Starting phenix.real_space_refine on Tue May 5 22:03:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xnu_38515/05_2026/8xnu_38515_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xnu_38515/05_2026/8xnu_38515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xnu_38515/05_2026/8xnu_38515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xnu_38515/05_2026/8xnu_38515.map" model { file = "/net/cci-nas-00/data/ceres_data/8xnu_38515/05_2026/8xnu_38515_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xnu_38515/05_2026/8xnu_38515_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.072 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 7 5.49 5 S 244 5.16 5 C 21577 2.51 5 N 5766 2.21 5 O 6110 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-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33733 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 762 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain breaks: 1 Chain: "B" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 10, 'TRANS': 145} Chain: "C" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1641 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3080 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 21, 'TRANS': 362} 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: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2495 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 22, 'TRANS': 289} Chain breaks: 2 Chain: "I" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1398 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 9, 'TRANS': 164} Chain breaks: 1 Chain: "P" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2730 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 19, 'TRANS': 320} Chain: "Q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 957 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "R" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 660 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "S" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 667 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "T" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "V" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1164 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "Z" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1152 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 9, 'TRANS': 129} Chain: "a" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 540 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "b" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 11, 'TRANS': 67} Chain: "q" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain breaks: 1 Chain: "r" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 413 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain breaks: 1 Chain: "s" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 226 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'UQ9': 1} Classifications: {'undetermined': 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: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1014 SG CYS B 99 83.619 58.926 103.142 1.00 29.52 S ATOM 1517 SG CYS B 164 81.066 55.458 108.260 1.00 28.96 S ATOM 1747 SG CYS B 194 86.168 55.243 107.227 1.00 29.28 S ATOM 1020 SG CYS B 100 82.212 54.985 102.381 1.00 30.11 S ATOM 7519 SG CYS E 134 145.625 49.156 146.340 1.00 56.01 S ATOM 7553 SG CYS E 139 148.091 50.748 145.485 1.00 56.50 S ATOM 7837 SG CYS E 175 143.440 52.649 149.115 1.00 54.42 S ATOM 7860 SG CYS E 179 146.768 54.272 149.062 1.00 57.95 S ATOM 11390 SG CYS F 425 127.246 58.654 150.231 1.00 45.60 S ATOM 11068 SG CYS F 385 126.936 56.195 144.439 1.00 39.95 S ATOM 11048 SG CYS F 382 122.816 57.417 146.935 1.00 40.29 S ATOM 11029 SG CYS F 379 124.863 53.312 149.680 1.00 43.09 S ATOM 12438 SG CYS G 131 105.745 46.569 134.256 1.00 31.31 S ATOM 12417 SG CYS G 128 107.572 50.397 129.575 1.00 30.26 S ATOM 12478 SG CYS G 137 105.584 52.471 135.718 1.00 33.13 S ATOM 13163 SG CYS G 226 107.731 46.509 142.751 1.00 34.31 S ATOM 12834 SG CYS G 182 111.148 44.756 148.324 1.00 36.31 S ATOM 12810 SG CYS G 179 110.485 50.357 145.840 1.00 35.62 S ATOM 12787 SG CYS G 176 113.723 46.046 143.174 1.00 34.05 S ATOM 11924 SG CYS G 64 112.099 56.363 147.801 1.00 35.53 S ATOM 12010 SG CYS G 75 112.769 58.403 146.108 1.00 36.47 S ATOM 12035 SG CYS G 78 111.848 62.858 148.295 1.00 36.76 S ATOM 12136 SG CYS G 92 111.764 60.941 151.474 1.00 39.04 S ATOM 20121 SG CYS I 123 90.483 49.998 116.081 1.00 27.30 S ATOM 20347 SG CYS I 152 89.972 48.862 110.981 1.00 27.39 S ATOM 20394 SG CYS I 158 95.730 48.927 112.810 1.00 26.60 S ATOM 20373 SG CYS I 155 92.679 53.395 112.663 1.00 27.04 S ATOM 20070 SG CYS I 116 100.613 45.764 122.959 1.00 29.24 S ATOM 20093 SG CYS I 119 96.084 45.522 119.818 1.00 28.85 S ATOM 20051 SG CYS I 113 99.232 40.664 119.727 1.00 28.61 S ATOM 20423 SG CYS I 162 102.088 45.235 117.509 1.00 28.07 S ATOM 24932 SG CYS R 79 115.700 38.296 121.441 1.00 32.60 S ATOM 25108 SG CYS R 104 113.296 36.897 122.999 1.00 32.49 S ATOM 25130 SG CYS R 107 112.469 37.574 119.615 1.00 30.78 S Time building chain proxies: 8.37, per 1000 atoms: 0.25 Number of scatterers: 33733 At special positions: 0 Unit cell: (174.9, 127.6, 199.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 244 16.00 P 7 15.00 O 6110 8.00 N 5766 7.00 C 21577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 24 " - pdb=" SG CYS S 58 " distance=2.04 Simple disulfide: pdb=" SG CYS X 46 " - pdb=" SG CYS X 56 " distance=2.03 Simple disulfide: pdb=" SG CYS X 88 " - pdb=" SG CYS X 100 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 179 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 139 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 134 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 175 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 78 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 64 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 75 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 92 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 100 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 164 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 194 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 99 " pdb=" SF4 F 502 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 382 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 379 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 425 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 385 " pdb=" SF4 G 801 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 131 " pdb="FE1 SF4 G 801 " - pdb=" NE2 HIS G 124 " pdb="FE3 SF4 G 801 " - pdb=" SG CYS G 128 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 137 " pdb=" SF4 G 802 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 176 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 226 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 179 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 182 " pdb=" SF4 I 302 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 123 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 152 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 155 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 158 " pdb="FE2 SF4 I 302 " - pdb=" NE2 HIS I 101 " pdb=" SF4 I 303 " pdb="FE3 SF4 I 303 " - pdb=" SG CYS I 113 " pdb="FE4 SF4 I 303 " - pdb=" SG CYS I 162 " pdb="FE1 SF4 I 303 " - pdb=" SG CYS I 116 " pdb="FE2 SF4 I 303 " - pdb=" SG CYS I 119 " 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 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7826 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 30 sheets defined 50.0% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 52 through 73 Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.313A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 108 Processing helix chain 'B' and resid 70 through 89 Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.584A pdb=" N GLU B 103 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 141 through 151 Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.588A pdb=" N TYR B 171 " --> pdb=" O GLY B 168 " (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: 3.602A 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: 4.321A pdb=" N GLN C 106 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.117A pdb=" N TYR C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 3.967A pdb=" N GLU D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 6.296A pdb=" N LEU D 130 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 140 removed outlier: 3.770A pdb=" N PHE D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.860A pdb=" N ASN D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 195 Processing helix chain 'D' and resid 197 through 218 removed outlier: 3.706A pdb=" N PHE D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU D 206 " --> pdb=" O TRP D 202 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 263 removed outlier: 3.691A pdb=" N ASP D 243 " --> pdb=" O GLY D 239 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N LEU D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 273 Processing helix chain 'D' and resid 279 through 286 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.669A pdb=" N SER D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 325 through 350 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 428 through 439 removed outlier: 3.531A pdb=" N LEU D 435 " --> pdb=" O HIS D 431 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 453 Processing helix chain 'D' and resid 457 through 463 removed outlier: 3.622A pdb=" N ILE D 461 " --> pdb=" O VAL D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 107 through 118 removed outlier: 3.524A pdb=" N VAL E 111 " --> pdb=" O PRO E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 142 Processing helix chain 'E' and resid 143 through 156 removed outlier: 3.684A pdb=" N THR E 150 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 209 removed outlier: 3.577A pdb=" N ILE E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 201 " --> pdb=" O PRO E 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 64 through 72 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 134 removed outlier: 3.553A pdb=" N GLU F 129 " --> pdb=" O CYS F 125 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 150 removed outlier: 3.921A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 148 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 180 removed outlier: 3.516A pdb=" N ALA F 166 " --> pdb=" O PHE F 162 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 removed outlier: 3.636A 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: 3.832A pdb=" N ILE F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 Processing helix chain 'F' and resid 245 through 266 removed outlier: 3.566A pdb=" N SER F 251 " --> pdb=" O THR F 247 " (cutoff:3.500A) Proline residue: F 252 - end of helix removed outlier: 5.534A pdb=" N GLY F 259 " --> pdb=" O CYS F 255 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N THR F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TRP F 261 " --> pdb=" O ARG F 257 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE F 265 " --> pdb=" O TRP F 261 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 303 removed outlier: 3.860A pdb=" N ILE F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 333 removed outlier: 4.157A pdb=" N GLU F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 345 removed outlier: 3.506A pdb=" N VAL F 343 " --> pdb=" O PHE F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 376 removed outlier: 3.545A pdb=" N LEU F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 402 removed outlier: 3.663A pdb=" N ASP F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.914A pdb=" N SER F 411 " --> pdb=" O ALA F 407 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 457 removed outlier: 4.349A pdb=" N ASP F 429 " --> pdb=" O CYS F 425 " (cutoff:3.500A) Proline residue: F 434 - end of helix removed outlier: 3.518A pdb=" N ARG F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) Proline residue: F 444 - end of helix Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.597A pdb=" N VAL G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 115 removed outlier: 3.774A pdb=" N LYS G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 123 removed outlier: 3.714A pdb=" N ASN G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 146 Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.932A pdb=" N ASP G 203 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET G 204 " --> pdb=" O GLY G 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 200 through 204' Processing helix chain 'G' and resid 220 through 226 removed outlier: 3.820A pdb=" N ASP G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 293 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 318 through 333 Processing helix chain 'G' and resid 347 through 360 Processing helix chain 'G' and resid 390 through 397 removed outlier: 3.671A 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: 4.025A 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: 4.008A pdb=" N VAL G 465 " --> pdb=" O SER G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 482 removed outlier: 3.636A pdb=" N LEU G 481 " --> pdb=" O GLY G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 505 Processing helix chain 'G' and resid 522 through 528 Processing helix chain 'G' and resid 534 through 540 Processing helix chain 'G' and resid 618 through 631 Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 651 through 655 Processing helix chain 'G' and resid 664 through 675 removed outlier: 3.523A pdb=" N ALA G 668 " --> pdb=" O TYR G 664 " (cutoff:3.500A) Processing helix chain 'G' and resid 690 through 696 removed outlier: 3.641A pdb=" N PHE G 694 " --> pdb=" O THR G 690 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET G 696 " --> pdb=" O LYS G 692 " (cutoff:3.500A) Processing helix chain 'G' and resid 698 through 703 Processing helix chain 'G' and resid 704 through 715 Processing helix chain 'H' and resid 3 through 8 Processing helix chain 'H' and resid 10 through 32 removed outlier: 3.750A pdb=" N THR H 21 " --> pdb=" O MET H 17 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY H 29 " --> pdb=" O ARG H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 58 removed outlier: 3.573A pdb=" N ASP H 51 " --> pdb=" O GLN H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 85 removed outlier: 3.740A pdb=" N THR H 76 " --> pdb=" O ILE H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 