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.075480 restraints weight = 24427.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.076145 restraints weight = 19241.631| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.6160 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= 0.168 Angle : 0.908 72.619 47853 Z= 0.360 Chirality : 0.045 0.228 5217 Planarity : 0.005 0.124 6066 Dihedral : 9.030 156.393 4970 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.03 % Favored : 95.95 % Rotamer: Outliers : 4.18 % Allowed : 22.17 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.22 (0.13), residues: 4193 helix: 0.63 (0.12), residues: 1876 sheet: -0.86 (0.26), residues: 389 loop : -0.68 (0.15), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 333 TYR 0.030 0.002 TYR H 215 PHE 0.036 0.002 PHE A 62 TRP 0.033 0.002 TRP a 45 HIS 0.011 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00394 (35248) covalent geometry : angle 0.71045 (47763) SS BOND : bond 0.00319 ( 3) SS BOND : angle 1.04948 ( 6) hydrogen bonds : bond 0.04142 ( 1461) hydrogen bonds : angle 5.25000 ( 4197) metal coordination : bond 0.01881 ( 37) metal coordination : angle 13.53155 ( 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 939 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 785 time to evaluate : 1.548 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 68 GLU cc_start: 0.8934 (tt0) cc_final: 0.8208 (tt0) REVERT: A 109 LYS cc_start: 0.8588 (mmmm) cc_final: 0.7962 (pttt) REVERT: B 147 LYS cc_start: 0.8339 (tptm) cc_final: 0.7865 (tptm) REVERT: B 150 ASP cc_start: 0.9051 (m-30) cc_final: 0.8602 (m-30) REVERT: B 151 GLN cc_start: 0.9119 (mt0) cc_final: 0.8655 (mt0) REVERT: D 84 PHE cc_start: 0.7789 (t80) cc_final: 0.7457 (t80) REVERT: D 261 MET cc_start: 0.9084 (tpp) cc_final: 0.8705 (tpp) REVERT: D 328 ASP cc_start: 0.8157 (t0) cc_final: 0.7796 (t0) REVERT: D 356 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9086 (pp) REVERT: D 371 MET cc_start: 0.9268 (ttp) cc_final: 0.8850 (ttt) REVERT: D 410 TYR cc_start: 0.8979 (t80) cc_final: 0.8589 (t80) REVERT: E 132 GLN cc_start: 0.7642 (mt0) cc_final: 0.7375 (mt0) REVERT: E 140 MET cc_start: 0.8920 (tmm) cc_final: 0.8671 (ppp) REVERT: E 181 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.7431 (t0) REVERT: F 155 TYR cc_start: 0.9297 (m-10) cc_final: 0.9000 (m-10) REVERT: F 337 MET cc_start: 0.8428 (mmm) cc_final: 0.7957 (mmm) REVERT: F 381 GLN cc_start: 0.8665 (tt0) cc_final: 0.8129 (mt0) REVERT: F 396 MET cc_start: 0.9358 (mmm) cc_final: 0.8549 (mmm) REVERT: G 42 MET cc_start: 0.8597 (mmt) cc_final: 0.8207 (mmm) REVERT: G 172 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9015 (tp) REVERT: G 329 MET cc_start: 0.8101 (mmm) cc_final: 0.7896 (tpp) REVERT: G 345 LEU cc_start: 0.9012 (mp) cc_final: 0.8484 (mt) REVERT: G 591 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7776 (mt-10) REVERT: H 47 GLN cc_start: 0.9356 (tp40) cc_final: 0.9046 (tp40) REVERT: H 78 SER cc_start: 0.9363 (m) cc_final: 0.9134 (p) REVERT: H 118 TRP cc_start: 0.9144 (m-10) cc_final: 0.8385 (m-90) REVERT: H 225 MET cc_start: 0.9323 (mtm) cc_final: 0.9109 (mtm) REVERT: H 227 GLU cc_start: 0.9052 (tp30) cc_final: 0.8718 (tp30) REVERT: H 235 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8156 (t0) REVERT: H 247 TYR cc_start: 0.8329 (t80) cc_final: 0.8012 (t80) REVERT: H 253 GLU cc_start: 0.8157 (pp20) cc_final: 0.7848 (mp0) REVERT: H 270 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7724 (t80) REVERT: H 271 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8410 (mt) REVERT: H 274 ARG cc_start: 0.9193 (ttt180) cc_final: 0.8774 (ttt180) REVERT: H 281 ARG cc_start: 0.8254 (ttp-170) cc_final: 0.7814 (ttp-170) REVERT: I 35 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.8913 (p) REVERT: I 40 ASN cc_start: 0.8601 (t0) cc_final: 0.8108 (t0) REVERT: I 72 MET cc_start: 0.9178 (tpp) cc_final: 0.8788 (tpp) REVERT: I 86 TYR cc_start: 0.8308 (t80) cc_final: 0.8101 (t80) REVERT: I 122 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9161 (tp) REVERT: I 159 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8550 (mt0) REVERT: I 174 GLU cc_start: 0.8476 (mp0) cc_final: 0.8183 (mp0) REVERT: I 208 ASP cc_start: 0.9135 (t0) cc_final: 0.8736 (t0) REVERT: P 45 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.7985 (tptp) REVERT: P 54 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8761 (t) REVERT: P 121 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7736 (mm110) REVERT: P 154 GLN cc_start: 0.8000 (tp-100) cc_final: 0.7603 (tp-100) REVERT: P 175 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7633 (mtmm) REVERT: P 269 ASN cc_start: 0.7173 (p0) cc_final: 0.6679 (p0) REVERT: P 271 TYR cc_start: 0.8300 (m-80) cc_final: 0.7997 (m-80) REVERT: P 351 GLU cc_start: 0.8367 (pt0) cc_final: 0.7838 (pm20) REVERT: Q 52 LEU cc_start: 0.9138 (mp) cc_final: 0.8902 (mp) REVERT: Q 133 ASP cc_start: 0.8854 (m-30) cc_final: 0.8632 (p0) REVERT: Q 148 GLU cc_start: 0.7887 (mp0) cc_final: 0.7516 (mp0) REVERT: R 42 ASP cc_start: 0.8006 (m-30) cc_final: 0.7497 (t0) REVERT: R 47 ARG cc_start: 0.9017 (ptp-170) cc_final: 0.8768 (ptt180) REVERT: R 106 TYR cc_start: 0.9261 (m-80) cc_final: 0.8948 (m-80) REVERT: S 59 SER cc_start: 0.8740 (t) cc_final: 0.8534 (p) REVERT: S 60 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7864 (tm-30) REVERT: S 62 GLN cc_start: 0.8435 (mt0) cc_final: 0.8186 (mt0) REVERT: S 80 ASN cc_start: 0.8629 (t0) cc_final: 0.8174 (t0) REVERT: S 89 ARG cc_start: 0.8193 (ptp-170) cc_final: 0.7807 (ptp-170) REVERT: T 81 ASP cc_start: 0.9409 (t0) cc_final: 0.9204 (m-30) REVERT: T 120 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8296 (ptp) REVERT: T 132 ASP cc_start: 0.7810 (t0) cc_final: 0.7528 (t0) REVERT: W 27 ASP cc_start: 0.8395 (t0) cc_final: 