Starting phenix.real_space_refine on Mon Jul 6 07:14:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xnx_38518/07_2026/8xnx_38518_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xnx_38518/07_2026/8xnx_38518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xnx_38518/07_2026/8xnx_38518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xnx_38518/07_2026/8xnx_38518.map" model { file = "/net/cci-nas-00/data/ceres_data/8xnx_38518/07_2026/8xnx_38518_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xnx_38518/07_2026/8xnx_38518_neut.cif" } resolution = 3.5 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= 0.001 sd= 0.075 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 21853 2.51 5 N 5800 2.21 5 O 6193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34132 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 735 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "B" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 10, 'TRANS': 144} Chain: "C" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1643 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 3083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3083 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 21, 'TRANS': 362} 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: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2493 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 22, 'TRANS': 289} Chain breaks: 1 Chain: "I" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1380 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain breaks: 1 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: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 940 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} 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: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1145 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} 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: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 628 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "q" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1025 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain breaks: 1 Chain: "r" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 686 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 10, 'TRANS': 73} Chain breaks: 2 Chain: "s" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 193 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 2, 'TRANS': 20} Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 86 Unusual residues: {'PC1': 2, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 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: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'3PE': 1, 'UQ9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "q" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 981 SG CYS B 99 84.170 61.703 105.283 1.00 29.52 S ATOM 987 SG CYS B 100 82.926 57.654 104.013 1.00 30.11 S ATOM 1484 SG CYS B 164 80.346 57.629 107.893 1.00 28.96 S ATOM 1714 SG CYS B 194 86.706 57.889 108.328 1.00 29.28 S ATOM 7491 SG CYS E 134 146.095 52.248 148.131 1.00 56.01 S ATOM 7525 SG CYS E 139 148.878 53.965 147.040 1.00 56.50 S ATOM 7809 SG CYS E 175 144.035 55.920 150.748 1.00 54.42 S ATOM 7832 SG CYS E 179 147.277 57.755 150.293 1.00 57.95 S ATOM 11362 SG CYS F 425 127.853 61.894 151.755 1.00 45.60 S ATOM 11040 SG CYS F 385 127.543 59.400 145.978 1.00 39.95 S ATOM 11020 SG CYS F 382 123.421 60.641 148.462 1.00 40.29 S ATOM 11001 SG CYS F 379 125.462 56.552 151.235 1.00 43.09 S ATOM 12410 SG CYS G 131 106.446 49.668 135.784 1.00 31.31 S ATOM 12389 SG CYS G 128 108.283 53.454 131.071 1.00 30.26 S ATOM 12450 SG CYS G 137 106.282 55.584 137.192 1.00 33.13 S ATOM 13135 SG CYS G 226 108.413 49.690 144.285 1.00 34.31 S ATOM 12806 SG CYS G 182 111.715 48.266 149.358 1.00 36.31 S ATOM 12782 SG CYS G 179 111.162 53.565 147.343 1.00 35.62 S ATOM 12759 SG CYS G 176 114.403 49.231 144.725 1.00 34.05 S ATOM 11896 SG CYS G 64 112.768 59.590 149.251 1.00 35.53 S ATOM 11982 SG CYS G 75 113.444 61.612 147.541 1.00 36.47 S ATOM 12007 SG CYS G 78 112.502 66.204 149.713 1.00 36.76 S ATOM 12108 SG CYS G 92 110.111 64.184 151.788 1.00 39.04 S ATOM 20299 SG CYS I 152 90.841 51.708 112.535 1.00 27.39 S ATOM 20073 SG CYS I 123 90.782 52.894 117.894 1.00 27.30 S ATOM 20325 SG CYS I 155 93.460 56.493 113.952 1.00 27.04 S ATOM 20346 SG CYS I 158 96.493 51.211 114.733 1.00 26.60 S ATOM 20045 SG CYS I 119 97.022 48.587 121.213 1.00 28.85 S ATOM 20375 SG CYS I 162 103.154 48.169 118.764 1.00 28.07 S ATOM 20003 SG CYS I 113 99.733 43.394 121.338 1.00 28.61 S ATOM 20022 SG CYS I 116 102.493 47.739 124.796 1.00 29.24 S ATOM 24857 SG CYS R 79 116.358 41.195 123.078 1.00 32.60 S ATOM 25033 SG CYS R 104 113.964 39.893 124.667 1.00 32.49 S ATOM 25055 SG CYS R 107 113.136 40.543 121.276 1.00 30.78 S Time building chain proxies: 6.08, per 1000 atoms: 0.18 Number of scatterers: 34132 At special positions: 0 Unit cell: (174.9, 129.8, 200.2, 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 6193 8.00 N 5800 7.00 C 21853 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS X 36 " - pdb=" SG CYS X 66 " distance=2.04 Simple disulfide: pdb=" SG CYS X 46 " - pdb=" SG CYS X 56 " distance=2.04 Simple disulfide: pdb=" SG CYS X 78 " - pdb=" SG CYS X 110 " distance=2.04 Simple disulfide: pdb=" SG CYS X 88 " - pdb=" SG CYS X 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.2 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 179 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 175 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 75 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 78 " 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="FE2 SF4 B 301 " - pdb=" SG CYS B 100 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 194 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 99 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 164 " 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="FE2 SF4 G 802 " - pdb=" SG CYS G 182 " 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=" SF4 I 301 " pdb="FE1 SF4 I 301 " - pdb=" SG CYS I 152 " pdb="FE2 SF4 I 301 " - pdb=" SG CYS I 123 " pdb="FE3 SF4 I 301 " - pdb=" SG CYS I 155 " pdb="FE4 SF4 I 301 " - pdb=" SG CYS I 158 " pdb="FE1 SF4 I 301 " - pdb=" NE2 HIS I 101 " pdb=" SF4 I 302 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 113 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 119 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 162 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 116 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 88 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 107 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 104 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 79 " Number of angles added : 3 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7878 Finding SS restraints... Secondary structure from input PDB file: 183 helices and 35 sheets defined 49.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 removed outlier: 3.508A pdb=" N ALA A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 71 removed outlier: 4.083A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 83 through 109 Processing helix chain 'B' and resid 71 through 89 Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.693A pdb=" N GLU B 103 " --> pdb=" O CYS B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 removed outlier: 3.911A pdb=" N ASP B 113 " --> pdb=" O PRO B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 110 through 113' 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 150 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.807A pdb=" N TYR B 171 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 4.228A pdb=" N ILE B 184 " --> pdb=" O GLY B 180 " (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: 3.960A pdb=" N HIS C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 102 through 106 removed outlier: 4.320A pdb=" N GLN C 106 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 159 through 160 No H-bonds generated for 'chain 'C' and resid 159 through 160' Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.034A pdb=" N TYR C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'D' and resid 119 through 125 removed outlier: 3.926A pdb=" N GLU D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 131 No H-bonds generated for 'chain 'D' and resid 129 through 131' Processing helix chain 'D' and resid 132 through 138 removed outlier: 3.736A pdb=" N PHE D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 132 through 138' Processing helix chain 'D' and resid 143 through 159 removed outlier: 4.132A pdb=" N ASN D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 195 Processing helix chain 'D' and resid 197 through 216 removed outlier: 3.828A pdb=" N PHE D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU D 206 " --> pdb=" O TRP D 202 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 263 removed outlier: 4.087A pdb=" N SER D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.850A 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: 3.751A pdb=" N SER D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 314 Processing helix chain 'D' and resid 325 through 350 Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.524A pdb=" N LYS D 372 " --> pdb=" O ARG D 368 " (cutoff:3.500A) 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: 3.677A pdb=" N VAL D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 463 removed outlier: 3.834A pdb=" N ILE D 461 " --> pdb=" O VAL D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 removed outlier: 3.609A pdb=" N ASN E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 3.705A 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 Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 143 through 156 removed outlier: 3.613A pdb=" N THR E 150 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'E' and resid 196 through 209 Processing helix chain 'F' and resid 36 through 40 Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 64 through 72 removed outlier: 3.558A pdb=" N GLY F 72 " --> pdb=" O ILE F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 84 Processing helix chain 'F' and resid 94 through 102 removed outlier: 4.295A pdb=" N MET F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 133 removed outlier: 4.184A pdb=" N ILE F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET F 131 " --> pdb=" O ASP F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 150 removed outlier: 4.032A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA F 148 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 180 Processing helix chain 'F' and resid 185 through 189 removed outlier: 3.635A pdb=" N GLY F 188 " --> pdb=" O ASN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 208 through 218 removed outlier: 4.260A 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 257 removed outlier: 3.587A pdb=" N SER F 251 " --> pdb=" O THR F 247 " (cutoff:3.500A) Proline residue: F 252 - end of helix Processing helix chain 'F' and resid 258 through 266 removed outlier: 4.015A pdb=" N PHE F 265 " --> pdb=" O TRP F 261 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 303 removed outlier: 3.861A pdb=" N ILE F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 333 removed outlier: 3.732A pdb=" N GLU F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 345 Processing helix chain 'F' and resid 362 through 376 removed outlier: 3.547A pdb=" N LEU F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 402 removed outlier: 3.662A pdb=" N ASP F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.723A pdb=" N SER F 411 " --> pdb=" O ALA F 407 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 457 removed outlier: 4.348A 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: 3.599A pdb=" N VAL G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 115 removed outlier: 3.775A pdb=" N LYS G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 123 removed outlier: 3.712A pdb=" N ASN G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 147 Processing helix chain 'G' and resid 180 through 189 Processing helix chain 'G' and resid 200 through 204 Processing helix chain 'G' and resid 220 through 226 removed outlier: 3.821A 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 361 Processing helix chain 'G' and resid 377 through 386 removed outlier: 4.303A pdb=" N LEU G 381 " --> pdb=" O GLY G 378 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG G 382 " --> pdb=" O THR G 379 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N SER G 383 " --> pdb=" O ASP G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 397 removed outlier: 3.589A 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: 4.009A pdb=" N VAL G 465 " --> pdb=" O SER G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 482 removed outlier: 3.677A 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 529 Processing helix chain 'G' and resid 534 through 540 Processing helix chain 'G' and resid 556 through 560 Processing helix chain 'G' and resid 618 through 631 Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 665 through 675 Processing helix chain 'G' and resid 690 through 696 removed outlier: 3.642A pdb=" N PHE G 694 " --> pdb=" O THR G 690 " (cutoff:3.500A) removed outlier: 4.353A 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 removed outlier: 3.604A pdb=" N VAL H 11 " --> pdb=" O LEU H 7 " (cutoff:3.500A) Proline residue: H 12 - end of helix removed outlier: 4.398A pdb=" N ALA H 16 " --> pdb=" O PRO H 12 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE H 19 " --> pdb=" O ILE H 15 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET H 31 " --> pdb=" O ILE H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 56 Processing helix chain 'H' and resid 67 through 72 Processing helix chain 'H' and resid 73 through 87 removed outlier: 3.705A pdb=" N LEU H 79 " --> pdb=" O PRO H 75 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU H 83 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 124 removed outlier: 3.671A pdb=" N SER H 112 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 158 removed outlier: 3.518A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN H 157 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 169 removed outlier: 3.675A pdb=" N LEU H 165 " --> pdb=" O SER H 161 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR H 167 " --> pdb=" O GLN H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 191 Processing helix chain 'H' and resid 216 through 226 removed outlier: 3.650A pdb=" N PHE H 223 " --> pdb=" O PRO H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 237 Processing helix chain 'H' and resid 237 through 242 Processing helix chain 'H' and resid 252 through 275 removed outlier: 4.395A pdb=" N SER H 256 " --> pdb=" O PRO H 252 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU H 265 " --> pdb=" O MET H 261 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE H 270 " --> pdb=" O LEU H 266 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU H 271 " --> pdb=" O SER H 267 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP H 272 " --> pdb=" O SER H 268 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE H 273 " --> pdb=" O THR