124 removed outlier: 3.688A pdb=" N SER H 112 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN H 124 " --> pdb=" O GLY H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 156 removed outlier: 3.855A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 164 through 169 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.734A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 214 removed outlier: 3.898A pdb=" N GLU H 214 " --> pdb=" O PHE H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 277 removed outlier: 3.540A pdb=" N SER H 256 " --> pdb=" O PRO H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 291 Processing helix chain 'H' and resid 293 through 311 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 49 through 62 Processing helix chain 'I' and resid 63 through 78 removed outlier: 3.529A pdb=" N THR I 73 " --> pdb=" O GLY I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 123 Processing helix chain 'I' and resid 156 through 162 Processing helix chain 'I' and resid 179 through 183 removed outlier: 3.865A pdb=" N LEU I 183 " --> pdb=" O THR I 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 179 through 183' Processing helix chain 'I' and resid 186 through 209 removed outlier: 5.145A pdb=" N ALA I 199 " --> pdb=" O ASP I 195 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLU I 200 " --> pdb=" O LYS I 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 77 removed outlier: 3.804A pdb=" N TYR P 68 " --> pdb=" O PHE P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 96 removed outlier: 4.873A pdb=" N HIS P 93 " --> pdb=" O TYR P 89 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU P 94 " --> pdb=" O ASP P 90 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU P 96 " --> pdb=" O MET P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 112 through 122 removed outlier: 4.105A pdb=" N ILE P 116 " --> pdb=" O ASP P 112 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N HIS P 122 " --> pdb=" O LYS P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 146 Processing helix chain 'P' and resid 146 through 160 removed outlier: 3.624A pdb=" N ALA P 153 " --> pdb=" O PRO P 149 " (cutoff:3.500A) Processing helix chain 'P' and resid 178 through 195 removed outlier: 3.755A pdb=" N ARG P 192 " --> pdb=" O GLU P 188 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER P 193 " --> pdb=" O LYS P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 219 removed outlier: 4.082A pdb=" N PHE P 217 " --> pdb=" O PHE P 213 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 222 No H-bonds generated for 'chain 'P' and resid 220 through 222' Processing helix chain 'P' and resid 229 through 232 Processing helix chain 'P' and resid 242 through 254 Processing helix chain 'P' and resid 272 through 285 Processing helix chain 'P' and resid 294 through 308 removed outlier: 3.620A pdb=" N TRP P 300 " --> pdb=" O PHE P 296 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 324 Processing helix chain 'P' and resid 344 through 354 removed outlier: 4.033A pdb=" N LYS P 348 " --> pdb=" O PRO P 344 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE P 350 " --> pdb=" O GLU P 346 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLU P 351 " --> pdb=" O LEU P 347 " (cutoff:3.500A) Processing helix chain 'P' and resid 355 through 357 No H-bonds generated for 'chain 'P' and resid 355 through 357' Processing helix chain 'P' and resid 360 through 364 Processing helix chain 'Q' and resid 61 through 66 removed outlier: 4.413A pdb=" N GLY Q 66 " --> pdb=" O THR Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 74 Processing helix chain 'Q' and resid 130 through 142 Processing helix chain 'Q' and resid 159 through 164 removed outlier: 4.200A pdb=" N ASN Q 163 " --> pdb=" O SER Q 159 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE Q 164 " --> pdb=" O TYR Q 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 159 through 164' Processing helix chain 'R' and resid 44 through 49 Processing helix chain 'R' and resid 59 through 64 removed outlier: 3.549A pdb=" N LEU R 63 " --> pdb=" O PHE R 59 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 59 through 64' Processing helix chain 'R' and resid 83 through 87 Processing helix chain 'S' and resid 30 through 48 removed outlier: 6.447A pdb=" N VAL S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLU S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 77 through 90 removed outlier: 3.811A pdb=" N TYR T 90 " --> pdb=" O VAL T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 127 Processing helix chain 'T' and resid 133 through 138 removed outlier: 3.624A pdb=" N LYS T 137 " --> pdb=" O ILE T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 150 Processing helix chain 'V' and resid 19 through 36 Processing helix chain 'V' and resid 42 through 62 Processing helix chain 'V' and resid 64 through 72 Processing helix chain 'V' and resid 76 through 98 removed outlier: 3.676A pdb=" N VAL V 80 " --> pdb=" O GLU V 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 53 removed outlier: 3.586A pdb=" N ARG W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) Proline residue: W 47 - end of helix Processing helix chain 'W' and resid 58 through 73 removed outlier: 3.616A pdb=" N ASN W 73 " --> pdb=" O MET W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 97 Processing helix chain 'W' and resid 98 through 100 No H-bonds generated for 'chain 'W' and resid 98 through 100' Processing helix chain 'W' and resid 102 through 108 removed outlier: 3.642A pdb=" N ARG W 108 " --> pdb=" O THR W 104 " (cutoff:3.500A) Processing helix chain 'W' and resid 109 through 111 No H-bonds generated for 'chain 'W' and resid 109 through 111' Processing helix chain 'W' and resid 120 through 128 Processing helix chain 'X' and resid 10 through 14 removed outlier: 3.528A pdb=" N LYS X 14 " --> pdb=" O GLU X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 36 removed outlier: 4.624A pdb=" N HIS X 30 " --> pdb=" O LYS X 26 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N HIS X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 51 Processing helix chain 'X' and resid 52 through 55 Processing helix chain 'X' and resid 56 through 77 Processing helix chain 'X' and resid 78 through 92 removed outlier: 3.944A pdb=" N SER X 92 " --> pdb=" O CYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 114 Processing helix chain 'X' and resid 140 through 144 removed outlier: 4.463A pdb=" N SER X 144 " --> pdb=" O PRO X 141 " (cutoff:3.500A) Processing helix chain 'Z' and resid 31 through 98 Proline residue: Z 73 - end of helix removed outlier: 3.904A pdb=" N MET Z 98 " --> pdb=" O GLU Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 126 Processing helix chain 'Z' and resid 129 through 139 Processing helix chain 'a' and resid 4 through 31 removed outlier: 4.499A pdb=" N GLY a 8 " --> pdb=" O GLU a 4 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS a 15 " --> pdb=" O ILE a 11 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 4.598A pdb=" N LYS a 28 " --> pdb=" O ALA a 24 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR a 30 " --> pdb=" O ILE a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 55 Processing helix chain 'b' and resid 7 through 15 Processing helix