0.8006 (p0) REVERT: W 45 GLU cc_start: 0.8606 (tp30) cc_final: 0.7986 (tp30) REVERT: W 100 TRP cc_start: 0.8788 (m-10) cc_final: 0.8189 (m-10) REVERT: W 101 LYS cc_start: 0.8353 (mmmt) cc_final: 0.8094 (tptt) REVERT: X 82 PHE cc_start: 0.8831 (t80) cc_final: 0.8569 (t80) REVERT: Z 10 MET cc_start: 0.9126 (tpp) cc_final: 0.8843 (mmm) REVERT: Z 24 ASN cc_start: 0.8367 (t0) cc_final: 0.7755 (t0) REVERT: Z 51 MET cc_start: 0.9045 (ttp) cc_final: 0.8773 (ptm) REVERT: Z 69 ILE cc_start: 0.8843 (mm) cc_final: 0.8564 (mm) REVERT: Z 79 LYS cc_start: 0.8408 (tptt) cc_final: 0.7924 (tppt) REVERT: Z 137 ASN cc_start: 0.9007 (m-40) cc_final: 0.8557 (m-40) REVERT: a 4 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8183 (mm-30) REVERT: b 9 LEU cc_start: 0.8678 (tp) cc_final: 0.8127 (mt) REVERT: q 42 ASP cc_start: 0.7201 (p0) cc_final: 0.6706 (m-30) REVERT: q 51 ASP cc_start: 0.7838 (t0) cc_final: 0.7484 (t0) REVERT: q 67 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7665 (tp30) REVERT: q 93 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8221 (tpp) REVERT: s 55 PHE cc_start: 0.8281 (m-80) cc_final: 0.7958 (m-10) outliers start: 154 outliers final: 92 residues processed: 867 average time/residue: 0.2114 time to fit residues: 306.8987 Evaluate side-chains 828 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 722 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 64 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 93 MET Chi-restraints excluded: chain B residue 97 LEU 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 203 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 223 VAL 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 147 ASN 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 137 THR 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 241 THR Chi-restraints excluded: chain F residue 315 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 172 ILE Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 273 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 27 ILE 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 235 ASN Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 271 LEU 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 35 THR Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 159 GLN 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 324 ILE Chi-restraints excluded: chain P residue 330 THR Chi-restraints excluded: chain P residue 366 ILE 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 167 ASN 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 79 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 V residue 58 MET 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 96 THR Chi-restraints excluded: chain X residue 56 CYS 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 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 2 GLU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 93 MET Chi-restraints excluded: chain q residue 104 THR Chi-restraints excluded: chain q residue 111 THR Chi-restraints excluded: chain r residue 5 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: 2.9990 chunk 205 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 363 optimal weight: 0.6980 chunk 399 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 240 optimal weight: 7.9990 chunk 304 optimal weight: 0.0970 chunk 197 optimal weight: 0.0170 chunk 354 optimal weight: 7.9990 overall best weight: 1.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN G 74 ASN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** W 73 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.083805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.070568 restraints weight = 128482.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.072715 restraints weight = 59488.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.074137 restraints weight = 35315.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.074987 restraints weight = 24576.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.075625 restraints weight = 19349.371| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.6352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 35288 Z= 0.171 Angle : 0.919 73.808 47853 Z= 0.362 Chirality : 0.045 0.211 5217 Planarity : 0.005 0.186 6066 Dihedral : 8.901 156.015 4970 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.03 % Favored : 95.95 % Rotamer: Outliers : 3.72 % Allowed : 23.12 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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: 0.70 (0.12), residues: 1875 sheet: -0.83 (0.26), residues: 388 loop : -0.63 (0.15), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 333 TYR 0.031 0.002 TYR Q 160 PHE 0.034 0.002 PHE Z 138 TRP 0.037 0.002 TRP a 45 HIS 0.012 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00397 (35248) covalent geometry : angle 0.72212 (47763) SS BOND : bond 0.00270 ( 3) SS BOND : angle 0.91489 ( 6) hydrogen bonds : bond 0.04068 ( 1461) hydrogen bonds : angle 5.22212 ( 4197) metal coordination : bond 0.01921 ( 37) metal coordination : angle 13.58635 ( 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 901 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 764 time to evaluate : 1.402 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 68 GLU cc_start: 0.8874 (tt0) cc_final: 0.8601 (tt0) REVERT: A 90 MET cc_start: 0.5453 (ptt) cc_final: 0.4721 (ttt) REVERT: A 109 LYS cc_start: 0.8606 (mmmm) cc_final: 0.7968 (pttt) REVERT: B 150 ASP cc_start: 0.9059 (m-30) cc_final: 0.8754 (m-30) REVERT: B 151 GLN cc_start: 0.9128 (mt0) cc_final: 0.8717 (mt0) REVERT: B 184 ILE cc_start: 0.9051 (mp) cc_final: 0.8841 (mt) REVERT: B 199 GLU cc_start: 0.8280 (mp0) cc_final: 0.7985 (mp0) REVERT: C 241 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.7263 (t80) REVERT: D 84 PHE