H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 292 removed outlier: 3.607A pdb=" N MET H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 312 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 49 through 58 Processing helix chain 'I' and resid 66 through 78 removed outlier: 3.769A pdb=" N MET I 72 " --> pdb=" O ARG I 68 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR I 76 " --> pdb=" O MET I 72 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU I 77 " --> pdb=" O THR I 73 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE I 78 " --> pdb=" O LEU I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 182 No H-bonds generated for 'chain 'I' and resid 180 through 182' Processing helix chain 'I' and resid 187 through 195 removed outlier: 3.584A pdb=" N ASN I 192 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN I 193 " --> pdb=" O LYS I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 209 removed outlier: 4.284A pdb=" N ALA I 203 " --> pdb=" O ALA I 199 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN I 204 " --> pdb=" O GLU I 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 76 Processing helix chain 'P' and resid 87 through 90 Processing helix chain 'P' and resid 91 through 96 removed outlier: 3.589A pdb=" N ARG P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 4.137A 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 114 through 122 removed outlier: 4.504A 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 Processing helix chain 'P' and resid 178 through 195 Processing helix chain 'P' and resid 213 through 220 Processing helix chain 'P' and resid 228 through 233 removed outlier: 3.773A pdb=" N LEU P 231 " --> pdb=" O LEU P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 254 Processing helix chain 'P' and resid 255 through 259 Processing helix chain 'P' and resid 273 through 284 removed outlier: 4.117A pdb=" N GLY P 282 " --> pdb=" O LYS P 278 " (cutoff:3.500A) Processing helix chain 'P' and resid 294 through 308 removed outlier: 3.937A pdb=" N LEU P 304 " --> pdb=" O TRP P 300 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE P 305 " --> pdb=" O ILE P 301 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 324 Processing helix chain 'P' and resid 334 through 339 Processing helix chain 'P' and resid 349 through 354 Processing helix chain 'Q' and resid 61 through 66 removed outlier: 4.446A pdb=" N GLY Q 66 " --> pdb=" O THR Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 72 Processing helix chain 'Q' and resid 130 through 142 removed outlier: 3.521A pdb=" N PHE Q 137 " --> pdb=" O ASP Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 165 Processing helix chain 'R' and resid 42 through 49 removed outlier: 4.167A pdb=" N ARG R 47 " --> pdb=" O ARG R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 64 Processing helix chain 'S' and resid 32 through 48 removed outlier: 6.311A pdb=" N VAL S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLU S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS S 46 " --> pdb=" O VAL S 42 " (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 127 removed outlier: 3.591A pdb=" N VAL T 116 " --> pdb=" O SER T 112 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU T 117 " --> pdb=" O LEU T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 131 through 138 Processing helix chain 'T' and resid 140 through 150 Processing helix chain 'V' and resid 19 through 35 Processing helix chain 'V' and resid 36 through 38 No H-bonds generated for 'chain 'V' and resid 36 through 38' Processing helix chain 'V' and resid 42 through 60 removed outlier: 3.708A pdb=" N GLN V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU V 54 " --> pdb=" O GLN V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 73 Processing helix chain 'V' and resid 76 through 98 removed outlier: 3.681A pdb=" N LYS V 96 " --> pdb=" O ARG V 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 53 removed outlier: 3.991A pdb=" N ARG W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA W 41 " --> pdb=" O GLU W 37 " (cutoff:3.500A) Proline residue: W 47 - end of helix Processing helix chain 'W' and resid 58 through 73 Processing helix chain 'W' and resid 78 through 98 removed outlier: 3.948A pdb=" N ILE W 87 " --> pdb=" O ASP W 83 " (cutoff:3.500A) 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 126 Processing helix chain 'X' and resid 9 through 14 Processing helix chain 'X' and resid 21 through 28 removed outlier: 3.544A pdb=" N LEU X 25 " --> pdb=" O SER X 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 35 Processing helix chain 'X' and resid 37 through 50 removed outlier: 3.679A pdb=" N GLU X 42 " --> pdb=" O LYS X 38 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE X 43 " --> pdb=" O THR X 39 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU X 49 " --> pdb=" O LEU X 45 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 77 removed outlier: 4.056A pdb=" N LEU X 68 " --> pdb=" O ASN X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 79 through 90 removed outlier: 3.894A pdb=" N CYS X 88 " --> pdb=" O GLU X 84 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 114 removed outlier: 3.900A pdb=" N ALA X 105 " --> pdb=" O ARG X 101 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS X 110 " --> pdb=" O LYS X 106 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 144 Processing helix chain 'Z' and resid 31 through 87 removed outlier: 3.544A pdb=" N GLY Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR Z 47 " --> pdb=" O LEU Z 43 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET Z 50 " --> pdb=" O GLY Z 46 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU Z 56 " --> pdb=" O ARG Z 52 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA Z 67 " --> pdb=" O GLU Z 63 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG Z 68 " --> pdb=" O ASP Z 64 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU Z 71 " --> pdb=" O ALA Z 67 " (cutoff:3.500A) Proline residue: Z 73 - end of helix removed outlier: 3.659A pdb=" N LEU Z 87 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 96 removed outlier: 3.717A pdb=" N GLU Z 93 " --> pdb=" O GLU Z 89 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 126 Processing helix chain 'Z' and resid 129 through 138 Processing helix chain 'a' and resid 5 through 13 Processing helix chain 'a' and resid 17 through 27 Processing helix chain 'a' and resid 41 through 55 removed outlier: 3.739A pdb=" N TRP a 45 " --> pdb=" O VAL a 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 15 removed outlier: 4.032A pdb=" N ASN b 11 " --> pdb=" O ALA b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 23 Processing helix chain 'b' and resid 24 through 35 removed outlier: 3.580A pdb=" N ALA b 29 " --> pdb=" O VAL b 25 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE b 30 " --> pdb=" O TRP b 26 " (cutoff:3.500A) Proline residue: b 33 - end of helix Processing helix chain 'b' and resid 38 through 40 No H-bonds generated for 'chain 'b' and resid 38 through 40' Processing helix chain 'b' and resid 41 through 49 removed outlier: 3.534A pdb=" N ASN b 46 " --> pdb=" O ALA b 42 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS b 47 " --> pdb=" O SER b 43 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR b 49 " --> pdb=" O ILE b 45 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 16 removed outlier: 3.740A pdb=" N LEU q 7 " --> pdb=" O LEU q 3 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS q 8 " --> pdb=" O VAL q 4 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 28 Processing helix chain 'q' and resid 43 through 45 No H-bonds generated for 'chain 'q' and resid 43 through 45' Processing helix chain 'q' and resid 78 through 82 removed outlier: 4.201A pdb=" N VAL q 82 " --> pdb=" O GLY q 79 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 91 removed outlier: 3.984A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 4.697A 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 58 through 63 removed outlier: 3.723A pdb=" N VAL r 63 " --> pdb=" O GLY r 59 " (cutoff:3.500A) Processing helix chain 's' and resid 78 through 87 Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94 removed outlier: 6.137A pdb=" N MET B 131 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N MET B 161 " --> pdb=" O MET B 131 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL B 133 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 189 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 109 through 117 removed outlier: 5.859A pdb=" N LEU C 110 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU C 132 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 116 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU C 83 " --> pdb=" O ARG C 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 152 through 153 removed outlier: 7.398A pdb=" N ILE C 152 " --> pdb=" O PHE C 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 207 through 211 Processing sheet with id=AA5, first strand: chain 'D' and resid 82 through 83 Processing sheet with id=AA6, first strand: chain 'D' and resid 101 through 102 removed outlier: 3.578A pdb=" N MET D 105 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 4.809A 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 168 through 171 removed outlier: 6.567A pdb=" N TYR E 129 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE E 171 " --> pdb=" O TYR E 129 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE E 131 " --> pdb=" O ILE E 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 195 through 199 removed outlier: 6.441A pdb=" N ALA F 154 " --> pdb=" O PHE F 196 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL F 198 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE F 156 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU F 113 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR F 157 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL F 115 " --> pdb=" O TYR F 157 " (cutoff:3.500A) removed outlier: 3.577A 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 288 removed outlier: 6.151A pdb=" N ASN F 277 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL F 356 " --> pdb=" O ASN F 277 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N SER F 279 " --> pdb=" O VAL F 356 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 294 through 295 removed outlier: 3.598A 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 33 Processing sheet with id=AB4, first strand: chain 'G' and resid 35 through 36 removed outlier: 6.776A pdb=" N PHE G 35 " --> pdb=" O ILE G 102 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU G 81 " --> pdb=" O LEU G 103 " (cutoff:3.500A) 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 196 through 198 Processing sheet with id=AB7, first strand: chain 'G' and resid 246 through 251 removed outlier: 6.350A pdb=" N ARG G 266 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL G 270 " --> pdb=" O ARG G 266 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 306 through 309 Processing sheet with id=AB9, first strand: chain 'G' and resid 531 through 532 removed outlier: 6.096A pdb=" N LEU G 366 " --> pdb=" O LYS G 531 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N CYS G 367 " --> pdb=" O VAL G 338 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ALA G 340 " --> pdb=" O CYS G 367 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU G 545 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 442 through 446 removed outlier: 6.323A pdb=" N VAL G 400 " --> pdb=" O ALA G 430 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE G 432 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU G 402 " --> pdb=" O ILE G 432 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ASN G 514 " --> pdb=" O PRO G 472 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL G 474 " --> pdb=" O ASN G 514 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 595 through 597 Processing sheet with id=AC3, first strand: chain 'I' and resid 101 through 103 Processing sheet with id=AC4, first strand: chain 'I' and resid 132 through 134 removed outlier: 3.573A pdb=" N ARG I 141 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 146 through 148 Processing sheet with id=AC6, first strand: chain 'P' and resid 56 through 58 removed outlier: 5.863A pdb=" N THR P 57 " --> pdb=" O ILE P 127 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE P 201 " --> pdb=" O PHE P 164 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N HIS P 166 " --> pdb=" O ILE P 201 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE P 200 " --> pdb=" O PHE P 263 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N PHE P 265 " --> pdb=" O ILE P 200 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ARG P 202 " --> pdb=" O PHE P 265 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 80 through 84 removed outlier: 3.848A pdb=" N LEU P 106 " --> pdb=" O ILE P 82 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 205 through 207 removed outlier: 6.368A pdb=" N ASP P 205 " --> pdb=" O VAL P 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'P' and resid 236 through 237 Processing sheet with id=AD1, first strand: chain 'Q' and resid 53 through 54 Processing sheet with id=AD2, first strand: chain 'Q' and resid 78 through 80 removed outlier: 4.055A pdb=" N GLU Q 100 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU Q 126 " --> pdb=" O MET Q 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 106 through 108 Processing sheet with id=AD4, first strand: chain 'R' and resid 76 through 77 Processing sheet with id=AD5, first strand: chain 'R' and resid 102 through 103 removed outlier: 3.507A pdb=" N GLY R 102 " --> pdb=" O PHE R 111 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 55 through 57 Processing sheet with id=AD7, first strand: chain 'X' and resid 130 through 131 Processing sheet with id=AD8, first strand: chain 'q' and resid 37 through 41 removed outlier: 3.825A pdb=" N THR q 37 " --> pdb=" O GLU q 50 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR q 48 " --> pdb=" O VAL q 39 " (cutoff:3.500A) 1329 hydrogen bonds defined for protein. 