chain 'b' and resid 18 through 32 Processing helix chain 'b' and resid 38 through 49 removed outlier: 3.758A pdb=" N ALA b 42 " --> pdb=" O TYR b 38 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER b 43 " --> pdb=" O THR b 39 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 17 removed outlier: 3.844A pdb=" N HIS q 17 " --> pdb=" O GLN q 13 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 31 removed outlier: 3.663A pdb=" N LEU q 23 " --> pdb=" O GLY q 19 " (cutoff:3.500A) Processing helix chain 'q' and resid 78 through 82 Processing helix chain 'q' and resid 83 through 91 removed outlier: 4.125A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 4.627A 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 's' and resid 43 through 54 removed outlier: 4.203A pdb=" N LYS s 54 " --> pdb=" O LEU s 50 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94 removed outlier: 6.371A pdb=" N MET B 131 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N MET B 161 " --> pdb=" O MET B 131 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N VAL B 133 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B 158 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL B 191 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER B 160 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 72 through 78 removed outlier: 3.523A pdb=" N GLN C 74 " --> pdb=" O CYS C 86 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 82 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU C 83 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LYS C 143 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE C 85 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL C 116 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU C 132 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU C 110 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 152 through 153 removed outlier: 7.148A pdb=" N ILE C 152 " --> pdb=" O PHE C 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 207 through 212 removed outlier: 3.563A pdb=" N ARG C 210 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 82 through 84 removed outlier: 3.818A pdb=" N LYS D 108 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER D 102 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 227 through 228 Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 320 removed outlier: 6.374A pdb=" N VAL D 318 " --> pdb=" O LYS I 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 397 through 401 Processing sheet with id=AA9, first strand: chain 'E' and resid 131 through 133 Processing sheet with id=AB1, 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: 7.392A 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: 6.722A 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=AB2, first strand: chain 'F' and resid 286 through 288 removed outlier: 6.152A pdb=" N ASN F 277 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL F 356 " --> pdb=" O ASN F 277 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER F 279 " --> pdb=" O VAL F 356 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 32 through 34 Processing sheet with id=AB4, first strand: chain 'G' and resid 89 through 90 removed outlier: 3.868A 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 246 through 251 removed outlier: 6.313A 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=AB7, first strand: chain 'G' and resid 306 through 308 Processing sheet with id=AB8, first strand: chain 'G' and resid 531 through 532 removed outlier: 6.454A pdb=" N LEU G 366 " --> pdb=" O LYS G 531 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU G 545 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 442 through 446 removed outlier: 6.202A pdb=" N VAL G 400 " --> pdb=" O ALA G 430 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ILE G 432 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU G 402 " --> pdb=" O ILE G 432 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 595 through 597 Processing sheet with id=AC2, first strand: chain 'I' and resid 100 through 103 Processing sheet with id=AC3, first strand: chain 'I' and resid 128 through 134 removed outlier: 6.408A pdb=" N GLU I 133 " --> pdb=" O THR I 142 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N THR I 142 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 103 through 107 removed outlier: 6.361A pdb=" N THR P 57 " --> pdb=" O ILE P 127 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 206 through 207 Processing sheet with id=AC6, first strand: chain 'P' and resid 226 through 227 removed outlier: 6.360A pdb=" N VAL P 226 " --> pdb=" O TYR P 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'Q' and resid 125 through 128 Processing sheet with id=AC8, first strand: chain 'Q' and resid 106 through 108 Processing sheet with id=AC9, first strand: chain 'R' and resid 76 through 77 Processing sheet with id=AD1, first strand: chain 'R' and resid 102 through 103 removed outlier: 3.506A pdb=" N GLY R 102 " --> pdb=" O PHE R 111 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 53 through 56 removed outlier: 3.671A pdb=" N GLN S 73 " --> pdb=" O TYR S 69 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'q' and resid 37 through 42 removed outlier: 6.240A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY q 40 " --> pdb=" O TYR q 48 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASN q 46 " --> pdb=" O ASP q 42 " (cutoff:3.500A) 1430 hydrogen bonds defined for protein. 4137 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.13 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.37: 11425 1.37 - 1.59: 22660 1.59 - 1.80: 253 1.80 - 2.02: 133 2.02 - 2.23: 80 Bond restraints: 34551 Sorted by residual: bond pdb=" O6 EHZ W 201 " pdb=" P1 EHZ W 201 " ideal model delta sigma weight residual 2.378 1.646 0.732 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 1.398 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C15 EHZ W 201 " pdb=" O4 EHZ W 201 " ideal model delta sigma weight residual 1.356 1.179 0.177 2.00e-02 2.50e+03 7.80e+01 bond pdb=" C VAL W 106 " pdb=" N MET W 107 " ideal model delta sigma weight residual 1.335 1.218 0.117 1.35e-02 5.49e+03 7.52e+01 bond pdb=" CA ASP R 39 " pdb=" C ASP R 39 " ideal model delta sigma weight residual 1.527 1.639 -0.111 1.41e-02 5.03e+03 6.25e+01 ... (remaining 34546 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.67: 46111 6.67 - 13.35: 574 13.35 - 20.02: 158 20.02 - 26.69: 3 26.69 - 33.37: 2 Bond angle restraints: 46848 Sorted by residual: angle pdb=" N VAL D 142 " pdb=" CA VAL D 142 " pdb=" CB VAL D 142 " ideal model delta sigma weight residual 110.65 132.48 -21.83 1.13e+00 7.83e-01 3.73e+02 angle pdb=" N VAL D 142 " pdb=" CA VAL D 142 " pdb=" C VAL D 142 " ideal model delta sigma weight residual 110.42 92.57 17.85 9.40e-01 1.13e+00 3.61e+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 89.05 25.59 1.52e+00 4.33e-01 2.83e+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 93.49 19.68 1.26e+00 6.30e-01 2.44e+02 angle pdb=" N ILE G 251 " pdb=" CA ILE G 251 " pdb=" C ILE G 251 " ideal model delta sigma weight residual 108.17 126.82 -18.65 1.40e+00 5.10e-01 1.77e+02 ... (remaining 46843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.81: 20072 26.81 - 53.62: 641 53.62 - 80.43: 75 80.43 - 