cc_start: 0.7713 (t80) cc_final: 0.7304 (t80) REVERT: D 261 MET cc_start: 0.9056 (tpp) cc_final: 0.8607 (tpp) REVERT: D 328 ASP cc_start: 0.8209 (t0) cc_final: 0.7782 (t0) REVERT: D 356 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.9112 (pp) REVERT: D 371 MET cc_start: 0.9268 (ttp) cc_final: 0.8788 (ttt) REVERT: E 132 GLN cc_start: 0.7734 (mt0) cc_final: 0.7417 (mt0) REVERT: E 140 MET cc_start: 0.8968 (tmm) cc_final: 0.8706 (ppp) REVERT: E 181 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7485 (t0) REVERT: E 205 ASP cc_start: 0.8932 (m-30) cc_final: 0.8694 (m-30) REVERT: F 155 TYR cc_start: 0.9295 (m-10) cc_final: 0.9072 (m-10) REVERT: F 337 MET cc_start: 0.8369 (mmm) cc_final: 0.7934 (mmm) REVERT: G 42 MET cc_start: 0.8611 (mmt) cc_final: 0.8200 (mmm) REVERT: G 97 MET cc_start: 0.7758 (tpp) cc_final: 0.7487 (mpp) REVERT: G 591 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7838 (mt-10) REVERT: H 78 SER cc_start: 0.9375 (m) cc_final: 0.9157 (p) REVERT: H 118 TRP cc_start: 0.9161 (m-10) cc_final: 0.8363 (m-90) REVERT: H 198 PHE cc_start: 0.9181 (m-80) cc_final: 0.8955 (m-10) REVERT: H 225 MET cc_start: 0.9298 (mtm) cc_final: 0.9074 (mtm) REVERT: H 227 GLU cc_start: 0.9061 (tp30) cc_final: 0.8732 (tp30) REVERT: H 247 TYR cc_start: 0.8373 (t80) cc_final: 0.7962 (t80) REVERT: H 253 GLU cc_start: 0.8019 (pp20) cc_final: 0.7777 (mp0) REVERT: H 270 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.7738 (t80) REVERT: H 274 ARG cc_start: 0.9206 (ttt180) cc_final: 0.8931 (ttt180) REVERT: H 281 ARG cc_start: 0.7760 (ttp-170) cc_final: 0.7535 (ttp-170) REVERT: H 284 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8737 (pm20) REVERT: I 40 ASN cc_start: 0.8643 (t0) cc_final: 0.8092 (t0) REVERT: I 72 MET cc_start: 0.9170 (tpp) cc_final: 0.8786 (tpp) REVERT: I 86 TYR cc_start: 0.8352 (t80) cc_final: 0.8131 (t80) REVERT: I 122 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9154 (tp) REVERT: I 159 GLN cc_start: 0.8784 (mt0) cc_final: 0.8558 (mt0) REVERT: I 208 ASP cc_start: 0.9115 (t0) cc_final: 0.8748 (t0) REVERT: P 45 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8115 (tptp) REVERT: P 54 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8805 (t) REVERT: P 121 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7741 (mm110) REVERT: P 154 GLN cc_start: 0.7932 (tp-100) cc_final: 0.7535 (tp-100) REVERT: P 175 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7558 (mtmm) REVERT: P 213 PHE cc_start: 0.8933 (t80) cc_final: 0.8715 (t80) REVERT: P 269 ASN cc_start: 0.7334 (p0) cc_final: 0.6875 (p0) REVERT: P 271 TYR cc_start: 0.8312 (m-80) cc_final: 0.8067 (m-80) REVERT: P 281 PHE cc_start: 0.9017 (m-80) cc_final: 0.8783 (m-80) REVERT: P 351 GLU cc_start: 0.8378 (pt0) cc_final: 0.7819 (pm20) REVERT: P 355 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6904 (mmt-90) REVERT: Q 148 GLU cc_start: 0.8007 (mp0) cc_final: 0.7683 (mp0) REVERT: R 38 TYR cc_start: 0.7895 (m-10) cc_final: 0.7284 (m-10) REVERT: R 42 ASP cc_start: 0.7882 (m-30) cc_final: 0.7505 (t0) REVERT: R 47 ARG cc_start: 0.9046 (ptp-170) cc_final: 0.8777 (ptt180) REVERT: R 106 TYR cc_start: 0.9310 (m-80) cc_final: 0.9026 (m-80) REVERT: S 60 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7861 (tm-30) REVERT: S 62 GLN cc_start: 0.8440 (mt0) cc_final: 0.8201 (mt0) REVERT: S 80 ASN cc_start: 0.8646 (t0) cc_final: 0.8173 (t0) REVERT: T 115 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8397 (tt0) REVERT: T 120 MET cc_start: 0.8550 (ptp) cc_final: 0.8253 (ptp) REVERT: V 94 MET cc_start: 0.8489 (tpp) cc_final: 0.8187 (mpp) REVERT: W 27 ASP cc_start: 0.8440 (t0) cc_final: 0.8036 (p0) REVERT: W 45 GLU cc_start: 0.8653 (tp30) cc_final: 0.7977 (tp30) REVERT: W 100 TRP cc_start: 0.8775 (m-10) cc_final: 0.8165 (m-10) REVERT: W 101 LYS cc_start: 0.8307 (mmmt) cc_final: 0.8054 (tptt) REVERT: X 82 PHE cc_start: 0.8876 (t80) cc_final: 0.8593 (t80) REVERT: Z 10 MET cc_start: 0.9129 (tpp) cc_final: 0.8844 (mmm) REVERT: Z 24 ASN cc_start: 0.8414 (t0) cc_final: 0.7744 (t0) REVERT: Z 69 ILE cc_start: 0.8881 (mm) cc_final: 0.8628 (mm) REVERT: Z 79 LYS cc_start: 0.8354 (tptt) cc_final: 0.7921 (tppt) REVERT: b 9 LEU cc_start: 0.8669 (tp) cc_final: 0.8114 (mt) REVERT: q 51 ASP cc_start: 0.7950 (t0) cc_final: 0.7674 (t0) REVERT: q 67 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7669 (tp30) REVERT: q 68 MET cc_start: 0.7375 (ttp) cc_final: 0.6710 (ttp) REVERT: q 93 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8254 (tpp) REVERT: s 55 PHE cc_start: 0.8262 (m-80) cc_final: 0.7968 (m-10) outliers start: 137 outliers final: 86 residues processed: 838 average time/residue: 0.2092 time to fit residues: 294.5611 Evaluate side-chains 816 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 719 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 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 C residue 116 VAL Chi-restraints excluded: chain C residue 223 VAL 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 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 137 THR 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 241 THR 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 172 ILE Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 261 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 11 VAL Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 31 MET Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 284 GLN 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 76 TYR Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 179 THR 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 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 99 MET Chi-restraints excluded: chain Q residue 124 MET Chi-restraints excluded: chain Q residue 167 ASN 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 