3762 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: 5.92 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.38: 13600 1.38 - 1.60: 20887 1.60 - 1.81: 325 1.81 - 2.02: 58 2.02 - 2.23: 80 Bond restraints: 34950 Sorted by residual: bond pdb=" O6 EHZ W 201 " pdb=" P1 EHZ W 201 " ideal model delta sigma weight residual 2.378 1.647 0.731 2.00e-02 2.50e+03 1.34e+03 bond pdb=" C20 EHZ W 201 " pdb=" O6 EHZ W 201 " ideal model delta sigma weight residual 1.191 1.399 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C ARG Q 106 " pdb=" O ARG Q 106 " ideal model delta sigma weight residual 1.236 1.338 -0.102 1.14e-02 7.69e+03 8.08e+01 bond pdb=" C15 EHZ W 201 " pdb=" O4 EHZ W 201 " ideal model delta sigma weight residual 1.356 1.181 0.175 2.00e-02 2.50e+03 7.61e+01 bond pdb=" CA LEU I 118 " pdb=" C LEU I 118 " ideal model delta sigma weight residual 1.522 1.636 -0.114 1.38e-02 5.25e+03 6.77e+01 ... (remaining 34945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.45: 46624 6.45 - 12.89: 560 12.89 - 19.34: 168 19.34 - 25.78: 3 25.78 - 32.23: 2 Bond angle restraints: 47357 Sorted by residual: angle pdb=" N ILE H 231 " pdb=" CA ILE H 231 " pdb=" C ILE H 231 " ideal model delta sigma weight residual 113.42 90.98 22.44 1.17e+00 7.31e-01 3.68e+02 angle pdb=" N THR G 174 " pdb=" CA THR G 174 " pdb=" C THR G 174 " ideal model delta sigma weight residual 114.64 89.03 25.61 1.52e+00 4.33e-01 2.84e+02 angle pdb=" N CYS F 125 " pdb=" CA CYS F 125 " pdb=" C CYS F 125 " ideal model delta sigma weight residual 113.17 93.45 19.72 1.26e+00 6.30e-01 2.45e+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 87.80 16.53 1.14e+00 7.69e-01 2.10e+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 87.58 16.75 1.20e+00 6.94e-01 1.95e+02 ... (remaining 47352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.94: 20490 27.94 - 55.88: 582 55.88 - 83.82: 50 83.82 - 111.76: 15 111.76 - 139.70: 4 Dihedral angle restraints: 21141 sinusoidal: 8923 harmonic: 12218 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 93.00 171.65 -78.65 1 1.00e+01 1.00e-02 7.71e+01 dihedral pdb=" CB CYS X 78 " pdb=" SG CYS X 78 " pdb=" SG CYS X 110 " pdb=" CB CYS X 110 " ideal model delta sinusoidal sigma weight residual 93.00 154.24 -61.24 1 1.00e+01 1.00e-02 4.98e+01 dihedral pdb=" N THR I 64 " pdb=" C THR I 64 " pdb=" CA THR I 64 " pdb=" CB THR I 64 " ideal model delta harmonic sigma weight residual 123.40 106.32 17.08 0 2.50e+00 1.60e-01 4.67e+01 ... (remaining 21138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.191: 4735 0.191 - 0.381: 393 0.381 - 0.572: 23 0.572 - 0.762: 2 0.762 - 0.953: 24 Chirality restraints: 5177 Sorted by residual: chirality pdb="FE3 SF4 I 301 " pdb=" S1 SF4 I 301 " pdb=" S2 SF4 I 301 " pdb=" S4 SF4 I 301 " both_signs ideal model delta sigma weight residual False -10.55 -9.60 -0.95 2.00e-01 2.50e+01 2.27e+01 chirality pdb="FE1 SF4 I 302 " pdb=" S2 SF4 I 302 " pdb=" S3 SF4 I 302 " pdb=" S4 SF4 I 302 " both_signs ideal model delta sigma weight residual False -10.55 -9.63 -0.92 2.00e-01 2.50e+01 2.13e+01 chirality pdb="FE2 SF4 I 301 " pdb=" S1 SF4 I 301 " pdb=" S3 SF4 I 301 " pdb=" S4 SF4 I 301 " both_signs ideal model delta sigma weight residual False 10.55 9.63 0.92 2.00e-01 2.50e+01 2.12e+01 ... (remaining 5174 not shown) Planarity restraints: 6010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C22 UQ9 H 401 " -0.340 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C23 UQ9 H 401 " 0.505 2.00e-02 2.50e+03 pdb=" C24 UQ9 H 401 " 0.106 2.00e-02 2.50e+03 pdb=" C25 UQ9 H 401 " -0.153 2.00e-02 2.50e+03 pdb=" C26 UQ9 H 401 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ9 H 401 " 0.337 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C13 UQ9 H 401 " -0.501 2.00e-02 2.50e+03 pdb=" C14 UQ9 H 401 " -0.104 2.00e-02 2.50e+03 pdb=" C15 UQ9 H 401 " 0.116 2.00e-02 2.50e+03 pdb=" C16 UQ9 H 401 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 H 401 " 0.020 2.00e-02 2.50e+03 1.35e-01 5.50e+02 pdb=" C1M UQ9 H 401 " 0.130 2.00e-02 2.50e+03 pdb=" C2 UQ9 H 401 " -0.064 2.00e-02 2.50e+03 pdb=" C3 UQ9 H 401 " 0.057 2.00e-02 2.50e+03 pdb=" C4 UQ9 H 401 " -0.041 2.00e-02 2.50e+03 pdb=" C5 UQ9 H 401 " 0.028 2.00e-02 2.50e+03 pdb=" C6 UQ9 H 401 " -0.004 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 401 " -0.074 2.00e-02 2.50e+03 pdb=" O2 UQ9 H 401 " -0.237 2.00e-02 2.50e+03 pdb=" O3 UQ9 H 401 " 0.270 2.00e-02 2.50e+03 pdb=" O4 UQ9 H 401 " -0.208 2.00e-02 2.50e+03 pdb=" O5 UQ9 H 401 " 0.123 2.00e-02 2.50e+03 ... (remaining 6007 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 407 2.53 - 3.13: 31083 3.13 - 3.72: 54428 3.72 - 4.31: 82239 4.31 - 4.90: 130086 Nonbonded interactions: 298243 Sorted by model distance: nonbonded pdb=" O ASN F 116 " pdb=" OD1 ASN F 116 " model vdw 1.942 3.040 nonbonded pdb=" OD1 ASP C 147 " pdb=" OE1 GLU C 148 " model vdw 1.999 3.040 nonbonded pdb=" O PHE G 63 " pdb=" SG CYS G 64 " model vdw 2.007 3.400 nonbonded pdb=" O ASN Z 24 " pdb=" OD1 ASN Z 24 " model vdw 2.045 3.040 nonbonded pdb=" N THR G 174 " pdb=" N ARG G 175 " model vdw 2.079 2.560 ... (remaining 298238 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: 3.450 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: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 35.220 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 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 : 0.021 1.241 34991 Z= 1.004 Angle : 2.173 56.911 47449 Z= 1.423 Chirality : 0.122 0.953 5177 Planarity : 0.009 0.290 6010 Dihedral : 12.949 139.696 13251 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 45.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.22 % Favored : 92.73 % Rotamer: Outliers : 0.44 % Allowed : 7.39 % Favored : 92.17 % Cbeta Deviations : 1.02 % 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: -3.28 (0.11), residues: 4153 helix: -1.85 (0.11), residues: 1769 sheet: -2.03 (0.28), residues: 308 loop : -2.48 (0.12), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 68 TYR 0.067 0.003 TYR D 135 PHE 0.031 0.002 PHE I 175 TRP 0.033 0.002 TRP G 285 HIS 0.012 0.002 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.01460 / 0.91 (34950) covalent geometry : angle 2.05258 / 1.42 (47357) SS BOND : bond 0.00906 / 0.46 ( 4) SS BOND : angle 1.31540 / 0.64 ( 8) hydrogen bonds : bond 0.25038 / 16.15 ( 1329) hydrogen bonds : angle 9.67553 / 7.02 ( 3762) metal coordination : bond 0.47978 / 31.17 ( 37) metal coordination : angle 17.11531 / 13.04 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1655 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 1639 time to evaluate : 1.274 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: 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: F 262 PHE cc_start: 0.5495 (m-80) cc_final: 0.5155 (m-80) REVERT: G 213 MET cc_start: 0.6216 (ptm) cc_final: 0.5779 (ptt) REVERT: G 261 ILE cc_start: 0.8614 (pp) cc_final: 0.8402 (pt) REVERT: G 564 CYS cc_start: 0.4587 (t) cc_final: 0.3110 (t) REVERT: H 172 MET cc_start: 0.5802 (ttp) cc_final: 0.5574 (ttp) REVERT: I 94 SER cc_start: 0.8483 (t) cc_final: 0.7910 (m) REVERT: P 227 PRO cc_start: 0.3902 (Cg_endo) cc_final: 0.3581 (Cg_exo) REVERT: Q 80 PHE cc_start: 0.7996 (p90) cc_final: 0.7139 (p90) REVERT: Q 85 ASN cc_start: 0.6891 (t0) cc_final: 0.6542 (t0) REVERT: R 80 ASP cc_start: 0.7865 (p0) cc_final: 0.7477 (p0) REVERT: T 148 ILE cc_start: 0.7034 (mm) cc_final: 0.6728 (mm) REVERT: V 104 VAL cc_start: 0.8817 (t) cc_final: 0.8559 (t) REVERT: W 104 THR cc_start: 0.7153 (m) cc_final: 0.6920 (m) REVERT: Z 83 THR cc_start: 0.6871 (t) cc_final: 0.6290 (t) REVERT: q 68 MET cc_start: 0.6483 (ptm) cc_final: 0.6210 (ptt) outliers start: 16 outliers final: 1 residues processed: 1646 average time/residue: 0.2132 time to fit residues: 557.3039 Evaluate side-chains 996 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 995 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 200 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN B 209 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS C 159 HIS C 195 HIS ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS D 147 ASN D 149 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 234 GLN D 270 ASN D 285 ASN D 313 GLN D 442 HIS E 68 ASN ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN E 86 GLN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN F 136 HIS F 164 ASN F 170 GLN F 220 GLN ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 HIS ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 388 ASN G 444 HIS G 495 ASN ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 HIS ** H 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 215 ASN P 216 HIS P 251 ASN ** P 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 123 ASN Q 163 ASN R 36 GLN R 70 ASN R 74 HIS ** R 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 81 ASN V 50 GLN W 102 GLN X 35 GLN Z 8 GLN Z 90 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 46 ASN b 71 GLN q 59 HIS r 21 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.114228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.089711 restraints weight = 89987.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.092937 restraints weight = 40096.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.095001 restraints weight = 24635.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.096249 restraints weight = 18375.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.096999 restraints weight = 15469.110| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 34991 Z= 0.237 Angle : 1.093 61.598 47449 Z= 0.449 Chirality : 0.051 0.355 5177 Planarity : 0.007 0.076 6010 Dihedral : 9.968 129.826 4950 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.11 % Allowed : 17.65 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.12), residues: 4153 helix: -0.61 (0.11), residues: 1836 sheet: -1.96 (0.26), residues: 324 loop : -1.71 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 79 TYR 0.035 0.003 TYR P 298 PHE 0.032 0.003 PHE W 109 TRP 0.029 0.002 TRP F 62 HIS 0.010 0.002 HIS q 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.24 (34950) covalent geometry : angle 0.86699 / 0.45 (47357) SS BOND : bond 0.00301 / 0.15 ( 4) SS BOND : angle 0.87938 / 0.46 ( 8) hydrogen bonds : bond 0.05960 / 3.90 ( 1329) hydrogen bonds : angle 5.97976 / 4.28 ( 3762) metal coordination : bond 0.02500 / 1.32 ( 37) metal coordination : angle 15.83608 / 11.62 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1228 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 1078 time to evaluate : 1.051 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: A 1 MET cc_start: 0.7361 (tpt) cc_final: 0.6639 (tmm) REVERT: A 93 ILE cc_start: 0.8734 (mm) cc_final: 0.8310 (mm) REVERT: A 96 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8789 (p) REVERT: A 105 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8656 (tt0) REVERT: B 73 TYR cc_start: 0.7890 (t80) cc_final: 0.7628 (t80) REVERT: B 88 SER cc_start: 0.9637 (t) cc_final: 0.8797 (p) REVERT: B 107 MET cc_start: 0.9017 (ttp) cc_final: 0.8749 (ttp) REVERT: B 113 ASP cc_start: 0.7858 (t70) cc_final: 0.7354 (p0) REVERT: B 114 MET cc_start: 0.8433 (ptp) cc_final: 0.8111 (ptm) REVERT: B 115 ASP cc_start: 0.9069 (t0) cc_final: 0.8845 (t0) REVERT: B 139 ASN cc_start: 0.8899 (m-40) cc_final: 0.8698 (m-40) REVERT: C 63 TYR cc_start: 0.8808 (t80) cc_final: 0.8462 (t80) REVERT: C 68 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8830 (tt) REVERT: C 71 TYR cc_start: 0.8754 (m-80) cc_final: 0.8418 (m-80) REVERT: C 216 LYS cc_start: 0.9305 (mmmt) cc_final: 0.9044 (mmmt) REVERT: D 99 LEU cc_start: 0.9292 (mt) cc_final: 0.9052 (mt) REVERT: D 105 MET cc_start: 0.4514 (tmm) cc_final: 0.3779 (tmm) REVERT: D 213 PHE cc_start: 0.8752 (m-10) cc_final: 0.8202 (m-10) REVERT: D 294 ARG cc_start: 0.8483 (mtm180) cc_final: 0.8210 (mtm-85) REVERT: E 40 HIS cc_start: 0.5879 (t-90) cc_final: 0.5497 (t-170) REVERT: E 82 LEU cc_start: 0.9246 (tp) cc_final: 0.8938 (tp) REVERT: E 86 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8256 (tp-100) REVERT: E 121 TYR cc_start: 0.8093 (m-10) cc_final: 0.7619 (m-10) REVERT: E 122 ASN cc_start: 0.7327 (t0) cc_final: 0.6868 (t0) REVERT: E 144 SER cc_start: 0.8521 (p) cc_final: 0.8043 (m) REVERT: E 147 ILE cc_start: 0.8959 (mp) cc_final: 0.8682 (mp) REVERT: E 152 GLN cc_start: 0.8546 (mt0) cc_final: 0.8073 (tt0) REVERT: E 157 ILE cc_start: 0.8644 (tt) cc_final: 0.8212 (mt) REVERT: E 184 MET cc_start: 0.7197 (ttp) cc_final: 0.6672 (mtp) REVERT: E 191 TYR cc_start: 0.6753 (OUTLIER) cc_final: 0.6454 (m-80) REVERT: F 101 PHE cc_start: 0.8742 (m-10) cc_final: 0.8074 (m-80) REVERT: F 149 MET cc_start: 0.8372 (mpp) cc_final: 0.7611 (mmt) REVERT: F 209 GLU cc_start: 0.8793 (tp30) cc_final: 0.8321 (tp30) REVERT: F 233 VAL cc_start: 0.8827 (t) cc_final: 0.8535 (p) REVERT: F 289 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6402 (tp30) REVERT: G 126 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8274 (pp) REVERT: G 136 GLU cc_start: 0.7336 (mt-10) cc_final: 0.7008 (mt-10) REVERT: G 210 ILE cc_start: 0.8707 (pt) cc_final: 0.8340 (mm) REVERT: G 269 GLU cc_start: 0.7732 (pm20) cc_final: 0.7436 (pm20) REVERT: H 31 MET cc_start: 0.9336 (mtt) cc_final: 0.8821 (mtt) REVERT: H 47 GLN cc_start: 0.8793 (tp40) cc_final: 0.8548 (tp40) REVERT: H 78 SER cc_start: 0.9673 (t) cc_final: 0.9425 (m) REVERT: H 121 TRP cc_start: 0.8908 (t60) cc_final: 0.8601 (t60) REVERT: H 156 MET cc_start: 0.8544 (mtp) cc_final: 0.8254 (mtp) REVERT: H 183 MET cc_start: 0.8281 (mmt) cc_final: 0.7494 (mtt) REVERT: H 195 ARG cc_start: 0.9202 (mmm-85) cc_final: 0.8385 (tpt90) REVERT: H 274 ARG cc_start: 0.9101 (ttt90) cc_final: 0.8844 (ttt180) REVERT: I 94 SER cc_start: 0.9178 (t) cc_final: 0.8207 (m) REVERT: I 117 LYS cc_start: 0.8473 (mttp) cc_final: 0.8180 (mmmm) REVERT: P 71 ASN cc_start: 0.8517 (t0) cc_final: 0.8026 (t0) REVERT: P 76 MET cc_start: 0.8321 (tpp) cc_final: 0.8119 (tpp) REVERT: P 92 MET cc_start: 0.8675 (mmt) cc_final: 0.8299 (mmm) REVERT: P 134 TRP cc_start: 0.8649 (p90) cc_final: 0.8434 (p90) REVERT: P 174 MET cc_start: 0.7407 (tpt) cc_final: 0.7076 (tpp) REVERT: P 177 SER cc_start: 0.8440 (t) cc_final: 0.8088 (p) REVERT: P 350 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7305 (tt) REVERT: Q 78 ARG cc_start: 0.8425 (ttp80) cc_final: 0.7829 (ptm-80) REVERT: Q 85 ASN cc_start: 0.7579 (t0) cc_final: 0.7356 (t0) REVERT: Q 108 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7866 (mm-30) REVERT: R 80 ASP cc_start: 0.8663 (p0) cc_final: 0.7748 (p0) REVERT: R 96 ASP cc_start: 0.7910 (t0) cc_final: 0.7688 (m-30) REVERT: S 50 ASN cc_start: 0.8004 (m110) cc_final: 0.6978 (t0) REVERT: S 79 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6509 (pt) REVERT: T 93 ILE cc_start: 0.6787 (mm) cc_final: 0.5907 (mm) REVERT: T 97 LYS cc_start: 0.6717 (ttpt) cc_final: 0.6507 (ttpt) REVERT: T 103 HIS cc_start: 0.7531 (OUTLIER) cc_final: 0.7030 (t-90) REVERT: T 114 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7587 (m-30) REVERT: V 26 ILE cc_start: 0.9326 (mm) cc_final: 0.9014 (mm) REVERT: V 27 LEU cc_start: 0.9376 (mt) cc_final: 0.9162 (tt) REVERT: V 44 TYR cc_start: 0.7932 (t80) cc_final: 0.6888 (t80) REVERT: V 69 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8222 (tm-30) REVERT: V 94 MET cc_start: 0.8950 (tpp) cc_final: 0.8312 (tpp) REVERT: V 113 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8047 (ttpp) REVERT: W 27 ASP cc_start: 0.8118 (t70) cc_final: 0.7855 (t70) REVERT: W 39 TYR cc_start: 0.8717 (t80) cc_final: 0.8415 (t80) REVERT: W 92 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8128 (mm-30) REVERT: W 99 VAL cc_start: 0.8533 (t) cc_final: 0.8266 (p) REVERT: W 107 MET cc_start: 0.8467 (mmm) cc_final: 0.8110 (tmm) REVERT: X 42 GLU cc_start: 0.8563 (pt0) cc_final: 0.8253 (pt0) REVERT: Z 72 MET cc_start: 0.7805 (mmt) cc_final: 0.7375 (mmm) REVERT: a 43 TYR cc_start: 0.8388 (t80) cc_final: 0.8041 (t80) REVERT: a 48 MET cc_start: 0.8867 (ttm) cc_final: 0.8520 (ttm) REVERT: b 41 TYR cc_start: 0.7488 (m-80) cc_final: 0.7065 (m-10) REVERT: q 68 MET cc_start: 0.6104 (ptm) cc_final: 0.5755 (ptt) REVERT: q 86 TRP cc_start: 0.8188 (m100) cc_final: 0.7982 (m-10) REVERT: s 77 THR cc_start: 0.5729 (p) cc_final: 0.5361 (t) REVERT: s 90 PHE cc_start: 0.8205 (m-80) cc_final: 0.7962 (m-80) outliers start: 150 outliers final: 74 residues processed: 1170 average time/residue: 0.2057 time to fit residues: 395.5434 Evaluate side-chains 961 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 876 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 670 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 173 TRP Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain P residue 124 ASN Chi-restraints excluded: chain P residue 205 ASP Chi-restraints excluded: chain P residue 213 PHE Chi-restraints excluded: chain P residue 228 LEU Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 297 VAL Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain Q residue 150 LYS Chi-restraints excluded: chain R residue 36 GLN Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain S residue 37 ILE Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain T residue 103 HIS Chi-restraints excluded: chain T residue 111 ASP Chi-restraints excluded: chain T residue 114 ASP Chi-restraints excluded: chain T residue 125 GLU Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain V residue 18 ASP Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 113 LYS Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain X residue 12 GLU Chi-restraints excluded: chain X residue 52 ASP Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain b residue 44 MET Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 39 VAL Chi-restraints excluded: chain q residue 59 HIS Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 138 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 307 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 253 optimal weight: 0.5980 chunk 294 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 238 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 322 optimal weight: 0.0370 chunk 318 optimal weight: 7.9990 overall best weight: 0.7264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 ASN ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN E 186 GLN F 136 HIS F 185 ASN ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN H 169 GLN ** H 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 275 HIS ** P 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 85 ASN Q 163 ASN S 62 GLN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 59 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.116087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.092643 restraints weight = 90330.