107.24: 8 107.24 - 134.06: 4 Dihedral angle restraints: 20800 sinusoidal: 8661 harmonic: 12139 Sorted by residual: dihedral pdb=" C ASP D 140 " pdb=" N ASP D 140 " pdb=" CA ASP D 140 " pdb=" CB ASP D 140 " ideal model delta harmonic sigma weight residual -122.60 -101.17 -21.43 0 2.50e+00 1.60e-01 7.35e+01 dihedral pdb=" CB CYS X 88 " pdb=" SG CYS X 88 " pdb=" SG CYS X 100 " pdb=" CB CYS X 100 " ideal model delta sinusoidal sigma weight residual 93.00 161.55 -68.55 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" C LEU G 387 " pdb=" N LEU G 387 " pdb=" CA LEU G 387 " pdb=" CB LEU G 387 " ideal model delta harmonic sigma weight residual -122.60 -105.67 -16.93 0 2.50e+00 1.60e-01 4.58e+01 ... (remaining 20797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 4550 0.183 - 0.367: 513 0.367 - 0.550: 47 0.550 - 0.733: 3 0.733 - 0.917: 24 Chirality restraints: 5137 Sorted by residual: chirality pdb="FE1 SF4 B 301 " pdb=" S2 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False -10.55 -9.64 -0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb="FE3 SF4 I 303 " pdb=" S1 SF4 I 303 " pdb=" S2 SF4 I 303 " pdb=" S4 SF4 I 303 " both_signs ideal model delta sigma weight residual False -10.55 -9.64 -0.91 2.00e-01 2.50e+01 2.08e+01 chirality pdb="FE4 SF4 I 303 " pdb=" S1 SF4 I 303 " pdb=" S2 SF4 I 303 " pdb=" S3 SF4 I 303 " both_signs ideal model delta sigma weight residual False 10.55 9.65 0.90 2.00e-01 2.50e+01 2.04e+01 ... (remaining 5134 not shown) Planarity restraints: 5964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ9 H 400 " -0.342 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C18 UQ9 H 400 " 0.508 2.00e-02 2.50e+03 pdb=" C19 UQ9 H 400 " 0.109 2.00e-02 2.50e+03 pdb=" C20 UQ9 H 400 " -0.135 2.00e-02 2.50e+03 pdb=" C21 UQ9 H 400 " -0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 UQ9 H 400 " -0.303 2.00e-02 2.50e+03 2.58e-01 8.29e+02 pdb=" C23 UQ9 H 400 " 0.439 2.00e-02 2.50e+03 pdb=" C24 UQ9 H 400 " 0.098 2.00e-02 2.50e+03 pdb=" C25 UQ9 H 400 " -0.045 2.00e-02 2.50e+03 pdb=" C26 UQ9 H 400 " -0.189 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 H 400 " 0.023 2.00e-02 2.50e+03 1.60e-01 7.71e+02 pdb=" C1M UQ9 H 400 " 0.110 2.00e-02 2.50e+03 pdb=" C2 UQ9 H 400 " -0.020 2.00e-02 2.50e+03 pdb=" C3 UQ9 H 400 " -0.043 2.00e-02 2.50e+03 pdb=" C4 UQ9 H 400 " 0.080 2.00e-02 2.50e+03 pdb=" C5 UQ9 H 400 " -0.094 2.00e-02 2.50e+03 pdb=" C6 UQ9 H 400 " -0.004 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 400 " 0.081 2.00e-02 2.50e+03 pdb=" O2 UQ9 H 400 " -0.030 2.00e-02 2.50e+03 pdb=" O3 UQ9 H 400 " -0.173 2.00e-02 2.50e+03 pdb=" O4 UQ9 H 400 " 0.381 2.00e-02 2.50e+03 pdb=" O5 UQ9 H 400 " -0.310 2.00e-02 2.50e+03 ... (remaining 5961 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 76 2.38 - 3.01: 22857 3.01 - 3.64: 52897 3.64 - 4.27: 83201 4.27 - 4.90: 134219 Nonbonded interactions: 293250 Sorted by model distance: nonbonded pdb=" O ASP I 208 " pdb=" OD1 ASP I 208 " model vdw 1.754 3.040 nonbonded pdb=" O ASN F 116 " pdb=" OD1 ASN F 116 " model vdw 1.941 3.040 nonbonded pdb=" O ASP Q 146 " pdb=" OD1 ASP Q 146 " model vdw 1.970 3.040 nonbonded pdb=" OD1 ASN P 376 " pdb=" N TYR P 377 " model vdw 1.981 3.120 nonbonded pdb=" O ASN H 97 " pdb=" OD1 ASN H 97 " model vdw 1.982 3.040 ... (remaining 293245 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: 3.850 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: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 42.170 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.140 34591 Z= 1.035 Angle : 2.245 52.602 46938 Z= 1.499 Chirality : 0.130 0.917 5137 Planarity : 0.010 0.292 5964 Dihedral : 12.950 134.056 12965 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 44.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.81 % Favored : 94.11 % Rotamer: Outliers : 0.28 % Allowed : 7.77 % Favored : 91.95 % Cbeta Deviations : 1.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.12), residues: 4129 helix: -0.83 (0.11), residues: 1795 sheet: -1.12 (0.29), residues: 337 loop : -2.03 (0.12), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 333 TYR 0.046 0.002 TYR B 112 PHE 0.032 0.002 PHE G 462 TRP 0.034 0.002 TRP G 285 HIS 0.017 0.002 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.01441 (34551) covalent geometry : angle 2.11429 (46848) SS BOND : bond 0.00777 ( 3) SS BOND : angle 2.16879 ( 6) hydrogen bonds : bond 0.24710 ( 1430) hydrogen bonds : angle 8.95729 ( 4137) metal coordination : bond 0.52293 ( 37) metal coordination : angle 17.98864 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1669 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1659 time to evaluate : 1.349 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: A 24 LEU cc_start: 0.8105 (tm) cc_final: 0.7148 (tt) REVERT: A 113 TRP cc_start: 0.3721 (p90) cc_final: 0.3511 (m-90) REVERT: B 88 SER cc_start: 0.7961 (p) cc_final: 0.7684 (t) REVERT: B 119 VAL cc_start: 0.8389 (t) cc_final: 0.8065 (t) REVERT: B 207 GLN cc_start: 0.7806 (tt0) cc_final: 0.7240 (tt0) REVERT: C 148 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7143 (mt-10) REVERT: C 168 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7196 (tm-30) REVERT: D 99 LEU cc_start: 0.7720 (mt) cc_final: 0.7142 (mt) REVERT: D 292 MET cc_start: 0.7342 (mmm) cc_final: 0.6601 (mpp) REVERT: D 308 TYR cc_start: 0.7329 (p90) cc_final: 0.7029 (p90) REVERT: D 371 MET cc_start: 0.7736 (ptm) cc_final: 0.7492 (ptt) REVERT: D 396 THR cc_start: 0.7752 (p) cc_final: 0.7530 (t) REVERT: E 121 TYR cc_start: 0.6403 (m-80) cc_final: 0.5775 (m-80) REVERT: F 138 LEU cc_start: 0.7862 (tp) cc_final: 0.7574 (tp) REVERT: F 433 TRP cc_start: 0.8311 (m-10) cc_final: 0.7987 (m-10) REVERT: G 261 ILE cc_start: 0.8729 (pp) cc_final: 0.8288 (pt) REVERT: H 43 TYR cc_start: 0.7625 (m-80) cc_final: 0.7377 (m-10) REVERT: H 173 TRP cc_start: 0.7184 (m-10) cc_final: 0.6325 (m-10) REVERT: H 255 TYR cc_start: 0.6432 (t80) cc_final: 0.6007 (t80) REVERT: H 285 LEU cc_start: 0.8288 (tt) cc_final: 0.7805 (tt) REVERT: H 296 LEU cc_start: 0.8403 (tp) cc_final: 0.8052 (tp) REVERT: P 71 ASN cc_start: 0.7326 (t0) cc_final: 0.6145 (t0) REVERT: P 97 MET cc_start: 0.7072 (ptp) cc_final: 0.6566 (ptp) REVERT: P 283 MET cc_start: 0.7056 (mmm) cc_final: 0.6644 (mmp) REVERT: Q 146 ASP cc_start: 0.6825 (p0) cc_final: 0.6311 (p0) REVERT: T 107 ASP cc_start: 0.6318 (p0) cc_final: 0.6100 (p0) REVERT: V 51 ILE cc_start: 0.8248 (mt) cc_final: 0.7640 (mt) REVERT: X 7 LEU cc_start: 0.7129 (mt) cc_final: 0.5964 (mt) REVERT: X 93 ASN cc_start: 0.7091 (p0) cc_final: 0.6738 (p0) REVERT: Z 96 ILE cc_start: 0.7529 (mt) cc_final: 0.7317 (tp) REVERT: Z 102 PRO cc_start: 0.7506 (Cg_exo) cc_final: 0.6747 (Cg_endo) outliers start: 10 outliers final: 1 residues processed: 1662 average time/residue: 0.2461 time to fit residues: 644.7097 Evaluate side-chains 978 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 977 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 242 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 197 optimal weight: 0.2980 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B 83 ASN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN C 73 GLN C 88 HIS D 117 HIS D 131 GLN ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN D 381 HIS D 454 GLN E 86 GLN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 451 GLN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 GLN G 164 ASN G 365 ASN G 444 HIS G 517 HIS ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 571 HIS ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN H 97 ASN H 235 ASN I 126 GLN P 154 GLN ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 216 HIS P 251 ASN P 356 HIS Q 51 GLN Q 88 GLN R 33 HIS ** T 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 HIS V 41 HIS V 50 GLN ** V 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 94 GLN W 105 HIS W 111 HIS X 77 HIS X 99 HIS X 109 GLN Z 103 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 46 ASN b 69 HIS q 12 GLN ** q 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 46 ASN q 87 HIS r 9 GLN r 21 GLN r 110 GLN s 49 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.104458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.082992 restraints weight = 102965.