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 58 MET 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 96 THR Chi-restraints excluded: chain X residue 50 GLU Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain Z residue 117 VAL 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 93 MET Chi-restraints excluded: chain q residue 104 THR Chi-restraints excluded: chain q residue 111 THR 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: 7.9990 chunk 294 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 298 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 401 optimal weight: 0.6980 chunk 235 optimal weight: 5.9990 chunk 202 optimal weight: 0.4980 chunk 281 optimal weight: 7.9990 chunk 302 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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** H 47 GLN ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.084501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.071505 restraints weight = 126501.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.073663 restraints weight = 58741.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.075058 restraints weight = 34732.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.075965 restraints weight = 24111.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.076571 restraints weight = 18658.456| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.6561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 35288 Z= 0.148 Angle : 0.911 72.732 47853 Z= 0.363 Chirality : 0.045 0.266 5217 Planarity : 0.005 0.162 6066 Dihedral : 8.796 155.950 4970 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.86 % Favored : 96.11 % Rotamer: Outliers : 3.12 % Allowed : 24.50 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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: -0.16 (0.13), residues: 4193 helix: 0.68 (0.12), residues: 1869 sheet: -0.85 (0.26), residues: 387 loop : -0.65 (0.15), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 217 TYR 0.030 0.002 TYR Q 160 PHE 0.043 0.002 PHE A 22 TRP 0.047 0.002 TRP q 86 HIS 0.011 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00341 (35248) covalent geometry : angle 0.72403 (47763) SS BOND : bond 0.00288 ( 3) SS BOND : angle 0.88666 ( 6) hydrogen bonds : bond 0.03978 ( 1461) hydrogen bonds : angle 5.15722 ( 4197) metal coordination : bond 0.01384 ( 37) metal coordination : angle 13.20824 ( 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 904 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 789 time to evaluate : 1.414 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: A 68 GLU cc_start: 0.8844 (tt0) cc_final: 0.8624 (tt0) REVERT: A 90 MET cc_start: 0.5311 (ptt) cc_final: 0.4464 (ttt) REVERT: A 109 LYS cc_start: 0.8662 (mmmm) cc_final: 0.7998 (pttt) REVERT: B 103 GLU cc_start: 0.8621 (mm-30) cc_final: 0.7790 (tm-30) REVERT: B 150 ASP cc_start: 0.9050 (m-30) cc_final: 0.8730 (m-30) REVERT: B 151 GLN cc_start: 0.9102 (mt0) cc_final: 0.8803 (mt0) REVERT: C 149 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8651 (pp) REVERT: C 228 GLU cc_start: 0.8180 (pm20) cc_final: 0.7898 (pm20) REVERT: C 241 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.7257 (t80) REVERT: D 84 PHE cc_start: 0.7724 (t80) cc_final: 0.7244 (t80) REVERT: D 261 MET cc_start: 0.8994 (tpp) cc_final: 0.8479 (tpp) REVERT: D 328 ASP cc_start: 0.8143 (t0) cc_final: 0.7688 (t0) REVERT: D 356 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9082 (pp) REVERT: D 371 MET cc_start: 0.9240 (ttp) cc_final: 0.8743 (ttt) REVERT: E 105 GLN cc_start: 0.8951 (mp10) cc_final: 0.8742 (mp10) REVERT: E 140 MET cc_start: 0.8887 (tmm) cc_final: 0.8652 (ppp) REVERT: E 181 ASN cc_start: 0.7795 (OUTLIER) cc_final: 0.7411 (t0) REVERT: F 337 MET cc_start: 0.8299 (mmm) cc_final: 0.7892 (mmm) REVERT: G 42 MET cc_start: 0.8598 (mmt) cc_final: 0.8187 (mmm) REVERT: G 97 MET cc_start: 0.7741 (tpp) cc_final: 0.7480 (mpp) REVERT: G 591 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7815 (mt-10) REVERT: H 78 SER cc_start: 0.9354 (m) cc_final: 0.9128 (p) REVERT: H 118 TRP cc_start: 0.9167 (m-10) cc_final: 0.8360 (m-90) REVERT: H 179 TRP cc_start: 0.8637 (p-90) cc_final: 0.8343 (p-90) REVERT: H 198 PHE cc_start: 0.9188 (m-80) cc_final: 0.8985 (m-10) REVERT: H 225 MET cc_start: 0.9314 (mtm) cc_final: 0.9109 (mtm) REVERT: H 227 GLU cc_start: 0.9097 (tp30) cc_final: 0.8735 (tp30) REVERT: H 235 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8301 (t0) REVERT: H 247 TYR cc_start: 0.8353 (t80) cc_final: 0.7990 (t80) REVERT: H 274 ARG cc_start: 0.9191 (ttt180) cc_final: 0.8831 (ttt180) REVERT: H 301 CYS cc_start: 0.9401 (t) cc_final: 0.9197 (p) REVERT: I 35 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.8940 (p) REVERT: I 40 ASN cc_start: 0.8577 (t0) cc_final: 0.8035 (t0) REVERT: I 72 MET cc_start: 0.9122 (tpp) cc_final: 0.8762 (tpp) REVERT: I 122 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9125 (tp) REVERT: I 149 MET cc_start: 0.8953 (mmm) cc_final: 0.7905 (mmm) REVERT: I 154 TYR cc_start: 0.9020 (m-80) cc_final: 0.8285 (m-80) REVERT: I 159 GLN cc_start: 0.8781 (mt0) cc_final: 0.8581 (mt0) REVERT: I 208 ASP cc_start: 0.9039 (t0) cc_final: 0.8699 (t0) REVERT: P 45 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8141 (tptp) REVERT: P 54 VAL cc_start: 0.9031 (t) cc_final: 0.8786 (t) REVERT: P 121 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7794 (mm110) REVERT: P 154 GLN cc_start: 0.7869 (tp-100) cc_final: 0.7446 (tp-100) REVERT: P 175 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7530 (mtmm) REVERT: P 269 ASN cc_start: 0.7356 (p0) cc_final: 0.6899 (p0) REVERT: P 281 PHE cc_start: 0.8916 (m-80) cc_final: 0.8716 (m-80) REVERT: P 351 GLU cc_start: 0.8329 (pt0) cc_final: 0.7784 (pm20) REVERT: P 355 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6725 (mmt-90) REVERT: Q 52 LEU cc_start: 0.9170 (mp) cc_final: 0.8880 (mp) REVERT: Q 148 GLU cc_start: 0.8034 (mp0) cc_final: 0.7702 (mp0) REVERT: R 38 TYR cc_start: 0.7943 (m-10) cc_final: 0.7518 (m-10) REVERT: R 42 ASP cc_start: 0.7891 (m-30) cc_final: 0.7497 (t0) REVERT: R 47 ARG cc_start: 0.9007 (ptp-170) cc_final: 0.8644 (ptt180) REVERT: S 60 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7859 (tm-30) REVERT: S 62 GLN cc_start: 0.8374 (mt0) cc_final: 0.8121 (mt0) REVERT: S 80 ASN cc_start: 0.8648 (t0) cc_final: 0.8186 (t0) REVERT: T 115 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8388 (tt0) REVERT: T 120 MET cc_start: 0.8507 (ptp) cc_final: 0.8254 (ptp) REVERT: T 132 ASP cc_start: 0.7827 (t0) cc_final: 0.7483 (t0) REVERT: V 94 MET cc_start: 0.8440 (tpp) cc_final: 0.8214 (mpp) REVERT: W 27 ASP cc_start: 0.8438 (t0) cc_final: 0.8113 (p0) REVERT: W 45 GLU cc_start: 0.8565 (tp30) cc_final: 0.7801 (tp30) REVERT: W 100 TRP cc_start: 0.8588 (m-10) cc_final: 0.8344 (m-10) REVERT: W 101 LYS cc_start: 0.8229 (mmmt) cc_final: 0.7980 (tptt) REVERT: X 82 PHE cc_start: 0.8874 (t80) cc_final: 0.8525 (t80) REVERT: Z 10 MET cc_start: 0.9170 (tpp) cc_final: 0.8953 (mmm) REVERT: Z 51 MET cc_start: 0.9018 (ttp) cc_final: 0.8611 (ptm) REVERT: Z 69 ILE cc_start: 0.8807 (mm) cc_final: 0.8556 (mm) REVERT: Z 79 LYS cc_start: 0.8341 (tptt) cc_final: 0.7917 (tppt) REVERT: b 9 LEU cc_start: 0.8645 (tp) cc_final: 0.8098 (mt) REVERT: q 51 ASP cc_start: 0.8051 (t0) cc_final: 0.7735 (t0) REVERT: q 67 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7682 (tp30) REVERT: q 68 MET cc_start: 0.7578 (ttp) cc_final: 0.6952 (ttp) REVERT: q 93 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8194 (tpp) REVERT: r 16 SER cc_start: 0.9437 (p) cc_final: 0.8335 (p) REVERT: s 55 PHE cc_start: 0.8225 (m-80) cc_final: 0.7962 (m-10) outliers start: 115 outliers final: 83 residues processed: 856 average time/residue: 0.2085 time to fit residues: 298.7312 Evaluate side-chains 822 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 728 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 C residue 116 VAL Chi-restraints excluded: chain C residue 128 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 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 241 THR Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 235 ASN Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 302 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 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 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 63 THR Chi-restraints excluded: chain Q residue 124 MET Chi-restraints excluded: chain Q residue 167 ASN 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 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 50 GLU Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain Z residue 117 VAL 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 93 MET Chi-restraints excluded: chain q residue 104 THR Chi-restraints excluded: chain q residue 111 THR 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 s residue 39 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 244 optimal weight: 7.9990 chunk 315 optimal weight: 0.2980 chunk 271 optimal weight: 0.1980 chunk 140 optimal weight: 3.9990 chunk 250 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 301 optimal weight: 5.9990 chunk 76 optimal weight: 0.0670 chunk 390 optimal weight: 9.9990 overall best weight: 1.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN G 51 GLN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN P 102 GLN 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 = 0.3586 r_free = 0.3586 target = 0.083649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.070667 restraints weight = 126320.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.072792 restraints weight = 58869.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.074176 restraints weight = 34816.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.075063 restraints weight = 24212.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.075653 restraints weight = 18937.817| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.6715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35288 Z= 0.167 Angle : 0.939 74.397 47853 Z= 0.374 Chirality : 0.046 0.364 5217 Planarity : 0.005 0.150 6066 Dihedral : 8.769 155.069 4970 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.08 % Favored : 95.90 % Rotamer: Outliers : 3.18 % Allowed : 24.94 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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: -0.12 (0.13), residues: 4193 helix: 0.72 (0.12), residues: 1875 sheet: -0.84 (0.26), residues: 382 loop : -0.64 (0.15), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 333 TYR 0.028 0.002 TYR Q 160 PHE 0.029 0.002 PHE A 62 TRP 0.033 0.002 TRP q 86 HIS 0.012 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00390 (35248) covalent geometry : angle 0.74405 (47763) SS BOND : bond 0.00256 ( 3) SS BOND : angle 0.80169 ( 6) hydrogen bonds : bond 0.03984 ( 1461) hydrogen bonds : angle 5.19204 ( 4197) metal coordination : bond 0.01855 ( 37) metal coordination : angle 13.70101 ( 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 875 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 758 time to evaluate : 1.430 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 83 LYS cc_start: 0.5750 (pttt) cc_final: 0.5523 (pttp) REVERT: A 90 MET cc_start: 0.5464 (ptt) cc_final: 0.4588 (ttt) REVERT: A 109 LYS cc_start: 0.8728 (mmmm) cc_final: 0.7990 (pttt) REVERT: B 103 GLU cc_start: 0.8662 (mm-30) cc_final: 0.7820 (tm-30) REVERT: B 150 ASP cc_start: 0.9056 (m-30) cc_final: 0.8592 (m-30) REVERT: B 199 GLU cc_start: 0.8237 (mp0) cc_final: 0.8004 (mp0) REVERT: C 149 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8572 (pp) REVERT: C 241 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.7222 (t80) REVERT: D 84 PHE cc_start: 0.7722 (t80) cc_final: 0.7176 (t80) REVERT: D 261 MET cc_start: 0.9023 (tpp) cc_final: 0.8530 (tpp) REVERT: D 328 ASP cc_start: 0.8205 (t0) cc_final: 0.7793 (t0) REVERT: D 356 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9083 (pp) REVERT: D 371 MET cc_start: 0.9275 (ttp) cc_final: 0.8788 (ttt) REVERT: E 105 GLN cc_start: 0.8946 (mp10) cc_final: 0.8708 (mp10) REVERT: E 143 ASP cc_start: 0.9057 (t0) cc_final: 0.8844 (t0) REVERT: E 181 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7557 (t0) REVERT: E 184 MET cc_start: 0.9065 (tmm) cc_final: 0.8754 (tmm) REVERT: F 337 MET cc_start: 0.8265 (mmm) cc_final: 0.7987 (mmm) REVERT: F 436 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7743 (mt0) REVERT: G 42 MET cc_start: 0.8595 (mmt) cc_final: 0.8187 (mmm) REVERT: G 97 MET cc_start: 0.7788 (tpp) cc_final: 0.7521 (mpp) REVERT: G 591 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7832 (mt-10) REVERT: H 118 TRP cc_start: 0.9186 (m-10) cc_final: 0.8357 (m-90) REVERT: H 134 ARG cc_start: 0.8533 (mmm-85) cc_final: 0.7597 (mmm-85) REVERT: H 179 TRP cc_start: 0.8589 (p-90) cc_final: 0.8367 (p-90) REVERT: H 185 TRP cc_start: 0.9010 (t-100) cc_final: 0.8769 (t-100) REVERT: H 227 GLU cc_start: 0.9067 (tp30) cc_final: 0.8719 (tp30) REVERT: H 235 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8252 (t0) REVERT: H 274 ARG cc_start: 0.9195 (ttt180) cc_final: 0.8869 (ttt180) REVERT: I 35 THR cc_start: 0.9213 (OUTLIER) cc_final: 0.8872 (p) REVERT: I 40 ASN cc_start: 0.8511 (t0) cc_final: 0.8121 (t0) REVERT: I 74 LEU cc_start: 0.9150 (tp) cc_final: 0.8929 (tt) REVERT: I 122 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9156 (tp) REVERT: I 149 MET cc_start: 0.8770 (mmm) cc_final: 0.7688 (mmm) REVERT: I 154 TYR cc_start: 0.8977 (m-80) cc_final: 0.8571 (m-80) REVERT: I 159 GLN cc_start: 0.8814 (mt0) cc_final: 0.8610 (mt0) REVERT: I 208 ASP cc_start: 0.9059 (t0) cc_final: 0.8724 (t0) REVERT: P 45 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8181 (tptp) REVERT: P 54 VAL cc_start: 0.9038 (t) cc_final: 0.8823 (t) REVERT: P 102 GLN cc_start: 0.8473 (tp-100) cc_final: 0.8191 (tp40) REVERT: P 121 GLN cc_start: 0.8285 (mm-40) cc_final: 0.7823 (mm110) REVERT: P 154 GLN cc_start: 0.7850 (tp-100) cc_final: 0.7430 (tp-100) REVERT: P 175 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7446 (mtmm) REVERT: P 269 ASN cc_start: 0.7477 (p0) cc_final: 0.7119 (p0) REVERT: P 351 GLU cc_start: 0.8380 (pt0) cc_final: 0.7774 (pm20) REVERT: P 355 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6824 (mmt-90) REVERT: Q 52 LEU cc_start: 0.9224 (mp) cc_final: 0.8921 (mp) REVERT: Q 69 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8479 (mm-30) REVERT: Q 143 TRP cc_start: 0.8685 (m-90) cc_final: 0.8000 (m-90) REVERT: Q 148 GLU cc_start: 0.8175 (mp0) cc_final: 0.7862 (mp0) REVERT: R 42 ASP cc_start: 0.7968 (m-30) cc_final: 0.7663 (t0) REVERT: R 47 ARG cc_start: 0.9033 (ptp-170) cc_final: 0.8656 (ptt180) REVERT: S 60 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7868 (tm-30) REVERT: S 62 GLN cc_start: 0.8388 (mt0) cc_final: 0.8148 (mt0) REVERT: S 80 ASN cc_start: 0.8647 (t0) cc_final: 0.8151 (t0) REVERT: S 89 ARG cc_start: 0.8210 (ptp-170) cc_final: 0.7990 (ptp-170) REVERT: T 120 MET cc_start: 0.8524 (ptp) cc_final: 0.8279 (ptp) REVERT: V 94 MET cc_start: 0.8466 (tpp) cc_final: 0.8236 (mpp) REVERT: W 27 ASP cc_start: 0.8445 (t0) cc_final: 0.8105 (p0) REVERT: W 45 GLU cc_start: 0.8413 (tp30) cc_final: 0.7849 (tp30) REVERT: X 82 PHE cc_start: 0.8797 (t80) cc_final: 0.8564 (t80) REVERT: Z 10 MET cc_start: 0.9165 (tpp) cc_final: 0.8946 (mmm) REVERT: Z 51 MET cc_start: 0.9022 (ttp) cc_final: 0.8625 (ptm) REVERT: Z 69 ILE cc_start: 0.8860 (mm) cc_final: 0.8642 (mm) REVERT: Z 72 MET cc_start: 0.7782 (mmt) cc_final: 0.7512 (mmt) REVERT: Z 79 LYS cc_start: 0.8364 (tptt) cc_final: 0.7946 (tppt) REVERT: b 9 LEU cc_start: 0.8650 (tp) cc_final: 0.8128 (mt) REVERT: q 41 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7620 (tm-30) REVERT: q 67 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7937 (tm-30) REVERT: q 93 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8206 (tpp) REVERT: s 55 PHE cc_start: 0.8244 (m-80) cc_final: 0.8006 (m-10) outliers start: 117 outliers final: 87 residues processed: 825 average time/residue: 0.2134 time to fit residues: 294.0407 Evaluate side-chains 817 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 718 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 116 VAL Chi-restraints excluded: chain C residue 149 LEU 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 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 419 ILE Chi-restraints excluded: chain F residue 422 HIS Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 235 ASN Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 76 TYR 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 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 P residue 366 ILE Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 124 MET Chi-restraints excluded: chain Q residue 167 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 104 PHE Chi-restraints excluded: chain T residue 125 GLU 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 50 GLU Chi-restraints excluded: chain X residue 56 CYS 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 142 TRP 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 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 24 LEU Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 93 MET Chi-restraints excluded: chain q residue 104 THR Chi-restraints excluded: chain q residue 111 THR Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 41 LEU Chi-restraints excluded: chain s residue 39 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 152 optimal weight: 0.9980 chunk 305 optimal weight: 0.9980 chunk 300 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 243 optimal weight: 0.9980 chunk 342 optimal weight: 5.9990 chunk 287 optimal weight: 5.9990 chunk 220 optimal weight: 0.6980 chunk 205 optimal weight: 0.9980 chunk 223 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 GLN ** 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** H 157 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 HIS Q 51 GLN Q 92 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 99 HIS ** 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 = 0.3627 r_free = 0.3627 target = 0.085448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.072303 restraints weight = 127895.