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.095893 restraints weight = 39716.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.097954 restraints weight = 24061.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.099208 restraints weight = 17758.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.099975 restraints weight = 14824.966| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 34991 Z= 0.166 Angle : 0.982 61.622 47449 Z= 0.386 Chirality : 0.046 0.244 5177 Planarity : 0.006 0.071 6010 Dihedral : 9.591 137.808 4948 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.71 % Allowed : 19.35 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.13), residues: 4153 helix: -0.15 (0.12), residues: 1846 sheet: -1.76 (0.26), residues: 355 loop : -1.38 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG S 20 TYR 0.031 0.002 TYR F 177 PHE 0.028 0.002 PHE W 109 TRP 0.034 0.002 TRP F 62 HIS 0.008 0.002 HIS q 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (34950) covalent geometry : angle 0.74796 / 0.38 (47357) SS BOND : bond 0.00192 / 0.10 ( 4) SS BOND : angle 0.54648 / 0.28 ( 8) hydrogen bonds : bond 0.04843 / 3.14 ( 1329) hydrogen bonds : angle 5.48027 / 3.90 ( 3762) metal coordination : bond 0.02068 / 1.43 ( 37) metal coordination : angle 15.13272 / 11.02 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 992 time to evaluate : 0.897 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 1 MET cc_start: 0.7286 (tpt) cc_final: 0.6549 (tmm) REVERT: A 23 TRP cc_start: 0.7546 (t60) cc_final: 0.6509 (t60) REVERT: A 54 LYS cc_start: 0.7936 (mttp) cc_final: 0.7408 (mtpp) REVERT: B 88 SER cc_start: 0.9528 (t) cc_final: 0.8723 (p) REVERT: B 94 THR cc_start: 0.9122 (p) cc_final: 0.8734 (p) REVERT: B 107 MET cc_start: 0.8974 (ttp) cc_final: 0.8693 (ttp) REVERT: B 113 ASP cc_start: 0.7887 (t70) cc_final: 0.7632 (p0) REVERT: B 114 MET cc_start: 0.8242 (ptp) cc_final: 0.7977 (ptm) REVERT: B 219 LYS cc_start: 0.8982 (mtpt) cc_final: 0.8766 (ttmm) REVERT: C 63 TYR cc_start: 0.8961 (t80) cc_final: 0.8618 (t80) REVERT: C 68 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8920 (tt) REVERT: C 104 ASN cc_start: 0.8453 (t0) cc_final: 0.7934 (t0) REVERT: C 122 GLN cc_start: 0.7014 (tm-30) cc_final: 0.6765 (tm-30) REVERT: C 214 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7737 (tm-30) REVERT: C 216 LYS cc_start: 0.9310 (mmmt) cc_final: 0.9058 (mmmt) REVERT: C 234 LEU cc_start: 0.9173 (pp) cc_final: 0.8966 (pp) REVERT: D 99 LEU cc_start: 0.9263 (mt) cc_final: 0.9040 (mt) REVERT: D 145 MET cc_start: 0.8361 (mmm) cc_final: 0.7690 (mmm) REVERT: D 184 ILE cc_start: 0.9147 (mm) cc_final: 0.8907 (mm) REVERT: D 213 PHE cc_start: 0.8608 (m-10) cc_final: 0.8105 (m-10) REVERT: D 250 ASN cc_start: 0.8593 (m-40) cc_final: 0.8200 (m-40) REVERT: D 261 MET cc_start: 0.9170 (tpp) cc_final: 0.8637 (tpt) REVERT: D 294 ARG cc_start: 0.8434 (mtm180) cc_final: 0.8150 (mtm-85) REVERT: E 40 HIS cc_start: 0.5750 (t-90) cc_final: 0.5454 (t-170) REVERT: E 82 LEU cc_start: 0.9186 (tp) cc_final: 0.8842 (tp) REVERT: E 112 TYR cc_start: 0.8252 (m-80) cc_final: 0.8043 (m-80) REVERT: E 121 TYR cc_start: 0.8042 (m-10) cc_final: 0.7733 (m-10) REVERT: E 157 ILE cc_start: 0.8514 (tt) cc_final: 0.8275 (mt) REVERT: E 184 MET cc_start: 0.7024 (ttp) cc_final: 0.6619 (mtp) REVERT: E 191 TYR cc_start: 0.6594 (OUTLIER) cc_final: 0.6021 (m-80) REVERT: E 225 GLU cc_start: 0.4186 (OUTLIER) cc_final: 0.3299 (tm-30) REVERT: E 242 PHE cc_start: 0.6901 (t80) cc_final: 0.6618 (t80) REVERT: F 209 GLU cc_start: 0.8891 (tp30) cc_final: 0.8629 (tp30) REVERT: F 233 VAL cc_start: 0.8882 (t) cc_final: 0.8631 (p) REVERT: F 289 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6253 (tp30) REVERT: G 136 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7027 (mt-10) REVERT: G 210 ILE cc_start: 0.8662 (pt) cc_final: 0.8330 (mm) REVERT: G 316 TYR cc_start: 0.7987 (m-80) cc_final: 0.7622 (m-80) REVERT: G 333 PHE cc_start: 0.6869 (m-10) cc_final: 0.6169 (m-10) REVERT: G 403 VAL cc_start: 0.9124 (OUTLIER) cc_final: 0.8917 (p) REVERT: H 31 MET cc_start: 0.9298 (mtt) cc_final: 0.8781 (mtt) REVERT: H 121 TRP cc_start: 0.8921 (t60) cc_final: 0.8656 (t60) REVERT: H 183 MET cc_start: 0.8519 (mmt) cc_final: 0.8138 (mtm) REVERT: H 214 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8149 (mt-10) REVERT: H 223 PHE cc_start: 0.8630 (m-80) cc_final: 0.8184 (m-80) REVERT: H 274 ARG cc_start: 0.9078 (ttt90) cc_final: 0.8642 (ttt180) REVERT: I 37 LYS cc_start: 0.8169 (ttmt) cc_final: 0.7962 (ttpt) REVERT: I 94 SER cc_start: 0.9127 (t) cc_final: 0.8455 (m) REVERT: P 71 ASN cc_start: 0.8476 (t0) cc_final: 0.8154 (t0) REVERT: P 92 MET cc_start: 0.8652 (mmt) cc_final: 0.8238 (mmm) REVERT: P 99 ASP cc_start: 0.8072 (t0) cc_final: 0.7613 (t0) REVERT: P 174 MET cc_start: 0.7685 (tpt) cc_final: 0.7347 (tpp) REVERT: P 177 SER cc_start: 0.8294 (t) cc_final: 0.7948 (p) REVERT: P 215 ASN cc_start: 0.8802 (m-40) cc_final: 0.7988 (m110) REVERT: P 237 LYS cc_start: 0.7346 (mttp) cc_final: 0.7125 (mttp) REVERT: P 241 TYR cc_start: 0.8585 (t80) cc_final: 0.8279 (t80) REVERT: P 255 ASP cc_start: 0.7803 (t0) cc_final: 0.7428 (t0) REVERT: P 280 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8721 (mp) REVERT: P 351 GLU cc_start: 0.8116 (mp0) cc_final: 0.7862 (mp0) REVERT: Q 78 ARG cc_start: 0.8483 (ttp80) cc_final: 0.8276 (ptm-80) REVERT: Q 85 ASN cc_start: 0.7468 (t0) cc_final: 0.7141 (t0) REVERT: Q 108 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8042 (mm-30) REVERT: Q 148 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7823 (tm-30) REVERT: R 80 ASP cc_start: 0.8621 (p0) cc_final: 0.7804 (p0) REVERT: R 112 LYS cc_start: 0.7360 (tppt) cc_final: 0.7122 (tppt) REVERT: S 50 ASN cc_start: 0.7725 (m110) cc_final: 0.6933 (t0) REVERT: T 111 ASP cc_start: 0.8590 (t70) cc_final: 0.8351 (p0) REVERT: T 114 ASP cc_start: 0.8366 (m-30) cc_final: 0.7807 (m-30) REVERT: T 142 GLN cc_start: 0.8009 (pt0) cc_final: 0.7773 (pt0) REVERT: V 27 LEU cc_start: 0.9345 (mt) cc_final: 0.9054 (tt) REVERT: V 94 MET cc_start: 0.8797 (tpp) cc_final: 0.8254 (tpp) REVERT: W 39 TYR cc_start: 0.8418 (t80) cc_final: 0.8217 (t80) REVERT: W 64 ASP cc_start: 0.8907 (m-30) cc_final: 0.8603 (m-30) REVERT: W 92 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8244 (mm-30) REVERT: W 95 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8820 (mt-10) REVERT: W 99 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8392 (m) REVERT: W 122 LEU cc_start: 0.8899 (tt) cc_final: 0.8692 (tt) REVERT: Z 72 MET cc_start: 0.8036 (mmt) cc_final: 0.7605 (mmm) REVERT: a 6 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8892 (mp) REVERT: a 50 ARG cc_start: 0.8557 (ttt90) cc_final: 0.8236 (tmt-80) REVERT: a 51 ASP cc_start: 0.8238 (m-30) cc_final: 0.7961 (m-30) REVERT: b 41 TYR cc_start: 0.7374 (m-80) cc_final: 0.6955 (m-10) REVERT: b 43 SER cc_start: 0.8990 (p) cc_final: 0.8600 (t) REVERT: b 46 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.8527 (t0) REVERT: q 42 ASP cc_start: 0.6683 (m-30) cc_final: 0.6440 (m-30) REVERT: q 68 MET cc_start: 0.6024 (ptm) cc_final: 0.5762 (ptt) REVERT: q 85 GLU cc_start: 0.8700 (tp30) cc_final: 0.8487 (tp30) REVERT: s 77 THR cc_start: 0.5860 (p) cc_final: 0.5580 (t) outliers start: 172 outliers final: 83 residues processed: 1087 average time/residue: 0.1973 time to fit residues: 355.3826 Evaluate side-chains 951 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 859 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 295 ASP Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 670 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 173 TRP Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain P residue 124 ASN Chi-restraints excluded: chain P residue 133 GLU Chi-restraints excluded: chain P residue 205 ASP Chi-restraints excluded: chain P residue 213 PHE Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 280 ILE Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain Q residue 150 LYS Chi-restraints excluded: chain S residue 37 ILE Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 78 SER Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 103 HIS Chi-restraints excluded: chain T residue 124 ASP Chi-restraints excluded: chain T residue 125 GLU Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 109 PHE Chi-restraints excluded: chain X residue 12 GLU Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 52 ASP Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 46 ASN Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 59 HIS Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 138 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 200 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 290 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 330 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 376 optimal weight: 2.9990 chunk 299 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN E 186 GLN F 133 HIS ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN H 38 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 HIS ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 219 ASN P 238 GLN P 285 HIS ** P 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 40 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 71 GLN q 59 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.112585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.088070 restraints weight = 89579.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.091227 restraints weight = 39867.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.093278 restraints weight = 24546.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.094493 restraints weight = 18260.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.095198 restraints weight = 15413.354| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 34991 Z= 0.170 Angle : 0.972 64.539 47449 Z= 0.371 Chirality : 0.046 0.211 5177 Planarity : 0.005 0.057 6010 Dihedral : 9.383 144.566 4948 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.68 % Allowed : 21.32 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.13), residues: 4153 helix: 0.08 (0.12), residues: 1844 sheet: -1.63 (0.26), residues: 385 loop : -1.29 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG q 60 TYR 0.041 0.002 TYR F 177 PHE 0.033 0.002 PHE C 173 TRP 0.031 0.002 TRP C 164 HIS 0.009 0.001 HIS q 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (34950) covalent geometry : angle 0.72336 / 0.37 (47357) SS BOND : bond 0.00246 / 0.12 ( 4) SS BOND : angle 0.62599 / 0.27 ( 8) hydrogen bonds : bond 0.04407 / 2.87 ( 1329) hydrogen bonds : angle 5.26060 / 3.75 ( 3762) metal coordination : bond 0.02050 / 1.26 ( 37) metal coordination : angle 15.45224 / 11.29 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 917 time to evaluate : 1.395 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: A 1 MET cc_start: 0.7328 (tpt) cc_final: 0.6549 (tmm) REVERT: A 23 TRP cc_start: 0.7627 (t60) cc_final: 0.6624 (t60) REVERT: A 54 LYS cc_start: 0.8139 (mttp) cc_final: 0.7599 (mtpp) REVERT: A 105 GLU cc_start: 0.8839 (tt0) cc_final: 0.8589 (tt0) REVERT: B 219 LYS cc_start: 0.9003 (mtpt) cc_final: 0.8776 (ttmm) REVERT: C 68 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8864 (tt) REVERT: C 71 TYR cc_start: 0.8880 (m-10) cc_final: 0.8599 (m-10) REVERT: C 104 ASN cc_start: 0.8509 (t0) cc_final: 0.8168 (t0) REVERT: C 122 GLN cc_start: 0.7148 (tm-30) cc_final: 0.6874 (tm-30) REVERT: C 214 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7827 (tm-30) REVERT: C 216 LYS cc_start: 0.9288 (mmmt) cc_final: 0.8918 (mmmt) REVERT: C 234 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8919 (pp) REVERT: D 135 TYR cc_start: 0.8371 (m-80) cc_final: 0.8128 (m-80) REVERT: D 213 PHE cc_start: 0.8568 (m-10) cc_final: 0.8005 (m-10) REVERT: D 215 GLU cc_start: 0.8285 (tt0) cc_final: 0.7932 (tm-30) REVERT: D 294 ARG cc_start: 0.8452 (mtm180) cc_final: 0.8203 (mtm-85) REVERT: D 371 MET cc_start: 0.8627 (ttp) cc_final: 0.8385 (ttp) REVERT: D 437 LYS cc_start: 0.8898 (mmtp) cc_final: 0.8625 (mmtp) REVERT: E 82 LEU cc_start: 0.9156 (tp) cc_final: 0.8748 (tp) REVERT: E 121 TYR cc_start: 0.8322 (m-10) cc_final: 0.7984 (m-10) REVERT: E 152 GLN cc_start: 0.8324 (mt0) cc_final: 0.7997 (tt0) REVERT: E 157 ILE cc_start: 0.8652 (tt) cc_final: 0.8227 (mt) REVERT: E 184 MET cc_start: 0.6819 (ttp) cc_final: 0.6419 (mtp) REVERT: E 191 TYR cc_start: 0.6656 (OUTLIER) cc_final: 0.5989 (m-80) REVERT: E 222 PHE cc_start: 0.6939 (m-80) cc_final: 0.6038 (m-10) REVERT: E 225 GLU cc_start: 0.3911 (OUTLIER) cc_final: 0.2883 (tm-30) REVERT: F 149 MET cc_start: 0.8411 (mmt) cc_final: 0.8193 (mmt) REVERT: F 209 GLU cc_start: 0.8974 (tp30) cc_final: 0.8673 (tp30) REVERT: F 289 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6248 (tp30) REVERT: F 372 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: G 136 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6821 (mt-10) REVERT: G 284 GLU cc_start: 0.7857 (tt0) cc_final: 0.7523 (tp30) REVERT: G 316 TYR cc_start: 0.8063 (m-80) cc_final: 0.7846 (m-80) REVERT: G 569 GLN cc_start: 0.8495 (tp40) cc_final: 0.8041 (tp-100) REVERT: G 659 