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.085844 restraints weight = 45202.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.087635 restraints weight = 27027.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.088738 restraints weight = 19722.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.089397 restraints weight = 16351.181| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 34591 Z= 0.219 Angle : 1.082 67.647 46938 Z= 0.458 Chirality : 0.050 0.278 5137 Planarity : 0.007 0.120 5964 Dihedral : 8.556 144.824 4719 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 4.00 % Allowed : 18.96 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.12), residues: 4129 helix: 0.14 (0.12), residues: 1874 sheet: -1.06 (0.26), residues: 351 loop : -1.41 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 67 TYR 0.030 0.003 TYR a 60 PHE 0.038 0.003 PHE H 270 TRP 0.037 0.002 TRP D 300 HIS 0.010 0.002 HIS P 122 Details of bonding type rmsd covalent geometry : bond 0.00490 (34551) covalent geometry : angle 0.88916 (46848) SS BOND : bond 0.00370 ( 3) SS BOND : angle 1.19963 ( 6) hydrogen bonds : bond 0.06314 ( 1430) hydrogen bonds : angle 5.88526 ( 4137) metal coordination : bond 0.03354 ( 37) metal coordination : angle 14.61017 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1226 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 1081 time to evaluate : 1.494 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 2 ASN cc_start: 0.7824 (m-40) cc_final: 0.6740 (t0) REVERT: A 11 ILE cc_start: 0.9472 (OUTLIER) cc_final: 0.9125 (mp) REVERT: A 13 LEU cc_start: 0.9172 (tp) cc_final: 0.8909 (tp) REVERT: A 98 LEU cc_start: 0.9516 (mt) cc_final: 0.8961 (mp) REVERT: A 113 TRP cc_start: 0.3866 (p90) cc_final: 0.3602 (m-90) REVERT: B 77 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7777 (mptt) REVERT: B 121 PHE cc_start: 0.8442 (t80) cc_final: 0.7913 (t80) REVERT: B 129 ASP cc_start: 0.8303 (m-30) cc_final: 0.7878 (m-30) REVERT: B 156 ARG cc_start: 0.8446 (ptt180) cc_final: 0.8072 (ptt180) REVERT: B 161 MET cc_start: 0.8382 (ttp) cc_final: 0.8147 (ttm) REVERT: B 166 ASN cc_start: 0.8751 (m110) cc_final: 0.8542 (m110) REVERT: B 221 TRP cc_start: 0.8321 (t60) cc_final: 0.8056 (t60) REVERT: C 75 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8416 (p) REVERT: C 114 THR cc_start: 0.9099 (m) cc_final: 0.8889 (p) REVERT: C 165 TYR cc_start: 0.8916 (m-80) cc_final: 0.8712 (m-80) REVERT: D 88 HIS cc_start: 0.6492 (p90) cc_final: 0.5795 (p90) REVERT: D 140 ASP cc_start: 0.7295 (t70) cc_final: 0.6816 (t0) REVERT: D 356 ILE cc_start: 0.8852 (pp) cc_final: 0.8534 (pp) REVERT: D 371 MET cc_start: 0.9042 (ptm) cc_final: 0.8734 (ppp) REVERT: E 68 ASN cc_start: 0.8684 (t0) cc_final: 0.8291 (m-40) REVERT: E 97 MET cc_start: 0.8497 (mtp) cc_final: 0.8250 (mtp) REVERT: E 118 TYR cc_start: 0.7985 (m-80) cc_final: 0.7657 (m-80) REVERT: E 167 LEU cc_start: 0.8470 (tp) cc_final: 0.8130 (tp) REVERT: E 170 LEU cc_start: 0.6847 (tp) cc_final: 0.6154 (pt) REVERT: F 75 TRP cc_start: 0.7986 (t60) cc_final: 0.7628 (t60) REVERT: F 214 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8604 (mt-10) REVERT: F 220 GLN cc_start: 0.6972 (pm20) cc_final: 0.5838 (pm20) REVERT: F 337 MET cc_start: 0.7842 (mmm) cc_final: 0.7631 (mmm) REVERT: G 74 ASN cc_start: 0.8394 (m110) cc_final: 0.8066 (m-40) REVERT: G 100 TRP cc_start: 0.6924 (m100) cc_final: 0.6649 (m100) REVERT: G 107 GLU cc_start: 0.8297 (tp30) cc_final: 0.8036 (tm-30) REVERT: G 271 MET cc_start: 0.8004 (mmm) cc_final: 0.7657 (mmm) REVERT: G 273 ILE cc_start: 0.9473 (mt) cc_final: 0.9215 (mm) REVERT: G 390 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8653 (t) REVERT: G 438 LEU cc_start: 0.8899 (mt) cc_final: 0.8661 (tp) REVERT: H 108 THR cc_start: 0.9517 (m) cc_final: 0.9180 (p) REVERT: H 156 MET cc_start: 0.7922 (ptm) cc_final: 0.7648 (ptt) REVERT: H 172 MET cc_start: 0.6821 (ppp) cc_final: 0.6458 (ppp) REVERT: H 225 MET cc_start: 0.8846 (mtm) cc_final: 0.8579 (ttm) REVERT: H 243 LEU cc_start: 0.8851 (mm) cc_final: 0.8478 (mm) REVERT: H 262 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8183 (tt0) REVERT: H 272 TRP cc_start: 0.8520 (t60) cc_final: 0.8299 (t60) REVERT: I 63 TRP cc_start: 0.8082 (m-10) cc_final: 0.7827 (m-10) REVERT: I 70 LEU cc_start: 0.9355 (mt) cc_final: 0.9104 (mt) REVERT: I 89 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7361 (pt0) REVERT: I 187 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8459 (ttmt) REVERT: P 134 TRP cc_start: 0.8118 (p90) cc_final: 0.7822 (p90) REVERT: P 210 GLU cc_start: 0.8354 (tp30) cc_final: 0.7916 (tp30) REVERT: P 214 LEU cc_start: 0.8720 (mm) cc_final: 0.8465 (mm) REVERT: P 338 LEU cc_start: 0.8946 (tp) cc_final: 0.8441 (tp) REVERT: P 350 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7816 (tp) REVERT: Q 69 GLU cc_start: 0.7757 (tp30) cc_final: 0.7484 (tp30) REVERT: Q 87 MET cc_start: 0.8222 (mmt) cc_final: 0.7567 (mmm) REVERT: Q 146 ASP cc_start: 0.7525 (p0) cc_final: 0.7202 (p0) REVERT: Q 164 PHE cc_start: 0.7753 (m-80) cc_final: 0.6903 (m-80) REVERT: R 80 ASP cc_start: 0.8170 (p0) cc_final: 0.7933 (p0) REVERT: R 95 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8118 (mt) REVERT: S 19 ILE cc_start: 0.8016 (mt) cc_final: 0.7667 (mp) REVERT: S 23 LEU cc_start: 0.9118 (pp) cc_final: 0.8814 (pt) REVERT: S 44 LEU cc_start: 0.9383 (tp) cc_final: 0.9136 (tp) REVERT: S 62 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8046 (pt0) REVERT: S 82 LEU cc_start: 0.7872 (mt) cc_final: 0.7601 (mt) REVERT: T 120 MET cc_start: 0.8852 (mtm) cc_final: 0.8648 (ttm) REVERT: T 147 TYR cc_start: 0.7563 (t80) cc_final: 0.7187 (t80) REVERT: V 38 PHE cc_start: 0.8101 (m-80) cc_final: 0.7630 (m-80) REVERT: V 44 TYR cc_start: 0.8611 (t80) cc_final: 0.8214 (t80) REVERT: V 51 ILE cc_start: 0.9256 (mt) cc_final: 0.8852 (mt) REVERT: W 37 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8602 (mm-30) REVERT: W 71 MET cc_start: 0.8533 (mmt) cc_final: 0.8221 (mmp) REVERT: W 100 TRP cc_start: 0.8051 (m-10) cc_final: 0.7652 (m-10) REVERT: X 22 SER cc_start: 0.9195 (p) cc_final: 0.8940 (m) REVERT: Z 50 MET cc_start: 0.7938 (tpp) cc_final: 0.7664 (tpp) REVERT: Z 83 THR cc_start: 0.9258 (p) cc_final: 0.8958 (t) REVERT: Z 124 MET cc_start: 0.8423 (mmm) cc_final: 0.8214 (mmm) REVERT: a 60 TYR cc_start: 0.7815 (p90) cc_final: 