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.074481 restraints weight = 59981.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.075935 restraints weight = 35584.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.076872 restraints weight = 24726.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.077427 restraints weight = 19242.973| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.6883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35288 Z= 0.148 Angle : 0.953 73.331 47853 Z= 0.376 Chirality : 0.046 0.340 5217 Planarity : 0.005 0.143 6066 Dihedral : 8.685 155.062 4970 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.94 % Favored : 96.04 % Rotamer: Outliers : 2.80 % Allowed : 25.62 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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: -0.11 (0.13), residues: 4193 helix: 0.72 (0.12), residues: 1873 sheet: -0.80 (0.26), residues: 393 loop : -0.63 (0.15), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 195 TYR 0.024 0.002 TYR I 86 PHE 0.030 0.002 PHE A 62 TRP 0.041 0.002 TRP W 100 HIS 0.011 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00347 (35248) covalent geometry : angle 0.75623 (47763) SS BOND : bond 0.00254 ( 3) SS BOND : angle 0.75828 ( 6) hydrogen bonds : bond 0.03962 ( 1461) hydrogen bonds : angle 5.18098 ( 4197) metal coordination : bond 0.01689 ( 37) metal coordination : angle 13.87383 ( 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 890 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 787 time to evaluate : 1.467 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 90 MET cc_start: 0.5431 (ptt) cc_final: 0.4531 (ttt) REVERT: A 109 LYS cc_start: 0.8738 (mmmm) cc_final: 0.7994 (pttt) REVERT: B 80 ASP cc_start: 0.8603 (m-30) cc_final: 0.8261 (t0) REVERT: B 103 GLU cc_start: 0.8624 (mm-30) cc_final: 0.7801 (tm-30) REVERT: B 150 ASP cc_start: 0.9072 (m-30) cc_final: 0.8595 (m-30) REVERT: B 151 GLN cc_start: 0.9098 (mt0) cc_final: 0.8715 (mt0) REVERT: B 161 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7938 (mtp) REVERT: B 175 TYR cc_start: 0.8840 (p90) cc_final: 0.8547 (p90) REVERT: B 199 GLU cc_start: 0.8214 (mp0) cc_final: 0.7986 (mp0) REVERT: C 114 THR cc_start: 0.7954 (m) cc_final: 0.7679 (m) REVERT: C 149 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8553 (pp) REVERT: C 227 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8474 (tp40) REVERT: C 241 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7202 (t80) REVERT: D 84 PHE cc_start: 0.7735 (t80) cc_final: 0.7207 (t80) REVERT: D 253 LEU cc_start: 0.8776 (tp) cc_final: 0.8482 (tp) REVERT: D 261 MET cc_start: 0.9051 (tpp) cc_final: 0.8657 (tpp) REVERT: D 328 ASP cc_start: 0.8109 (t0) cc_final: 0.7771 (t0) REVERT: D 356 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.9068 (pp) REVERT: D 371 MET cc_start: 0.9209 (ttp) cc_final: 0.7851 (tmm) REVERT: E 105 GLN cc_start: 0.8932 (mp10) cc_final: 0.8677 (mp10) REVERT: E 143 ASP cc_start: 0.8995 (t0) cc_final: 0.8793 (t0) REVERT: E 181 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7467 (t0) REVERT: E 184 MET cc_start: 0.9079 (tmm) cc_final: 0.8777 (tmm) REVERT: F 337 MET cc_start: 0.8120 (mmm) cc_final: 0.7890 (mmm) REVERT: F 381 GLN cc_start: 0.8896 (tp40) cc_final: 0.8631 (tp40) REVERT: G 42 MET cc_start: 0.8592 (mmt) cc_final: 0.8180 (mmm) REVERT: G 97 MET cc_start: 0.7752 (tpp) cc_final: 0.7503 (mpp) REVERT: G 395 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8578 (mp0) REVERT: G 591 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7796 (mt-10) REVERT: H 118 TRP cc_start: 0.9173 (m-10) cc_final: 0.8340 (m-90) REVERT: H 134 ARG cc_start: 0.8533 (mmm-85) cc_final: 0.7654 (mmm-85) REVERT: H 179 TRP cc_start: 0.8572 (p-90) cc_final: 0.8340 (p-90) REVERT: H 185 TRP cc_start: 0.8939 (t-100) cc_final: 0.8669 (t-100) REVERT: H 225 MET cc_start: 0.9299 (mtm) cc_final: 0.8551 (mtm) REVERT: H 227 GLU cc_start: 0.9055 (tp30) cc_final: 0.8646 (tp30) REVERT: H 235 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8386 (t0) REVERT: H 270 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7728 (t80) REVERT: H 274 ARG cc_start: 0.9168 (ttt180) cc_final: 0.8856 (ttt180) REVERT: H 284 GLN cc_start: 0.9098 (pm20) cc_final: 0.8889 (pm20) REVERT: I 40 ASN cc_start: 0.8500 (t0) cc_final: 0.8117 (t0) REVERT: I 122 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9117 (tp) REVERT: I 208 ASP cc_start: 0.8979 (t0) cc_final: 0.8704 (t0) REVERT: P 45 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8398 (tppt) REVERT: P 54 VAL cc_start: 0.9010 (t) cc_final: 0.8789 (t) REVERT: P 102 GLN cc_start: 0.8317 (tp-100) cc_final: 0.7985 (tp-100) REVERT: P 121 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7875 (mm110) REVERT: P 154 GLN cc_start: 0.7830 (tp-100) cc_final: 0.7378 (tp-100) REVERT: P 175 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7150 (mmmt) REVERT: P 269 ASN cc_start: 0.7374 (p0) cc_final: 0.6996 (p0) REVERT: P 351 GLU