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8845 (tt) REVERT: H 143 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7685 (mt-10) REVERT: H 183 MET cc_start: 0.8489 (mmt) cc_final: 0.8212 (mtm) REVERT: H 214 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8282 (mt-10) REVERT: H 222 LEU cc_start: 0.9622 (mp) cc_final: 0.9361 (mp) REVERT: H 223 PHE cc_start: 0.8656 (m-80) cc_final: 0.8277 (m-80) REVERT: I 85 ASN cc_start: 0.8030 (t0) cc_final: 0.7817 (t0) REVERT: I 94 SER cc_start: 0.9104 (t) cc_final: 0.7749 (m) REVERT: P 71 ASN cc_start: 0.8533 (t0) cc_final: 0.8189 (t0) REVERT: P 174 MET cc_start: 0.7844 (tpt) cc_final: 0.7374 (tpp) REVERT: P 177 SER cc_start: 0.8189 (t) cc_final: 0.7847 (p) REVERT: P 215 ASN cc_start: 0.8779 (m-40) cc_final: 0.7936 (m110) REVERT: P 237 LYS cc_start: 0.6857 (mttp) cc_final: 0.6625 (mttp) REVERT: P 241 TYR cc_start: 0.8689 (t80) cc_final: 0.8436 (t80) REVERT: P 255 ASP cc_start: 0.7820 (t0) cc_final: 0.7544 (t0) REVERT: P 280 ILE cc_start: 0.9049 (mt) cc_final: 0.8847 (mp) REVERT: P 350 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.6884 (tt) REVERT: P 351 GLU cc_start: 0.8261 (mp0) cc_final: 0.7984 (mp0) REVERT: Q 78 ARG cc_start: 0.8505 (ttp80) cc_final: 0.7652 (ptm-80) REVERT: Q 85 ASN cc_start: 0.7797 (t0) cc_final: 0.7450 (t0) REVERT: Q 86 ASN cc_start: 0.8045 (t0) cc_final: 0.7834 (t0) REVERT: Q 108 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8026 (mm-30) REVERT: Q 151 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7924 (mmmt) REVERT: R 80 ASP cc_start: 0.8594 (p0) cc_final: 0.7794 (p0) REVERT: S 50 ASN cc_start: 0.7905 (m110) cc_final: 0.7202 (t0) REVERT: T 111 ASP cc_start: 0.8594 (t70) cc_final: 0.8307 (p0) REVERT: T 114 ASP cc_start: 0.8413 (m-30) cc_final: 0.7902 (m-30) REVERT: W 64 ASP cc_start: 0.8878 (m-30) cc_final: 0.8672 (m-30) REVERT: W 92 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8234 (mm-30) REVERT: W 95 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8495 (mt-10) REVERT: W 99 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8374 (m) REVERT: W 122 LEU cc_start: 0.8932 (tt) cc_final: 0.8628 (tt) REVERT: W 126 TYR cc_start: 0.8875 (m-10) cc_final: 0.8624 (m-80) REVERT: Z 72 MET cc_start: 0.8101 (mmt) cc_final: 0.7456 (mtp) REVERT: a 26 ILE cc_start: 0.9307 (mm) cc_final: 0.9100 (mp) REVERT: a 50 ARG cc_start: 0.8619 (ttt90) cc_final: 0.8324 (tmt-80) REVERT: b 32 MET cc_start: 0.7822 (ttt) cc_final: 0.7465 (ttt) REVERT: b 41 TYR cc_start: 0.7490 (m-80) cc_final: 0.7238 (m-80) REVERT: b 43 SER cc_start: 0.8954 (p) cc_final: 0.8543 (t) REVERT: b 46 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8481 (t0) REVERT: q 17 HIS cc_start: 0.7070 (t70) cc_final: 0.6600 (t-170) REVERT: q 68 MET cc_start: 0.6032 (ptm) cc_final: 0.5693 (ptt) REVERT: r 10 LYS cc_start: 0.6545 (mtpp) cc_final: 0.5583 (tmtt) REVERT: s 77 THR cc_start: 0.6076 (p) cc_final: 0.5682 (t) REVERT: s 94 GLN cc_start: 0.5983 (pm20) cc_final: 0.4964 (mt0) outliers start: 171 outliers final: 95 residues processed: 1018 average time/residue: 0.2093 time to fit residues: 352.1918 Evaluate side-chains 935 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 830 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 295 ASP Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 670 GLU Chi-restraints excluded: chain G residue 710 CYS Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 173 TRP Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 305 ILE Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain P residue 124 ASN Chi-restraints excluded: chain P residue 205 ASP Chi-restraints excluded: chain P residue 213 PHE Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain Q residue 150 LYS Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain S residue 37 ILE Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 103 HIS Chi-restraints excluded: chain T residue 113 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 124 ASP Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain X residue 12 GLU Chi-restraints excluded: chain X residue 52 ASP Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 23 PHE Chi-restraints excluded: chain b residue 46 ASN Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 59 HIS Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain r residue 63 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 232 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 356 optimal weight: 7.9990 chunk 287 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 279 optimal weight: 10.0000 chunk 179 optimal weight: 0.5980 chunk 373 optimal weight: 10.0000 chunk 313 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 overall best weight: 4.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 HIS ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 569 GLN G 571 HIS G 572 HIS ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 ASN ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 238 GLN S 80 ASN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 59 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.107466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.082836 restraints weight = 90914.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.085792 restraints weight = 41708.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.087700 restraints weight = 26165.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.088839 restraints weight = 19794.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.089523 restraints weight = 16826.638| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.6024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 34991 Z= 0.302 Angle : 1.093 66.923 47449 Z= 0.413 Chirality : 0.050 0.246 5177 Planarity : 0.006 0.056 6010 Dihedral : 9.516 157.217 4948 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 5.53 % Allowed : 21.59 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.13), residues: 4153 helix: 0.11 (0.12), residues: 1841 sheet: -1.72 (0.25), residues: 393 loop : -1.27 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG q 60 TYR 0.039 0.002 TYR C 63 PHE 0.037 0.002 PHE C 173 TRP 0.046 0.002 TRP C 164 HIS 0.022 0.002 HIS q 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00688 / 0.30 (34950) covalent geometry : angle 0.80034 / 0.41 (47357) SS BOND : bond 0.00453 / 0.23 ( 4) SS BOND : angle 1.07659 / 0.55 ( 8) hydrogen bonds : bond 0.04692 / 3.07 ( 1329) hydrogen bonds : angle 5.43046 / 3.86 ( 3762) metal coordination : bond 0.03253 / 1.91 ( 37) metal coordination : angle 17.69206 / 12.64 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1023 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 821 time to evaluate : 1.183 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: A 1 MET cc_start: 0.7352 (tpt) cc_final: 0.6653 (tmm) REVERT: A 54 LYS cc_start: 0.8269 (mttp) cc_final: 0.7739 (mtpp) REVERT: B 216 GLN cc_start: 0.7359 (mm-40) cc_final: 0.7059 (mm-40) REVERT: C 71 TYR cc_start: 0.9222 (m-10) cc_final: 0.8873 (m-10) REVERT: C 122 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7304 (tm-30) REVERT: C 186 ILE cc_start: 0.9347 (tp) cc_final: 0.9000 (tp) REVERT: C 211 TYR cc_start: 0.9053 (t80) cc_final: 0.8658 (t80) REVERT: C 214 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8023 (tm-30) REVERT: C 234 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8932 (pp) REVERT: D 105 MET cc_start: 0.5399 (tmm) cc_final: 0.4691 (tmm) REVERT: D 213 PHE cc_start: 0.8798 (m-10) cc_final: 0.8338 (m-10) REVERT: D 294 ARG cc_start: 0.8598 (mtm180) cc_final: 0.8182 (mtm-85) REVERT: D 330 TYR cc_start: 0.8526 (t80) cc_final: 0.7733 (t80) REVERT: D 371 MET cc_start: 0.8893 (ttp) cc_final: 0.8669 (ttp) REVERT: D 389 TYR cc_start: 0.8423 (m-10) cc_final: 0.8142 (m-10) REVERT: D 440 LYS cc_start: 0.8206 (ptpp) cc_final: 0.7964 (ptpp) REVERT: E 82 LEU cc_start: 0.9143 (tp) cc_final: 0.8768 (tp) REVERT: E 121 TYR cc_start: 0.8359 (m-10) cc_final: 0.7904 (m-10) REVERT: E 191 TYR cc_start: 0.6713 (OUTLIER) cc_final: 0.6208 (m-80) REVERT: E 222 PHE cc_start: 0.6938 (m-80) cc_final: 0.5827 (m-10) REVERT: E 225 GLU cc_start: 0.4202 (OUTLIER) cc_final: 0.3147 (tm-30) REVERT: F 41 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9087 (mm) REVERT: F 209 GLU cc_start: 0.8980 (tp30) cc_final: 0.8774 (tp30) REVERT: F 214 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8740 (mm-30) REVERT: F 289 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6340 (pt0) REVERT: F 372 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8022 (mt-10) REVERT: F 455 GLN cc_start: 0.8994 (mp10) cc_final: 0.8775 (mp10) REVERT: G 59 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7703 (mm110) REVERT: G 136 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6909 (mt-10) REVERT: G 138 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8213 (t0) REVERT: G 284 GLU cc_start: 0.7965 (tt0) cc_final: 0.7593 (tt0) REVERT: G 316 TYR cc_start: 0.8509 (m-80) cc_final: 0.8014 (m-80) REVERT: G 632 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7258 (pp) REVERT: G 659 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8750 (tt) REVERT: H 3 PHE cc_start: 0.7202 (t80) cc_final: 0.6952 (t80) REVERT: H 31 MET cc_start: 0.9414 (mtp) cc_final: 0.8649 (mtp) REVERT: H 59 GLU cc_start: 0.8560 (tp30) cc_final: 0.8003 (tp30) REVERT: H 143 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7834 (mt-10) REVERT: H 183 MET cc_start: 0.8594 (mmt) cc_final: 0.8015 (mtm) REVERT: H 200 LEU cc_start: 0.8327 (mt) cc_final: 0.7982 (mt) REVERT: H 223 PHE cc_start: 0.8675 (m-80) cc_final: 0.8386 (m-80) REVERT: H 258 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.8027 (t0) REVERT: I 94 SER cc_start: 0.9293 (t) cc_final: 0.8728 (m) REVERT: P 78 SER cc_start: 0.8029 (OUTLIER) cc_final: 0.7574 (p) REVERT: P 174 MET cc_start: 0.7842 (tpt) cc_final: 0.7372 (tpp) REVERT: P 177 SER cc_start: 0.8233 (t) cc_final: 0.7880 (p) REVERT: P 215 ASN cc_start: 0.8818 (m-40) cc_final: 0.7888 (m110) REVERT: P 300 TRP cc_start: 0.7009 (m100) cc_final: 0.5856 (m-10) REVERT: P 350 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7257 (tt) REVERT: P 351 GLU cc_start: 0.8288 (mp0) cc_final: 0.8032 (mp0) REVERT: Q 78 ARG cc_start: 0.8667 (ttp80) cc_final: 0.7543 (ptm-80) REVERT: Q 85 ASN cc_start: 0.8088 (t0) cc_final: 0.7775 (t0) REVERT: Q 86 ASN cc_start: 0.8450 (t0) cc_final: 0.8218 (t0) REVERT: Q 108 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8043 (mm-30) REVERT: R 80 ASP cc_start: 0.8721 (p0) cc_final: 0.8009 (p0) REVERT: S 50 ASN cc_start: 0.8039 (m110) cc_final: 0.7676 (t0) REVERT: T 77 ASP cc_start: 0.7789 (p0) cc_final: 0.6783 (t0) REVERT: T 111 ASP cc_start: 0.8746 (t70) cc_final: 0.8376 (p0) REVERT: T 114 ASP cc_start: 0.8448 (m-30) cc_final: 0.7918 (m-30) REVERT: T 125 GLU cc_start: 0.8480 (tp30) cc_final: 0.7962 (tm-30) REVERT: V 113 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8495 (ttpp) REVERT: W 42 TRP cc_start: 0.9520 (m100) cc_final: 0.8907 (m100) REVERT: W 73 ASN cc_start: 0.8737 (m-40) cc_final: 0.8526 (m-40) REVERT: W 92 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8165 (mm-30) REVERT: W 95 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8266 (mt-10) REVERT: W 99 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8494 (m) REVERT: W 122 LEU cc_start: 0.8957 (tt) cc_final: 0.8659 (tt) REVERT: W 126 TYR cc_start: 0.9000 (m-10) cc_final: 0.8589 (m-80) REVERT: Z 72 MET cc_start: 0.8204 (mmt) cc_final: 0.7640 (mtp) REVERT: a 61 TYR cc_start: 0.7067 (t80) cc_final: 0.6861 (t80) REVERT: b 43 SER cc_start: 0.9128 (p) cc_final: 0.8605 (t) REVERT: b 46 ASN cc_start: 0.8869 (t160) cc_final: 0.8570 (t0) REVERT: q 68 MET cc_start: 0.6319 (ptm) cc_final: 0.5828 (ptt) REVERT: r 10 LYS cc_start: 0.6634 (mtpp) cc_final: 0.5646 (tmtt) REVERT: s 77 THR cc_start: 0.6313 (p) cc_final: 0.5899 (t) outliers start: 202 outliers final: 124 residues processed: 943 average time/residue: 0.2057 time to fit residues: 323.0843 Evaluate side-chains 897 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 758 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 288 ASP Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 670 GLU Chi-restraints excluded: chain G residue 674 LEU Chi-restraints excluded: chain G residue 710 CYS Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 173 TRP Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 258 ASN Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 124 ASN Chi-restraints excluded: chain P residue 133 GLU Chi-restraints excluded: chain P residue 213 PHE Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 341 GLN Chi-restraints excluded: chain P residue 343 THR Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 150 LYS Chi-restraints excluded: chain R residue 96 ASP Chi-restraints excluded: chain S residue 37 ILE Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 48 HIS Chi-restraints excluded: chain T residue 113 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 113 LYS Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 12 GLU Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 52 ASP Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 127 LYS Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 44 MET Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 59 HIS Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain r residue 107 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 411 optimal weight: 10.0000 chunk 377 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 367 optimal weight: 2.9990 chunk 328 optimal weight: 9.9990 chunk 317 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 chunk 234 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 HIS E 186 GLN ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 ASN ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 238 GLN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 102 GLN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 94 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.111820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.089052 restraints weight = 91232.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.091557 restraints weight = 41069.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.094790 restraints weight = 23843.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.094424 restraints weight = 17763.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.094610 restraints weight = 16260.929| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 34991 Z= 0.167 Angle : 1.004 65.239 47449 Z= 0.369 Chirality : 0.046 0.235 5177 Planarity : 0.005 0.064 6010 Dihedral : 9.280 160.104 4948 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.43 % Allowed : 23.10 % Favored : 72.47 % 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: -0.95 (0.13), residues: 4153 helix: 0.23 (0.12), residues: 1852 sheet: -1.55 (0.26), residues: 379 loop : -1.24 (0.14), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 107 TYR 0.032 0.002 TYR C 63 PHE 0.029 0.002 PHE D 84 TRP 0.030 0.002 TRP E 91 HIS 0.008 0.001 HIS E 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (34950) covalent geometry : angle 0.72619 / 0.36 (47357) SS BOND : bond 0.00518 / 0.25 ( 4) SS BOND : angle 2.99440 / 1.07 ( 8) hydrogen bonds : bond 0.04264 / 2.80 ( 1329) hydrogen bonds : angle 5.19859 / 3.69 ( 3762) metal coordination : bond 0.01977 / 1.33 ( 37) metal coordination : angle 16.48187 / 12.06 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 831 time to evaluate : 1.390 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: A 1 MET cc_start: 0.7299 (tpt) cc_final: 0.6635 (tmm) REVERT: A 23 TRP cc_start: 0.7525 (t60) cc_final: 0.6390 (t60) REVERT: A 54 LYS cc_start: 0.8217 (mttp) cc_final: 0.7790 (mtpp) REVERT: A 87 MET cc_start: 0.8200 (ttp) cc_final: 0.7989 (ttp) REVERT: B 104 MET cc_start: 0.8252 (tmm) cc_final: 0.7223 (tmm) REVERT: B 107 MET cc_start: 0.8967 (ttp) cc_final: 0.8718 (ttm) REVERT: B 216 GLN cc_start: 0.7464 (mm-40) cc_final: 0.6991 (tp40) REVERT: C 71 TYR cc_start: 0.9140 (m-80) cc_final: 0.8790 (m-10) REVERT: C 164 TRP cc_start: 0.8617 (m-10) cc_final: 0.8399 (m-10) REVERT: C 214 GLU cc_start: 0.8479 (tm-30) cc_final: 0.7974 (tm-30) REVERT: C 216 LYS cc_start: 0.9380 (mmmt) cc_final: 0.9148 (mmmt) REVERT: C 234 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8897 (pp) REVERT: D 202 TRP cc_start: 0.8772 (m-10) cc_final: 0.8433 (m-10) REVERT: D 213 PHE cc_start: 0.8652 (m-10) cc_final: 0.8196 (m-10) REVERT: D 261 MET cc_start: 0.9102 (tpp) cc_final: 0.8783 (tpp) REVERT: D 294 ARG cc_start: 0.8517 (mtm180) cc_final: 0.8143 (mtm-85) REVERT: D 371 MET cc_start: 0.8783 (ttp) cc_final: 0.8564 (ttp) REVERT: D 389 TYR cc_start: 0.8364 (m-10) cc_final: 0.8024 (m-10) REVERT: D 454 GLN cc_start: 0.8474 (tp40) cc_final: 0.7897 (tp40) REVERT: E 82 LEU cc_start: 0.9089 (tp) cc_final: 0.8697 (tp) REVERT: E 121 TYR cc_start: 0.8385 (m-10) cc_final: 0.8163 (m-10) REVERT: E 152 GLN cc_start: 0.8495 (mt0) cc_final: 0.8212 (tt0) REVERT: E 184 MET cc_start: 0.6950 (ttp) cc_final: 0.6386 (mtm) REVERT: E 191 TYR cc_start: 0.6639 (OUTLIER) cc_final: 0.5844 (m-80) REVERT: E 222 PHE cc_start: 0.6797 (m-80) cc_final: 0.5744 (m-10) REVERT: E 225 GLU cc_start: 0.4284 (OUTLIER) cc_final: 0.3436 (tm-30) REVERT: F 64 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8089 (mmmt) REVERT: F 115 VAL cc_start: 0.8259 (t) cc_final: 0.7930 (p) REVERT: F 182 ILE cc_start: 0.7294 (pp) cc_final: 0.7064 (pp) REVERT: F 209 GLU cc_start: 0.8914 (tp30) cc_final: 0.8657 (tp30) REVERT: F 372 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: F 455 GLN cc_start: 0.8867 (mp10) cc_final: 0.8624 (mp10) REVERT: G 94 MET cc_start: 0.8726 (ttm) cc_final: 0.8005 (ttm) REVERT: G 136 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6806 (mt-10) REVERT: G 138 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8355 (t0) REVERT: G 223 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.9165 (mt) REVERT: G 284 GLU cc_start: 0.7883 (tt0) cc_final: 0.7624 (tt0) REVERT: G 632 ILE cc_start: 0.7532 (OUTLIER) cc_final: 0.7172 (pp) REVERT: G 659 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8799 (tt) REVERT: H 31 MET cc_start: 0.9417 (mtp) cc_final: 0.8604 (mtp) REVERT: H 47 GLN cc_start: 0.8781 (tp40) cc_final: 0.8557 (tp40) REVERT: H 58 LYS cc_start: 0.8612 (mttp) cc_final: 0.8291 (mmmt) REVERT: H 59 GLU cc_start: 0.8468 (tp30) cc_final: 0.7936 (mm-30) REVERT: H 143 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7726 (mt-10) REVERT: H 172 MET cc_start: 0.7698 (ttp) cc_final: 0.7493 (ppp) REVERT: H 183 MET cc_start: 0.8594 (mmt) cc_final: 0.8051 (mtm) REVERT: H 223 PHE cc_start: 0.8635 (m-80) cc_final: 0.8275 (m-80) REVERT: H 262 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7429 (mt-10) REVERT: H 274 ARG cc_start: 0.9039 (ttt180) cc_final: 0.8371 (ttt180) REVERT: I 94 SER cc_start: 0.9318 (t) cc_final: 0.8784 (m) REVERT: P 174 MET cc_start: 0.7983 (tpt) cc_final: 0.7484 (tpp) REVERT: P 177 SER cc_start: 0.8143 (t) cc_final: 0.7791 (p) REVERT: P 215 ASN cc_start: 0.8852 (m-40) cc_final: 0.7968 (m110) REVERT: P 241 TYR cc_start: 0.8683 (t80) cc_final: 0.8452 (t80) REVERT: P 300 TRP cc_start: 0.6995 (OUTLIER) cc_final: 0.5829 (m-10) REVERT: P 323 HIS cc_start: 0.6888 (t-90) cc_final: 0.6551 (t-90) REVERT: P 350 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.6965 (tt) REVERT: P 351 GLU cc_start: 0.8323 (mp0) cc_final: 0.8088 (mp0) REVERT: Q 85 ASN cc_start: 0.8050 (t0) cc_final: 0.7588 (t0) REVERT: Q 86 ASN cc_start: 0.8364 (t0) cc_final: 0.8097 (t0) REVERT: Q 108 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8063 (mm-30) REVERT: Q 135 ILE cc_start: 0.9306 (pt) cc_final: 0.8889 (mt) REVERT: Q 141 ASN cc_start: 0.8898 (m-40) cc_final: 0.8672 (t0) REVERT: R 80 ASP cc_start: 0.8585 (p0) cc_final: 0.7912 (p0) REVERT: S 50 ASN cc_start: 0.7893 (m110) cc_final: 0.7665 (t0) REVERT: T 132 ASP cc_start: 0.6896 (t0) cc_final: 0.5894 (t0) REVERT: T 137 LYS cc_start: 0.8530 (mtmm) cc_final: 0.8249 (mmtt) REVERT: V 113 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8300 (ttpp) REVERT: W 61 GLN cc_start: 0.8781 (mt0) cc_final: 0.8572 (mp10) REVERT: W 92 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8220 (mm-30) REVERT: W 95 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8145 (mt-10) REVERT: W 99 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8307 (m) REVERT: W 122 LEU cc_start: 0.8950 (tt) cc_final: 0.8625 (tt) REVERT: W 126 TYR cc_start: 0.8918 (m-10) cc_final: 0.8462 (m-80) REVERT: X 47 ARG cc_start: 0.8288 (tpt170) cc_final: 0.7613 (tmt-80) REVERT: Z 72 MET cc_start: 0.8183 (mmt) cc_final: 0.7566 (mtp) REVERT: a 50 ARG cc_start: 0.8607 (ttt90) cc_final: 0.8114 (tpt170) REVERT: b 26 TRP cc_start: 0.8765 (t60) cc_final: 0.8080 (t60) REVERT: b 43 SER cc_start: 0.9074 (p) cc_final: 0.8559 (t) REVERT: b 46 ASN cc_start: 0.8878 (t160) cc_final: 0.8550 (t0) REVERT: q 12 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.7197 (pt0) REVERT: q 68 MET cc_start: 0.6103 (ptm) cc_final: 0.5705 (ptt) REVERT: r 10 LYS cc_start: 0.6641 (mtpp) cc_final: 0.5714 (tmtt) REVERT: s 77 THR cc_start: 0.6091 (p) cc_final: 0.5687 (t) outliers start: 162 outliers final: 107 residues processed: 933 average time/residue: 0.2098 time to fit residues: 325.1137 Evaluate side-chains 896 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 775 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 670 GLU Chi-restraints excluded: chain G residue 674 LEU Chi-restraints excluded: chain G residue 710 CYS Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 173 TRP Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 172 ASN Chi-restraints excluded: chain P residue 133 GLU Chi-restraints excluded: chain P residue 213 PHE Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 300 TRP Chi-restraints excluded: chain P residue 338 LEU Chi-restraints excluded: chain P residue 343 THR Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain Q residue 150 LYS Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain T residue 113 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 113 LYS Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 12 GLU Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 52 ASP Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 127 LYS Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain Z residue 112 HIS Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 12 GLN Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 59 HIS Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain s residue 94 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 88 optimal weight: 1.9990 chunk 276 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 256 optimal weight: 0.0570 chunk 341 optimal weight: 0.9980 chunk 327 optimal weight: 9.9990 chunk 202 optimal weight: 0.9980 chunk 313 optimal weight: 10.0000 overall best weight: 1.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 HIS ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 59 HIS r 110 GLN ** s 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 94 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.111658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.088676 restraints weight = 91684.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.091486 restraints weight = 40749.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.094172 restraints weight = 23437.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.093992 restraints weight = 18171.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.094200 restraints weight = 16751.384| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.6465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 34991 Z= 0.176 Angle : 0.997 65.001 47449 Z= 0.368 Chirality : 0.045 0.287 5177 Planarity : 0.005 0.072 6010 Dihedral : 9.139 161.150 4948 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.63 % Allowed : 23.43 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.13), residues: 4153 helix: 0.31 (0.12), residues: 1857 sheet: -1.61 (0.26), residues: 382 loop : -1.16 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 417 TYR 0.030 0.002 TYR a 43 PHE 0.027 0.002 PHE G 462 TRP 0.029 0.002 TRP b 80 HIS 0.008 0.001 HIS F 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (34950) covalent geometry : angle 0.72611 / 0.36 (47357) SS BOND : bond 0.00506 / 0.25 ( 4) SS BOND : angle 1.90018 / 0.67 ( 8) hydrogen bonds : bond 0.04140 / 2.73 ( 1329) hydrogen bonds : angle 5.17936 / 3.68 ( 3762) metal coordination : bond 0.02062 / 1.33 ( 37) metal coordination : angle 16.25901 / 11.94 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 804 time to evaluate : 1.368 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: A 1 MET cc_start: 0.7167 (tpt) cc_final: 0.6519 (tmm) REVERT: A 23 TRP cc_start: 0.7467 (t60) cc_final: 0.6306 (t60) REVERT: A 54 LYS cc_start: 0.8258 (mttp) cc_final: 0.7750 (mtpp) REVERT: B 216 GLN cc_start: 0.7468 (mm-40) cc_final: 0.7049 (mm-40) REVERT: C 49 ARG cc_start: 0.4673 (ptt-90) cc_final: 0.4085 (ptt90) REVERT: C 71 TYR cc_start: 0.9171 (m-80) cc_final: 0.8774 (m-10) REVERT: C 189 ASP cc_start: 0.8021 (t70) cc_final: 0.7779 (t70) REVERT: C 214 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8018 (tm-30) REVERT: C 216 LYS cc_start: 0.9343 (mmmt) cc_final: 0.9070 (mmmt) REVERT: C 234 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8826 (pp) REVERT: D 202 TRP cc_start: 0.8754 (m-10) cc_final: 0.8433 (m-10) REVERT: D 213 PHE cc_start: 0.8636 (m-10) cc_final: 0.8117 (m-10) REVERT: D 294 ARG cc_start: 0.8517 (mtm180) cc_final: 0.8161 (mtm-85) REVERT: D 389 TYR cc_start: 0.8379 (m-10) cc_final: 0.8037 (m-10) REVERT: D 411 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8610 (tp) REVERT: E 82 LEU cc_start: 0.9089 (tp) cc_final: 0.8760 (tp) REVERT: E 184 MET cc_start: 0.6845 (ttp) cc_final: 0.6319 (mtm) REVERT: E 191 TYR cc_start: 0.6413 (OUTLIER) cc_final: 0.5712 (m-80) REVERT: E 222 PHE cc_start: 0.6761 (m-80) cc_final: 0.5763 (m-10) REVERT: E 225 GLU cc_start: 0.4299 (OUTLIER) cc_final: 0.3460 (tm-30) REVERT: F 64 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8071 (mmmt) REVERT: F 209 GLU cc_start: 0.8916 (tp30) cc_final: 0.8670 (tp30) REVERT: F 214 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8671 (mm-30) REVERT: F 289 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.5735 (tp30) REVERT: F 292 MET cc_start: 0.3726 (ppp) cc_final: 0.3230 (ppp) REVERT: F 455 GLN cc_start: 0.8797 (mp10) cc_final: 0.8591 (mp10) REVERT: G 136 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6745 (mt-10) REVERT: G 138 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8359 (t0) REVERT: G 223 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9158 (mt) REVERT: G 632 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7207 (pp) REVERT: G 659 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8779 (tt) REVERT: H 31 MET cc_start: 0.9413 (mtp) cc_final: 0.8643 (mtp) REVERT: H 47 GLN cc_start: 0.8835 (tp40) cc_final: 0.8584 (tp40) REVERT: H 59 GLU cc_start: 0.8465 (tp30) cc_final: 0.8006 (mm-30) REVERT: H 143 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7708 (mt-10) REVERT: H 183 MET cc_start: 0.8710 (mmt) cc_final: 0.8130 (mtm) REVERT: H 223 PHE cc_start: 0.8594 (m-80) cc_final: 0.8229 (m-80) REVERT: H 224 PHE cc_start: 0.8072 (t80) cc_final: 0.7754 (t80) REVERT: I 94 SER cc_start: 0.9305 (t) cc_final: 0.8734 (m) REVERT: P 174 MET cc_start: 0.8107 (tpt) cc_final: 0.7503 (tpp) REVERT: P 177 SER cc_start: 0.8147 (t) cc_final: 0.7790 (p) REVERT: P 215 ASN cc_start: 0.8840 (m-40) cc_final: 0.7958 (m110) REVERT: P 300 TRP cc_start: 0.6946 (m100) cc_final: 0.5726 (m-10) REVERT: P 350 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.6945 (tt) REVERT: P 351 GLU cc_start: 0.8346 (mp0) cc_final: 0.8089 (mp0) REVERT: Q 85 ASN cc_start: 0.8144 (t0) cc_final: 0.7589 (t0) REVERT: Q 86 ASN cc_start: 0.8377 (t0) cc_final: 0.8021 (t0) REVERT: Q 108 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8052 (mm-30) REVERT: Q 135 ILE cc_start: 0.9314 (pt) cc_final: 0.8879 (mt) REVERT: Q 141 ASN cc_start: 0.8890 (m-40) cc_final: 0.8654 (t0) REVERT: R 80 ASP cc_start: 0.8575 (p0) cc_final: 0.7909 (p0) REVERT: R 96 ASP cc_start: 0.6588 (m-30) cc_final: 0.6376 (m-30) REVERT: T 77 ASP cc_start: 0.7970 (p0) cc_final: 0.6993 (t0) REVERT: T 80 LYS cc_start: 0.8331 (mmmt) cc_final: 0.8042 (mmmt) REVERT: T 111 ASP cc_start: 0.8706 (t70) cc_final: 0.8336 (p0) REVERT: T 114 ASP cc_start: 0.8455 (m-30) cc_final: 0.7986 (m-30) REVERT: T 137 LYS cc_start: 0.8710 (mtmm) cc_final: 0.8130 (mmtt) REVERT: V 113 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8326 (ttpp) REVERT: W 42 TRP cc_start: 0.9501 (m100) cc_final: 0.8882 (m100) REVERT: W 92 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8308 (mm-30) REVERT: W 95 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8300 (mt-10) REVERT: W 99 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8287 (m) REVERT: W 122 LEU cc_start: 0.8967 (tt) cc_final: 0.8693 (tt) REVERT: W 126 TYR cc_start: 0.8945 (m-10) cc_final: 0.8575 (m-80) REVERT: X 47 ARG cc_start: 0.8251 (tpt170) cc_final: 0.7620 (tmt-80) REVERT: Z 72 MET cc_start: 0.8210 (mmt) cc_final: 0.7596 (mtp) REVERT: a 25 TYR cc_start: 0.8173 (m-80) cc_final: 0.7792 (m-80) REVERT: a 54 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8901 (mt) REVERT: b 26 TRP cc_start: 0.8766 (t60) cc_final: 0.8039 (t60) REVERT: b 32 MET cc_start: 0.8269 (ttp) cc_final: 0.8063 (ttp) REVERT: b 41 TYR cc_start: 0.7765 (m-80) cc_final: 0.7420 (m-10) REVERT: b 43 SER cc_start: 0.9023 (p) cc_final: 0.8491 (t) REVERT: b 46 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8552 (t0) REVERT: q 12 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7287 (pt0) REVERT: r 10 LYS cc_start: 0.6738 (mtpp) cc_final: 0.5780 (tmtt) REVERT: s 77 THR cc_start: 0.6071 (p) cc_final: 0.5807 (t) outliers start: 169 outliers final: 117 residues processed: 904 average time/residue: 0.1941 time to fit residues: 292.2829 Evaluate side-chains 903 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 770 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 670 GLU Chi-restraints excluded: chain G residue 674 LEU Chi-restraints excluded: chain G residue 710 CYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 173 TRP Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 305 ILE Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain P residue 133 GLU Chi-restraints excluded: chain P residue 213 PHE Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 338 LEU Chi-restraints excluded: chain P residue 341 GLN Chi-restraints excluded: chain P residue 343 THR Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain Q residue 150 LYS Chi-restraints excluded: chain R residue 36 GLN Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 48 HIS Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain T residue 113 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 41 HIS Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 113 LYS Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 12 GLU Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 52 ASP Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 127 LYS Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 44 MET Chi-restraints excluded: chain b residue 46 ASN Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain q residue 11 VAL Chi-restraints excluded: chain q residue 12 GLN Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 59 HIS Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 138 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 148 optimal weight: 5.9990 chunk 404 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 179 optimal weight: 0.7980 chunk 373 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 157 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 384 ASN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN I 172 ASN ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 59 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.112503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.089752 restraints weight = 91264.