cc_start: 0.8319 (pt0) cc_final: 0.7748 (pm20) REVERT: P 355 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6903 (mmt-90) REVERT: Q 52 LEU cc_start: 0.9200 (mp) cc_final: 0.8896 (mp) REVERT: Q 69 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8405 (mm-30) REVERT: Q 143 TRP cc_start: 0.8607 (m-90) cc_final: 0.8018 (m-90) REVERT: Q 148 GLU cc_start: 0.8200 (mp0) cc_final: 0.7896 (mp0) REVERT: R 41 LYS cc_start: 0.4323 (tppt) cc_final: 0.3460 (tttt) REVERT: R 42 ASP cc_start: 0.8083 (m-30) cc_final: 0.7721 (t0) REVERT: R 47 ARG cc_start: 0.8989 (ptp-170) cc_final: 0.8660 (ptt180) REVERT: S 62 GLN cc_start: 0.8369 (mt0) cc_final: 0.8130 (mt0) REVERT: S 80 ASN cc_start: 0.8670 (t0) cc_final: 0.8268 (t0) REVERT: S 89 ARG cc_start: 0.8218 (ptp-170) cc_final: 0.7973 (ptp-170) REVERT: T 115 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8200 (tt0) REVERT: T 120 MET cc_start: 0.8518 (ptp) cc_final: 0.8289 (ptp) REVERT: T 132 ASP cc_start: 0.7622 (t0) cc_final: 0.7302 (t0) REVERT: V 94 MET cc_start: 0.8382 (tpp) cc_final: 0.8161 (mpp) REVERT: W 27 ASP cc_start: 0.8399 (t0) cc_final: 0.8093 (p0) REVERT: W 45 GLU cc_start: 0.8395 (tp30) cc_final: 0.7741 (tp30) REVERT: X 56 CYS cc_start: 0.5205 (OUTLIER) cc_final: 0.4117 (t) REVERT: X 82 PHE cc_start: 0.8765 (t80) cc_final: 0.8301 (t80) REVERT: X 99 HIS cc_start: 0.6542 (m-70) cc_final: 0.6307 (m-70) REVERT: Z 10 MET cc_start: 0.9166 (tpp) cc_final: 0.8900 (mmm) REVERT: Z 51 MET cc_start: 0.8991 (ttp) cc_final: 0.8618 (ptm) REVERT: Z 69 ILE cc_start: 0.8846 (mm) cc_final: 0.8631 (mm) REVERT: Z 72 MET cc_start: 0.7605 (mmt) cc_final: 0.7319 (mmt) REVERT: Z 79 LYS cc_start: 0.8358 (tptt) cc_final: 0.7942 (tppt) REVERT: a 59 ARG cc_start: 0.8560 (tmm-80) cc_final: 0.8339 (tmm-80) REVERT: b 9 LEU cc_start: 0.8617 (tp) cc_final: 0.8093 (mt) REVERT: q 67 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7777 (tp30) REVERT: q 93 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8178 (tpp) REVERT: r 54 TYR cc_start: 0.7662 (t80) cc_final: 0.7358 (t80) REVERT: s 43 TYR cc_start: 0.8190 (m-10) cc_final: 0.7858 (m-80) outliers start: 103 outliers final: 74 residues processed: 853 average time/residue: 0.2120 time to fit residues: 303.8775 Evaluate side-chains 833 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 745 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU 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 161 MET Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 128 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 109 CYS 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 277 VAL Chi-restraints excluded: chain D residue 278 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 241 THR Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 235 ASN Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 76 TYR 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 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 63 THR Chi-restraints excluded: chain Q residue 124 MET 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 104 PHE Chi-restraints excluded: chain T residue 125 GLU 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 53 MET Chi-restraints excluded: chain X residue 40 ASN Chi-restraints excluded: chain X residue 50 GLU Chi-restraints excluded: chain X residue 56 CYS 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 142 TRP 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 24 LEU Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 93 MET Chi-restraints excluded: chain q residue 104 THR Chi-restraints excluded: chain r residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 324 optimal weight: 4.9990 chunk 339 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 230 optimal weight: 7.9990 chunk 252 optimal weight: 1.9990 chunk 371 optimal weight: 4.9990 chunk 291 optimal weight: 0.4980 chunk 43 optimal weight: 20.0000 chunk 393 optimal weight: 0.7980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 HIS Q 51 GLN Q 92 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 31 HIS ** X 99 HIS ** 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 = 0.3607 r_free = 0.3607 target = 0.084457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.071314 restraints weight = 128018.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.073462 restraints weight = 60237.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.074891 restraints weight = 35865.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.075764 restraints weight = 25034.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.076398 restraints weight = 19645.231| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.6985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 35288 Z= 0.171 Angle : 0.966 75.770 47853 Z= 0.385 Chirality : 0.046 0.324 5217 Planarity : 0.005 0.139 6066 Dihedral : 8.687 154.302 4970 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.22 % Favored : 95.75 % Rotamer: Outliers : 2.80 % Allowed : 26.21 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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: -0.15 (0.13), residues: 4193 helix: 0.68 (0.12), residues: 1875 sheet: -0.80 (0.26), residues: 389 loop : -0.65 (0.15), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG r 103 TYR 0.022 0.002 TYR I 211 PHE 0.030 0.002 PHE A 62 TRP 0.035 0.002 TRP H 290 HIS 0.012 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00405 (35248) covalent geometry : angle 0.76693 (47763) SS BOND : bond 0.00432 ( 3) SS BOND : angle 1.14931 ( 6) hydrogen bonds : bond 0.04056 ( 1461) hydrogen bonds : angle 5.24464 ( 4197) metal coordination : bond 0.01803 ( 37) metal coordination : angle 14.02858 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7772.41 seconds wall clock time: 135 minutes 4.46 seconds (8104.46 seconds total)