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.092665 restraints weight = 42100.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.095403 restraints weight = 23433.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.095206 restraints weight = 17398.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.095313 restraints weight = 16182.093| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.6648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 34991 Z= 0.156 Angle : 0.989 64.433 47449 Z= 0.367 Chirality : 0.045 0.298 5177 Planarity : 0.005 0.062 6010 Dihedral : 9.044 162.328 4948 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.60 % Allowed : 24.27 % Favored : 71.13 % 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: -0.70 (0.13), residues: 4153 helix: 0.42 (0.12), residues: 1840 sheet: -1.45 (0.27), residues: 377 loop : -1.08 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 153 TYR 0.030 0.002 TYR q 124 PHE 0.024 0.002 PHE G 462 TRP 0.037 0.002 TRP b 80 HIS 0.009 0.001 HIS P 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (34950) covalent geometry : angle 0.73096 / 0.36 (47357) SS BOND : bond 0.00288 / 0.15 ( 4) SS BOND : angle 1.51043 / 0.54 ( 8) hydrogen bonds : bond 0.04019 / 2.64 ( 1329) hydrogen bonds : angle 5.13406 / 3.64 ( 3762) metal coordination : bond 0.01866 / 1.26 ( 37) metal coordination : angle 15.85111 / 11.74 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 822 time to evaluate : 0.864 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: A 1 MET cc_start: 0.7203 (tpt) cc_final: 0.6574 (tmm) REVERT: A 23 TRP cc_start: 0.7467 (t60) cc_final: 0.6304 (t60) REVERT: A 54 LYS cc_start: 0.8264 (mttp) cc_final: 0.7863 (mtpp) REVERT: B 112 TYR cc_start: 0.7022 (OUTLIER) cc_final: 0.6574 (m-80) REVERT: B 216 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7225 (mm-40) REVERT: C 71 TYR cc_start: 0.9143 (m-80) cc_final: 0.8719 (m-10) REVERT: C 186 ILE cc_start: 0.9180 (tp) cc_final: 0.8653 (tp) REVERT: C 214 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8119 (tm-30) REVERT: C 216 LYS cc_start: 0.9337 (mmmt) cc_final: 0.9097 (mmmt) REVERT: C 234 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8765 (pp) REVERT: D 184 ILE cc_start: 0.8975 (mm) cc_final: 0.8774 (mm) REVERT: D 202 TRP cc_start: 0.8701 (m-10) cc_final: 0.8335 (m-10) REVERT: D 213 PHE cc_start: 0.8572 (m-10) cc_final: 0.7962 (m-10) REVERT: D 261 MET cc_start: 0.9024 (tpp) cc_final: 0.8705 (tpp) REVERT: D 294 ARG cc_start: 0.8464 (mtm180) cc_final: 0.7952 (mtm-85) REVERT: D 389 TYR cc_start: 0.8381 (m-10) cc_final: 0.8064 (m-10) REVERT: D 458 PHE cc_start: 0.8203 (m-80) cc_final: 0.7852 (m-80) REVERT: E 60 LYS cc_start: 0.9380 (mtmt) cc_final: 0.9118 (mmtt) REVERT: E 152 GLN cc_start: 0.8525 (mt0) cc_final: 0.8196 (tt0) REVERT: E 184 MET cc_start: 0.6647 (ttp) cc_final: 0.6346 (mtm) REVERT: E 191 TYR cc_start: 0.6361 (OUTLIER) cc_final: 0.6124 (m-80) REVERT: E 222 PHE cc_start: 0.6789 (m-80) cc_final: 0.5986 (m-10) REVERT: E 225 GLU cc_start: 0.4260 (OUTLIER) cc_final: 0.2319 (tt0) REVERT: F 191 TYR cc_start: 0.6300 (t80) cc_final: 0.6069 (t80) REVERT: F 192 ASP cc_start: 0.7323 (p0) cc_final: 0.6866 (t0) REVERT: F 209 GLU cc_start: 0.8905 (tp30) cc_final: 0.8644 (tp30) REVERT: F 214 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8714 (mm-30) REVERT: F 289 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.5632 (tp30) REVERT: F 292 MET cc_start: 0.3651 (ppp) cc_final: 0.3144 (ppp) REVERT: F 344 GLN cc_start: 0.8697 (pp30) cc_final: 0.8475 (pp30) REVERT: F 455 GLN cc_start: 0.8787 (mp10) cc_final: 0.8580 (mp10) REVERT: G 138 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8297 (t0) REVERT: G 255 ASP cc_start: 0.8330 (t0) cc_final: 0.8094 (t0) REVERT: G 632 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7380 (pp) REVERT: G 659 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8734 (tt) REVERT: H 31 MET cc_start: 0.9383 (mtp) cc_final: 0.8615 (mtp) REVERT: H 47 GLN cc_start: 0.8826 (tp40) cc_final: 0.8532 (tp40) REVERT: H 59 GLU cc_start: 0.8401 (tp30) cc_final: 0.7875 (mm-30) REVERT: H 143 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7675 (mt-10) REVERT: H 183 MET cc_start: 0.8705 (mmt) cc_final: 0.8179 (mtm) REVERT: H 195 ARG cc_start: 0.9076 (mmm160) cc_final: 0.8175 (tpt90) REVERT: H 222 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9310 (tp) REVERT: H 223 PHE cc_start: 0.8561 (m-80) cc_final: 0.8214 (m-80) REVERT: H 224 PHE cc_start: 0.7990 (t80) cc_final: 0.7681 (t80) REVERT: I 50 MET cc_start: 0.7075 (mmp) cc_final: 0.5544 (ptt) REVERT: I 72 MET cc_start: 0.8807 (tpp) cc_final: 0.8439 (tpp) REVERT: I 94 SER cc_start: 0.9253 (t) cc_final: 0.8710 (m) REVERT: I 195 ASP cc_start: 0.8773 (t0) cc_final: 0.8557 (t0) REVERT: P 174 MET cc_start: 0.8055 (tpt) cc_final: 0.7493 (tpp) REVERT: P 177 SER cc_start: 0.8103 (t) cc_final: 0.7703 (p) REVERT: P 215 ASN cc_start: 0.8863 (m-40) cc_final: 0.7948 (m110) REVERT: P 300 TRP cc_start: 0.6896 (m100) cc_final: 0.5717 (m-10) REVERT: P 350 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.6914 (tt) REVERT: P 351 GLU cc_start: 0.8350 (mp0) cc_final: 0.8093 (mp0) REVERT: Q 85 ASN cc_start: 0.8136 (t0) cc_final: 0.7823 (t0) REVERT: Q 86 ASN cc_start: 0.8355 (t0) cc_final: 0.7953 (t0) REVERT: Q 108 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8074 (mm-30) REVERT: Q 135 ILE cc_start: 0.9362 (pt) cc_final: 0.8921 (mt) REVERT: R 80 ASP cc_start: 0.8554 (p0) cc_final: 0.7650 (p0) REVERT: T 111 ASP cc_start: 0.8635 (t70) cc_final: 0.8262 (p0) REVERT: T 114 ASP cc_start: 0.8474 (m-30) cc_final: 0.7275 (m-30) REVERT: T 117 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7685 (mt-10) REVERT: T 137 LYS cc_start: 0.8747 (mtmm) cc_final: 0.8214 (mmtt) REVERT: V 113 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8371 (ttpp) REVERT: W 71 MET cc_start: 0.8898 (mmm) cc_final: 0.8562 (mmm) REVERT: W 92 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8340 (mm-30) REVERT: W 95 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8247 (mt-10) REVERT: W 99 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8295 (m) REVERT: W 122 LEU cc_start: 0.8967 (tt) cc_final: 0.8700 (tt) REVERT: W 126 TYR cc_start: 0.8932 (m-10) cc_final: 0.8553 (m-10) REVERT: X 47 ARG cc_start: 0.8256 (tpt170) cc_final: 0.7735 (tmt-80) REVERT: X 124 GLN cc_start: 0.7679 (mt0) cc_final: 0.7115 (pp30) REVERT: Z 72 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7669 (mtp) REVERT: Z 79 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8179 (mptt) REVERT: a 25 TYR cc_start: 0.8100 (m-80) cc_final: 0.7718 (m-80) REVERT: a 48 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.7460 (mpp) REVERT: b 26 TRP cc_start: 0.8763 (t60) cc_final: 0.8174 (t60) REVERT: b 43 SER cc_start: 0.8893 (p) cc_final: 0.8288 (t) REVERT: b 44 MET cc_start: 0.7801 (mtt) cc_final: 0.7218 (ptm) REVERT: b 46 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8531 (t0) REVERT: q 12 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7319 (tm-30) REVERT: q 68 MET cc_start: 0.5981 (ptm) cc_final: 0.5671 (ptt) REVERT: s 77 THR cc_start: 0.5963 (p) cc_final: 0.5583 (t) outliers start: 168 outliers final: 114 residues processed: 914 average time/residue: 0.1979 time to fit residues: 299.1541 Evaluate side-chains 905 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 775 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 670 GLU Chi-restraints excluded: chain G residue 674 LEU Chi-restraints excluded: chain G residue 710 CYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 173 TRP Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 287 HIS Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 172 ASN Chi-restraints excluded: chain P residue 206 ILE Chi-restraints excluded: chain P residue 213 PHE Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 338 LEU Chi-restraints excluded: chain P residue 341 GLN Chi-restraints excluded: chain P residue 343 THR Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain R residue 36 GLN Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain T residue 113 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 41 HIS Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 113 LYS Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 77 HIS Chi-restraints excluded: chain X residue 127 LYS Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain Z residue 72 MET Chi-restraints excluded: chain Z residue 84 LEU Chi-restraints excluded: chain Z residue 112 HIS Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 48 MET Chi-restraints excluded: chain b residue 46 ASN Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 11 VAL Chi-restraints excluded: chain q residue 12 GLN Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 59 HIS Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 138 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 262 optimal weight: 0.9990 chunk 395 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 35 optimal weight: 0.4980 chunk 110 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 167 optimal weight: 0.3980 chunk 100 optimal weight: 9.9990 chunk 303 optimal weight: 0.0970 chunk 305 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS D 112 HIS ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN I 172 ASN ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 166 HIS S 80 ASN ** T 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 31 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.113987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.091321 restraints weight = 91057.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.094644 restraints weight = 40659.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.096970 restraints weight = 22266.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.096715 restraints weight = 17378.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.096974 restraints weight = 16545.160| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.6833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 34991 Z= 0.142 Angle : 0.992 63.220 47449 Z= 0.376 Chirality : 0.045 0.250 5177 Planarity : 0.005 0.065 6010 Dihedral : 8.910 162.324 4948 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.50 % Allowed : 25.70 % Favored : 70.80 % 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: -0.71 (0.13), residues: 4153 helix: 0.42 (0.12), residues: 1831 sheet: -1.38 (0.27), residues: 381 loop : -1.09 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 369 TYR 0.037 0.002 TYR q 124 PHE 0.024 0.002 PHE a 3 TRP 0.038 0.002 TRP b 80 HIS 0.014 0.001 HIS P 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (34950) covalent geometry : angle 0.75482 / 0.37 (47357) SS BOND : bond 0.00249 / 0.13 ( 4) SS BOND : angle 1.34273 / 0.48 ( 8) hydrogen bonds : bond 0.03947 / 2.62 ( 1329) hydrogen bonds : angle 5.11186 / 3.61 ( 3762) metal coordination : bond 0.01508 / 1.02 ( 37) metal coordination : angle 15.32339 / 11.41 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 844 time to evaluate : 1.334 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: A 1 MET cc_start: 0.7214 (tpt) cc_final: 0.6579 (tmm) REVERT: A 23 TRP cc_start: 0.7438 (t60) cc_final: 0.6241 (t60) REVERT: A 54 LYS cc_start: 0.8260 (mttp) cc_final: 0.7743 (mtpp) REVERT: A 77 TRP cc_start: 0.8250 (m-10) cc_final: 0.7267 (t60) REVERT: A 105 GLU cc_start: 0.8885 (tt0) cc_final: 0.8622 (tm-30) REVERT: B 106 HIS cc_start: 0.8274 (m90) cc_final: 0.7993 (m90) REVERT: B 112 TYR cc_start: 0.7112 (OUTLIER) cc_final: 0.6431 (m-80) REVERT: B 216 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7199 (mm-40) REVERT: C 71 TYR cc_start: 0.9120 (m-80) cc_final: 0.8719 (m-10) REVERT: C 164 TRP cc_start: 0.8633 (m-10) cc_final: 0.8351 (m-10) REVERT: C 216 LYS cc_start: 0.9334 (mmmt) cc_final: 0.9070 (mmmt) REVERT: C 234 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8696 (pp) REVERT: D 184 ILE cc_start: 0.8926 (mm) cc_final: 0.8705 (mm) REVERT: D 202 TRP cc_start: 0.8657 (m-10) cc_final: 0.8314 (m-10) REVERT: D 213 PHE cc_start: 0.8443 (m-10) cc_final: 0.8017 (m-10) REVERT: D 261 MET cc_start: 0.9005 (tpp) cc_final: 0.8707 (tpp) REVERT: D 389 TYR cc_start: 0.8328 (m-10) cc_final: 0.7958 (m-10) REVERT: E 60 LYS cc_start: 0.9383 (mtmt) cc_final: 0.9141 (mmtt) REVERT: E 122 ASN cc_start: 0.8574 (m-40) cc_final: 0.7985 (p0) REVERT: E 184 MET cc_start: 0.6539 (ttp) cc_final: 0.6298 (mtm) REVERT: E 191 TYR cc_start: 0.6691 (OUTLIER) cc_final: 0.6087 (m-80) REVERT: E 222 PHE cc_start: 0.6666 (m-80) cc_final: 0.6281 (m-10) REVERT: E 225 GLU cc_start: 0.4167 (OUTLIER) cc_final: 0.1977 (tt0) REVERT: F 170 GLN cc_start: 0.9362 (mm110) cc_final: 0.9078 (mm-40) REVERT: F 192 ASP cc_start: 0.7143 (p0) cc_final: 0.6857 (t0) REVERT: F 209 GLU cc_start: 0.8888 (tp30) cc_final: 0.8626 (tp30) REVERT: F 214 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8692 (mm-30) REVERT: F 289 GLU cc_start: 0.6382 (OUTLIER) cc_final: 0.6178 (pt0) REVERT: F 292 MET cc_start: 0.3575 (ppp) cc_final: 0.3048 (ppp) REVERT: F 455 GLN cc_start: 0.8772 (mp10) cc_final: 0.8561 (mp10) REVERT: G 138 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8231 (t0) REVERT: G 223 ILE cc_start: 0.9302 (mp) cc_final: 0.9100 (mt) REVERT: G 255 ASP cc_start: 0.8319 (t0) cc_final: 0.8097 (t0) REVERT: G 632 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7388 (pp) REVERT: G 659 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8742 (tt) REVERT: H 47 GLN cc_start: 0.8796 (tp40) cc_final: 0.8532 (tp40) REVERT: H 59 GLU cc_start: 0.8201 (tp30) cc_final: 0.7791 (mm-30) REVERT: H 143 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7604 (mt-10) REVERT: H 183 MET cc_start: 0.8667 (mmt) cc_final: 0.8224 (mtm) REVERT: H 195 ARG cc_start: 0.8980 (mmm160) cc_final: 0.8097 (tpt90) REVERT: H 222 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9275 (tp) REVERT: H 223 PHE cc_start: 0.8515 (m-80) cc_final: 0.8187 (m-80) REVERT: H 224 PHE cc_start: 0.7953 (t80) cc_final: 0.7667 (t80) REVERT: I 50 MET cc_start: 0.7153 (mmp) cc_final: 0.5498 (ptt) REVERT: I 62 MET cc_start: 0.8015 (ttp) cc_final: 0.7716 (ptp) REVERT: I 72 MET cc_start: 0.8766 (tpp) cc_final: 0.8386 (tpp) REVERT: I 94 SER cc_start: 0.9243 (t) cc_final: 0.8661 (m) REVERT: I 160 GLU cc_start: 0.7779 (pt0) cc_final: 0.7519 (pt0) REVERT: I 195 ASP cc_start: 0.8689 (t0) cc_final: 0.8466 (t0) REVERT: P 174 MET cc_start: 0.8073 (tpt) cc_final: 0.7443 (tpp) REVERT: P 177 SER cc_start: 0.8124 (t) cc_final: 0.7753 (p) REVERT: P 215 ASN cc_start: 0.8823 (m-40) cc_final: 0.7899 (m110) REVERT: P 300 TRP cc_start: 0.6921 (m100) cc_final: 0.5775 (m-10) REVERT: P 350 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.6864 (tt) REVERT: P 351 GLU cc_start: 0.8330 (mp0) cc_final: 0.8054 (mp0) REVERT: Q 85 ASN cc_start: 0.8099 (t0) cc_final: 0.7836 (t0) REVERT: Q 86 ASN cc_start: 0.8280 (t0) cc_final: 0.7929 (t0) REVERT: Q 108 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8051 (mm-30) REVERT: Q 135 ILE cc_start: 0.9355 (pt) cc_final: 0.8963 (mt) REVERT: R 80 ASP cc_start: 0.8547 (p0) cc_final: 0.7625 (p0) REVERT: R 96 ASP cc_start: 0.6830 (m-30) cc_final: 0.6608 (m-30) REVERT: T 111 ASP cc_start: 0.8662 (t70) cc_final: 0.8341 (p0) REVERT: T 114 ASP cc_start: 0.8472 (m-30) cc_final: 0.7293 (m-30) REVERT: T 117 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7735 (mt-10) REVERT: T 137 LYS cc_start: 0.8731 (mtmm) cc_final: 0.8223 (mmtt) REVERT: W 42 TRP cc_start: 0.9495 (m100) cc_final: 0.8866 (m100) REVERT: W 61 GLN cc_start: 0.8821 (mt0) cc_final: 0.8600 (mt0) REVERT: W 71 MET cc_start: 0.8943 (mmm) cc_final: 0.8650 (mmm) REVERT: W 92 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8341 (mm-30) REVERT: W 95 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8184 (mt-10) REVERT: W 99 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8148 (m) REVERT: W 126 TYR cc_start: 0.8904 (m-10) cc_final: 0.8637 (m-80) REVERT: X 47 ARG cc_start: 0.8254 (tpt170) cc_final: 0.7646 (tmt-80) REVERT: Z 72 MET cc_start: 0.8209 (mmt) cc_final: 0.7652 (mtp) REVERT: Z 79 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8027 (mmtm) REVERT: a 25 TYR cc_start: 0.8067 (m-80) cc_final: 0.7617 (m-80) REVERT: a 46 TYR cc_start: 0.8556 (t80) cc_final: 0.8190 (t80) REVERT: a 48 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.7446 (mpp) REVERT: b 26 TRP cc_start: 0.8757 (t60) cc_final: 0.8256 (t60) REVERT: b 41 TYR cc_start: 0.7562 (m-80) cc_final: 0.7306 (m-10) REVERT: b 43 SER cc_start: 0.8848 (p) cc_final: 0.8428 (t) REVERT: b 46 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8466 (t0) REVERT: b 82 LYS cc_start: 0.8793 (pttm) cc_final: 0.8526 (ptpp) REVERT: s 77 THR cc_start: 0.6101 (p) cc_final: 0.5739 (t) outliers start: 128 outliers final: 88 residues processed: 906 average time/residue: 0.1914 time to fit residues: 286.4117 Evaluate side-chains 900 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 799 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 528 LEU Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 670 GLU Chi-restraints excluded: chain G residue 674 LEU Chi-restraints excluded: chain G residue 710 CYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 173 TRP Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 287 HIS Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain P residue 206 ILE Chi-restraints excluded: chain P residue 213 PHE Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 338 LEU Chi-restraints excluded: chain P residue 343 THR Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain T residue 113 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain V residue 41 HIS Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 85 LEU Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain Z residue 50 MET Chi-restraints excluded: chain Z residue 84 LEU Chi-restraints excluded: chain Z residue 112 HIS Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 48 MET Chi-restraints excluded: chain b residue 46 ASN Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 11 VAL Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 59 HIS Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 18 optimal weight: 7.9990 chunk 388 optimal weight: 9.9990 chunk 315 optimal weight: 0.9990 chunk 184 optimal weight: 0.0010 chunk 394 optimal weight: 0.7980 chunk 284 optimal weight: 8.9990 chunk 265 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 304 optimal weight: 9.9990 chunk 319 optimal weight: 7.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 ASN ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 76 GLN q 59 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.110270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.085830 restraints weight = 89552.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.088892 restraints weight = 40800.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.090791 restraints weight = 25263.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.091975 restraints weight = 19036.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.092673 restraints weight = 16082.510| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.6942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 34991 Z= 0.165 Angle : 1.000 63.197 47449 Z= 0.379 Chirality : 0.046 0.272 5177 Planarity : 0.005 0.059 6010 Dihedral : 8.834 163.882 4948 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.28 % Allowed : 26.38 % Favored : 70.33 % 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: -0.67 (0.13), residues: 4153 helix: 0.44 (0.12), residues: 1833 sheet: -1.22 (0.27), residues: 383 loop : -1.08 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 153 TYR 0.040 0.002 TYR q 124 PHE 0.038 0.002 PHE G 462 TRP 0.038 0.002 TRP B 221 HIS 0.014 0.001 HIS P 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (34950) covalent geometry : angle 0.76261 / 0.38 (47357) SS BOND : bond 0.00241 / 0.12 ( 4) SS BOND : angle 1.88999 / 0.68 ( 8) hydrogen bonds : bond 0.03980 / 2.63 ( 1329) hydrogen bonds : angle 5.12859 / 3.64 ( 3762) metal coordination : bond 0.01771 / 1.14 ( 37) metal coordination : angle 15.39564 / 11.36 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 828 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7281 (tpt) cc_final: 0.6626 (tmm) REVERT: A 23 TRP cc_start: 0.7411 (t60) cc_final: 0.6242 (t60) REVERT: A 54 LYS cc_start: 0.8325 (mttp) cc_final: 0.7826 (mtpp) REVERT: A 77 TRP cc_start: 0.8210 (m-10) cc_final: 0.7138 (t60) REVERT: A 105 GLU cc_start: 0.8925 (tt0) cc_final: 0.8642 (tm-30) REVERT: B 106 HIS cc_start: 0.8319 (m90) cc_final: 0.8078 (m90) REVERT: B 112 TYR cc_start: 0.7151 (OUTLIER) cc_final: 0.6263 (m-80) REVERT: B 216 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7177 (mm-40) REVERT: C 71 TYR cc_start: 0.9168 (m-80) cc_final: 0.8721 (m-10) REVERT: C 234 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8719 (pp) REVERT: D 184 ILE cc_start: 0.8937 (mm) cc_final: 0.8714 (mm) REVERT: D 202 TRP cc_start: 0.8700 (m-10) cc_final: 0.8326 (m-10) REVERT: D 213 PHE cc_start: 0.8365 (m-10) cc_final: 0.7971 (m-10) REVERT: D 261 MET cc_start: 0.8960 (tpp) cc_final: 0.8667 (tpp) REVERT: D 389 TYR cc_start: 0.8360 (m-10) cc_final: 0.7997 (m-10) REVERT: E 60 LYS cc_start: 0.9389 (mtmt) cc_final: 0.9134 (mmtt) REVERT: E 122 ASN cc_start: 0.8625 (m-40) cc_final: 0.8034 (p0) REVERT: E 152 GLN cc_start: 0.8528 (mt0) cc_final: 0.8187 (tt0) REVERT: E 184 MET cc_start: 0.6587 (ttp) cc_final: 0.6336 (mtm) REVERT: E 191 TYR cc_start: 0.6683 (OUTLIER) cc_final: 0.6060 (m-80) REVERT: E 222 PHE cc_start: 0.6719 (m-80) cc_final: 0.6103 (m-10) REVERT: E 225 GLU cc_start: 0.4174 (OUTLIER) cc_final: 0.3810 (tm-30) REVERT: F 170 GLN cc_start: 0.9373 (mm110) cc_final: 0.9068 (mm-40) REVERT: F 192 ASP cc_start: 0.7302 (p0) cc_final: 0.6840 (t0) REVERT: F 209 GLU cc_start: 0.8940 (tp30) cc_final: 0.8702 (tp30) REVERT: F 289 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.6150 (pt0) REVERT: F 292 MET cc_start: 0.3514 (ppp) cc_final: 0.3004 (ppp) REVERT: G 136 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6506 (mt-10) REVERT: G 138 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8248 (t0) REVERT: G 223 ILE cc_start: 0.9351 (mp) cc_final: 0.9119 (mt) REVERT: G 255 ASP cc_start: 0.8295 (t0) cc_final: 0.8038 (t0) REVERT: G 632 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7427 (pp) REVERT: G 659 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8677 (tt) REVERT: H 33 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8746 (mp) REVERT: H 47 GLN cc_start: 0.8813 (tp40) cc_final: 0.8553 (tp40) REVERT: H 59 GLU cc_start: 0.8293 (tp30) cc_final: 0.7863 (tp30) REVERT: H 143 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7631 (mt-10) REVERT: H 172 MET cc_start: 0.7366 (tmm) cc_final: 0.7102 (ppp) REVERT: H 183 MET cc_start: 0.8609 (mmt) cc_final: 0.8197 (mtm) REVERT: H 214 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8208 (mt-10) REVERT: H 222 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9302 (tp) REVERT: H 223 PHE cc_start: 0.8477 (m-80) cc_final: 0.8157 (m-80) REVERT: H 224 PHE cc_start: 0.7983 (t80) cc_final: 0.7692 (t80) REVERT: H 258 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.7568 (t0) REVERT: I 50 MET cc_start: 0.7087 (mmp) cc_final: 0.5405 (ptt) REVERT: I 55 ASP cc_start: 0.8516 (p0) cc_final: 0.8015 (p0) REVERT: I 62 MET cc_start: 0.8077 (ttp) cc_final: 0.7720 (ptp) REVERT: I 72 MET cc_start: 0.8816 (tpp) cc_final: 0.8451 (tpp) REVERT: I 94 SER cc_start: 0.9246 (t) cc_final: 0.8681 (m) REVERT: I 160 GLU cc_start: 0.7920 (pt0) cc_final: 0.7661 (pt0) REVERT: I 195 ASP cc_start: 0.8567 (t0) cc_final: 0.8336 (t0) REVERT: P 174 MET cc_start: 0.8121 (tpt) cc_final: 0.7481 (tpp) REVERT: P 177 SER cc_start: 0.8081 (t) cc_final: 0.7718 (p) REVERT: P 215 ASN cc_start: 0.8862 (m-40) cc_final: 0.7925 (m110) REVERT: P 300 TRP cc_start: 0.6919 (m100) cc_final: 0.5763 (m-10) REVERT: P 350 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.6900 (tt) REVERT: P 351 GLU cc_start: 0.8318 (mp0) cc_final: 0.8031 (mp0) REVERT: Q 86 ASN cc_start: 0.8315 (t0) cc_final: 0.7948 (t0) REVERT: Q 108 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8090 (mm-30) REVERT: Q 135 ILE cc_start: 0.9359 (pt) cc_final: 0.8962 (mt) REVERT: R 80 ASP cc_start: 0.8451 (p0) cc_final: 0.7567 (p0) REVERT: T 111 ASP cc_start: 0.8577 (t70) cc_final: 0.8355 (p0) REVERT: T 114 ASP cc_start: 0.8521 (m-30) cc_final: 0.7264 (m-30) REVERT: T 117 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7741 (mt-10) REVERT: T 137 LYS cc_start: 0.8709 (mtmm) cc_final: 0.8189 (mmtt) REVERT: W 33 ARG cc_start: 0.8640 (ttp80) cc_final: 0.7810 (ttp-110) REVERT: W 42 TRP cc_start: 0.9502 (m100) cc_final: 0.9238 (m100) REVERT: W 71 MET cc_start: 0.8958 (mmm) cc_final: 0.8674 (mmm) REVERT: W 99 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.8205 (m) REVERT: W 126 TYR cc_start: 0.8909 (m-10) cc_final: 0.8658 (m-80) REVERT: X 47 ARG cc_start: 0.8140 (tpt170) cc_final: 0.7659 (tmt-80) REVERT: X 124 GLN cc_start: 0.7745 (mt0) cc_final: 0.7518 (tt0) REVERT: Z 72 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7703 (mtp) REVERT: Z 79 LYS cc_start: 0.8587 (mmtt) cc_final: 0.7913 (mmtm) REVERT: a 12 MET cc_start: 0.8653 (tpp) cc_final: 0.8354 (tpp) REVERT: a 25 TYR cc_start: 0.8108 (m-80) cc_final: 0.7650 (m-10) REVERT: a 46 TYR cc_start: 0.8496 (t80) cc_final: 0.8069 (t80) REVERT: a 48 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.7480 (mpp) REVERT: a 50 ARG cc_start: 0.8758 (tmt-80) cc_final: 0.8257 (tpt170) REVERT: b 26 TRP cc_start: 0.8708 (t60) cc_final: 0.8263 (t60) REVERT: b 43 SER cc_start: 0.8883 (p) cc_final: 0.8271 (t) REVERT: b 46 ASN cc_start: 0.8881 (OUTLIER) cc_final: 0.8480 (t0) REVERT: q 89 TRP cc_start: 0.8307 (t60) cc_final: 0.7459 (t60) REVERT: s 77 THR cc_start: 0.6232 (p) cc_final: 0.5856 (t) outliers start: 120 outliers final: 91 residues processed: 890 average time/residue: 0.1992 time to fit residues: 294.4366 Evaluate side-chains 900 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 793 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 528 LEU Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 670 GLU Chi-restraints excluded: chain G residue 674 LEU Chi-restraints excluded: chain G residue 710 CYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 173 TRP Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 258 ASN Chi-restraints excluded: chain H residue 287 HIS Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 172 ASN Chi-restraints excluded: chain P residue 206 ILE Chi-restraints excluded: chain P residue 213 PHE Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 338 LEU Chi-restraints excluded: chain P residue 343 THR Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain Z residue 50 MET Chi-restraints excluded: chain Z residue 72 MET Chi-restraints excluded: chain Z residue 84 LEU Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 48 MET Chi-restraints excluded: chain b residue 46 ASN Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 11 VAL Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 59 HIS Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 39 optimal weight: 0.0980 chunk 296 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 343 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 108 optimal weight: 0.0470 chunk 70 optimal weight: 0.3980 chunk 307 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 179 optimal weight: 0.8980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 ASN ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 102 GLN s 94 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.114289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.091531 restraints weight = 90791.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.094987 restraints weight = 41102.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.096936 restraints weight = 22540.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.096960 restraints weight = 17987.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.097149 restraints weight = 16755.186| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.7072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 34991 Z= 0.144 Angle : 1.014 62.744 47449 Z= 0.389 Chirality : 0.046 0.263 5177 Planarity : 0.005 0.060 6010 Dihedral : 8.767 164.156 4948 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.31 % Allowed : 26.46 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.13), residues: 4153 helix: 0.38 (0.12), residues: 1842 sheet: -1.13 (0.28), residues: 372 loop : -1.08 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 643 TYR 0.050 0.002 TYR q 124 PHE 0.030 0.002 PHE G 462 TRP 0.039 0.002 TRP B 221 HIS 0.013 0.001 HIS P 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (34950) covalent geometry : angle 0.78592 / 0.38 (47357) SS BOND : bond 0.00255 / 0.13 ( 4) SS BOND : angle 1.62006 / 0.60 ( 8) hydrogen bonds : bond 0.03955 / 2.64 ( 1329) hydrogen bonds : angle 5.13471 / 3.63 ( 3762) metal coordination : bond 0.01476 / 1.03 ( 37) metal coordination : angle 15.22946 / 11.31 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8003.65 seconds wall clock time: 138 minutes 30.64 seconds (8310.64 seconds total)