0.7572 (p90) REVERT: q 48 TYR cc_start: 0.8112 (m-80) cc_final: 0.7741 (m-10) REVERT: q 62 VAL cc_start: 0.7980 (p) cc_final: 0.6405 (p) outliers start: 145 outliers final: 59 residues processed: 1162 average time/residue: 0.2191 time to fit residues: 419.4970 Evaluate side-chains 939 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 872 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 387 GLU Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 284 GLU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 111 GLU Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 187 LYS Chi-restraints excluded: chain P residue 253 THR Chi-restraints excluded: chain P residue 345 LEU Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain S residue 62 GLN Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain W residue 57 ILE Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain q residue 11 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 77 optimal weight: 4.9990 chunk 206 optimal weight: 5.9990 chunk 372 optimal weight: 4.9990 chunk 362 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 139 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 382 optimal weight: 8.9990 chunk 304 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS D 112 HIS ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 221 ASN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 705 GLN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 HIS I 126 GLN I 159 GLN P 166 HIS ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 HIS Q 85 ASN R 33 HIS R 56 ASN ** T 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 111 GLN W 51 HIS W 111 HIS Z 76 GLN q 12 GLN q 31 ASN q 72 ASN ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 GLN ** s 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.096650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.075382 restraints weight = 106376.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.077908 restraints weight = 48655.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.079816 restraints weight = 27080.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.079700 restraints weight = 20781.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.079971 restraints weight = 20191.582| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 34591 Z= 0.369 Angle : 1.252 80.572 46938 Z= 0.472 Chirality : 0.054 0.283 5137 Planarity : 0.007 0.132 5964 Dihedral : 8.348 137.893 4718 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.15 % Rotamer: Outliers : 6.39 % Allowed : 19.76 % Favored : 73.84 % 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: -1.00 (0.13), residues: 4129 helix: 0.02 (0.11), residues: 1873 sheet: -1.12 (0.26), residues: 381 loop : -1.20 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG a 37 TYR 0.047 0.003 TYR H 142 PHE 0.029 0.003 PHE Q 128 TRP 0.040 0.003 TRP q 86 HIS 0.011 0.002 HIS H 304 Details of bonding type rmsd covalent geometry : bond 0.00820 (34551) covalent geometry : angle 0.91559 (46848) SS BOND : bond 0.00396 ( 3) SS BOND : angle 1.29431 ( 6) hydrogen bonds : bond 0.05530 ( 1430) hydrogen bonds : angle 5.85320 ( 4137) metal coordination : bond 0.04649 ( 37) metal coordination : angle 20.20588 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 849 time to evaluate : 1.351 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: A 2 ASN cc_start: 0.8189 (m-40) cc_final: 0.7425 (m-40) REVERT: A 3 LEU cc_start: 0.8663 (tp) cc_final: 0.8369 (tt) REVERT: A 27 MET cc_start: 0.6428 (pmm) cc_final: 0.5792 (mmt) REVERT: A 88 MET cc_start: 0.8178 (ttp) cc_final: 0.7952 (tmm) REVERT: B 124 SER cc_start: 0.8741 (m) cc_final: 0.8412 (p) REVERT: B 129 ASP cc_start: 0.8721 (m-30) cc_final: 0.8204 (m-30) REVERT: B 137 LEU cc_start: 0.9332 (tp) cc_final: 0.9075 (tt) REVERT: B 154 GLU cc_start: 0.7248 (tp30) cc_final: 0.6550 (tp30) REVERT: B 161 MET cc_start: 0.8692 (ttp) cc_final: 0.8455 (ttm) REVERT: B 166 ASN cc_start: 0.8656 (m-40) cc_final: 0.8447 (m110) REVERT: B 170 TYR cc_start: 0.9202 (t80) cc_final: 0.8687 (t80) REVERT: B 215 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8679 (tm-30) REVERT: C 114 THR cc_start: 0.9028 (m) cc_final: 0.8699 (p) REVERT: C 165 TYR cc_start: 0.9092 (m-80) cc_final: 0.8736 (m-80) REVERT: C 168 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8237 (tm-30) REVERT: C 227 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: D 337 MET cc_start: 0.9104 (mtt) cc_final: 0.8716 (mtt) REVERT: E 67 LYS cc_start: 0.9153 (mtpt) cc_final: 0.8943 (mtmm) REVERT: E 69 TYR cc_start: 0.8531 (m-80) cc_final: 0.8300 (m-80) REVERT: E 153 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7451 (ttp80) REVERT: F 75 TRP cc_start: 0.8250 (t60) cc_final: 0.7917 (t60) REVERT: F 214 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8998 (mm-30) REVERT: G 126 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8658 (pp) REVERT: G 138 ASP cc_start: 0.9444 (OUTLIER) cc_final: 0.9194 (t0) REVERT: G 278 HIS cc_start: 0.8617 (OUTLIER) cc_final: 0.8400 (t-90) REVERT: G 410 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7451 (mt-10) REVERT: G 598 ASN cc_start: 0.8650 (p0) cc_final: 0.8287 (p0) REVERT: H 31 MET cc_start: 0.9106 (mtt) cc_final: 0.8853 (mtp) REVERT: H 47 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8708 (tm-30) REVERT: H 142 TYR cc_start: 0.8783 (m-80) cc_final: 0.8537 (m-10) REVERT: H 152 SER cc_start: 0.9266 (OUTLIER) cc_final: 0.8864 (t) REVERT: H 156 MET cc_start: 0.8411 (ptm) cc_final: 0.8132 (ptt) REVERT: H 172 MET cc_start: 0.7407 (ppp) cc_final: 0.7056 (ppp) REVERT: H 262 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8305 (tt0) REVERT: H 291 LYS cc_start: 0.9107 (mmmt) cc_final: 0.8674 (mtmt) REVERT: I 187 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.7842 (ttmt) REVERT: I 206 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8417 (tm-30) REVERT: I 208 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8073 (t70) REVERT: P 210 GLU cc_start: 0.8664 (tp30) cc_final: 0.8148 (tp30) REVERT: P 214 LEU cc_start: 0.8881 (mm) cc_final: 0.8663 (mm) REVERT: P 220 TYR cc_start: 0.7464 (m-10) cc_final: 0.7243 (m-10) REVERT: P 276 LEU cc_start: 0.8909 (mt) cc_final: 0.8706 (tp) REVERT: P 338 LEU cc_start: 0.8966 (tp) cc_final: 0.8646 (tp) REVERT: P 350 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8056 (mp) REVERT: Q 146 ASP cc_start: 0.7908 (p0) cc_final: 0.7483 (p0) REVERT: Q 148 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7457 (mm-30) REVERT: Q 164 PHE cc_start: 0.7723 (m-80) cc_final: 0.7341 (m-80) REVERT: R 95 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8008 (mt) REVERT: S 62 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8278 (pt0) REVERT: T 82 ARG cc_start: 0.7061 (mmp80) cc_final: 0.6837 (mmp80) REVERT: T 101 ASN cc_start: 0.9137 (p0) cc_final: 0.8267 (t0) REVERT: T 117 GLU cc_start: 0.9255 (mt-10) cc_final: 0.9026 (pt0) REVERT: T 120 MET cc_start: 0.8826 (mtm) cc_final: 0.8383 (ttm) REVERT: T 147 TYR cc_start: 0.7679 (t80) cc_final: 0.7328 (t80) REVERT: W 45 GLU cc_start: 0.8497 (tp30) cc_final: 0.8174 (tp30) REVERT: W 48 ASN cc_start: 0.9384 (m110) cc_final: 0.9182 (m110) REVERT: W 94 GLN cc_start: 0.8873 (mm-40) cc_final: 0.7923 (tt0) REVERT: W 98 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8504 (mtmm) REVERT: X 32 TYR cc_start: 0.8619 (t80) cc_final: 0.8056 (t80) REVERT: X 57 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7677 (tp) REVERT: X 98 ARG cc_start: 0.9256 (tmm-80) cc_final: 0.9038 (tmm-80) REVERT: Z 50 MET cc_start: 0.8142 (tpp) cc_final: 0.7138 (tpp) REVERT: Z 54 ASN cc_start: 0.8956 (m-40) cc_final: 0.8658 (m110) REVERT: Z 121 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.8021 (tp) REVERT: a 60 TYR cc_start: 0.7984 (p90) cc_final: 0.7534 (p90) REVERT: b 44 MET cc_start: 0.8394 (ptt) cc_final: 0.7801 (ptt) REVERT: b 80 TRP cc_start: 0.7773 (p-90) cc_final: 0.7184 (p-90) REVERT: b 81 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9343 (mt) REVERT: q 8 LYS cc_start: 0.7766 (ttmt) cc_final: 0.7120 (mmtt) REVERT: q 48 TYR cc_start: 0.7945 (m-80) cc_final: 0.7484 (m-80) REVERT: q 62 VAL cc_start: 0.7544 (p) cc_final: 0.7340 (p) REVERT: q 89 TRP cc_start: 0.8848 (t60) cc_final: 0.8012 (t60) REVERT: q 142 THR cc_start: 0.8742 (m) cc_final: 0.8337 (t) outliers start: 232 outliers final: 126 residues processed: 981 average time/residue: 0.2037 time to fit residues: 331.3542 Evaluate side-chains 896 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 757 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 287 THR 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 383 THR Chi-restraints excluded: chain F residue 411 SER Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 277 MET Chi-restraints excluded: chain G residue 278 HIS Chi-restraints excluded: chain G residue 284 GLU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 365 ASN Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain G residue 548 LEU Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 696 MET Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain H residue 301 CYS Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 187 LYS Chi-restraints excluded: chain I residue 195 ASP Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain P residue 43 HIS Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 253 THR Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 335 LEU Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 131 LYS Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 167 ASN Chi-restraints excluded: chain R residue 56 ASN Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 62 GLN Chi-restraints excluded: chain S residue 93 ASN Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain V residue 18 ASP Chi-restraints excluded: chain W residue 19 SER Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 59 VAL Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 35 MET Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain Z residue 97 ILE Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 58 ARG 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 379 optimal weight: 2.9990 chunk 345 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 397 optimal weight: 0.9990 chunk 296 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 196 optimal weight: 0.6980 chunk 313 optimal weight: 0.9990 chunk 274 optimal weight: 6.9990 chunk 329 optimal weight: 3.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN C 180 HIS ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 HIS ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 569 GLN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN ** T 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 94 GLN W 111 HIS X 102 GLN Z 76 GLN a 31 ASN q 17 HIS ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 110 GLN ** s 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.104521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.083766 restraints weight = 106323.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.086412 restraints weight = 46571.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.088060 restraints weight = 27917.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.089093 restraints weight = 20441.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.089627 restraints weight = 16974.726| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 34591 Z= 0.161 Angle : 1.032 76.357 46938 Z= 0.381 Chirality : 0.047 0.346 5137 Planarity : 0.006 0.129 5964 Dihedral : 8.186 142.064 4718 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.46 % Favored : 96.51 % Rotamer: Outliers : 4.74 % Allowed : 22.19 % Favored : 73.07 % 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: -0.56 (0.13), residues: 4129 helix: 0.51 (0.12), residues: 1855 sheet: -1.08 (0.25), residues: 391 loop : -1.04 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 59 TYR 0.043 0.002 TYR T 85 PHE 0.022 0.002 PHE D 458 TRP 0.037 0.002 TRP X 117 HIS 0.006 0.001 HIS F 281 Details of bonding type rmsd covalent geometry : bond 0.00368 (34551) covalent geometry : angle 0.75301 (46848) SS BOND : bond 0.00399 ( 3) SS BOND : angle 1.09755 ( 6) hydrogen bonds : bond 0.04622 ( 1430) hydrogen bonds : angle 5.31329 ( 4137) metal coordination : bond 0.02025 ( 37) metal coordination : angle 16.70202 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1049 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 877 time to evaluate : 1.401 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 75 LEU cc_start: 0.9376 (mt) cc_final: 0.9115 (mt) REVERT: A 98 LEU cc_start: 0.9538 (mt) cc_final: 0.8416 (mt) REVERT: B 129 ASP cc_start: 0.8580 (m-30) cc_final: 0.7949 (m-30) REVERT: B 170 TYR cc_start: 0.9094 (t80) cc_final: 0.8565 (t80) REVERT: B 190 TYR cc_start: 0.9402 (m-80) cc_final: 0.9183 (m-80) REVERT: B 215 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8444 (tm-30) REVERT: C 114 THR cc_start: 0.8978 (m) cc_final: 0.8617 (p) REVERT: C 165 TYR cc_start: 0.9114 (m-80) cc_final: 0.8645 (m-80) REVERT: C 168 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8254 (tm-30) REVERT: C 227 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: D 300 TRP cc_start: 0.8701 (t-100) cc_final: 0.8397 (t-100) REVERT: D 356 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9098 (pp) REVERT: E 167 LEU cc_start: 0.8431 (tp) cc_final: 0.8137 (tp) REVERT: F 149 MET cc_start: 0.8253 (mtm) cc_final: 0.8040 (ptp) REVERT: F 214 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8850 (mm-30) REVERT: F 387 GLU cc_start: 0.8168 (mp0) cc_final: 0.7651 (mp0) REVERT: G 126 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8458 (pp) REVERT: G 138 ASP cc_start: 0.9257 (OUTLIER) cc_final: 0.8927 (t0) REVERT: G 144 MET cc_start: 0.8840 (mmm) cc_final: 0.8487 (tpp) REVERT: G 254 MET cc_start: 0.8206 (mtm) cc_final: 0.7957 (mtt) REVERT: G 255 ASP cc_start: 0.8237 (m-30) cc_final: 0.8026 (m-30) REVERT: G 410 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7371 (mt-10) REVERT: G 511 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8305 (mmtp) REVERT: G 598 ASN cc_start: 0.8649 (p0) cc_final: 0.8215 (p0) REVERT: H 31 MET cc_start: 0.9036 (mtt) cc_final: 0.8787 (mtp) REVERT: H 47 GLN cc_start: 0.9138 (tm-30) cc_final: 0.7870 (tm-30) REVERT: H 51 ASP cc_start: 0.8820 (p0) cc_final: 0.8515 (p0) REVERT: H 152 SER cc_start: 0.9318 (m) cc_final: 0.8879 (t) REVERT: H 156 MET cc_start: 0.8365 (ptm) cc_final: 0.7994 (ptt) REVERT: H 172 MET cc_start: 0.7490 (ppp) cc_final: 0.7228 (ppp) REVERT: H 173 TRP cc_start: 0.8466 (m-10) cc_final: 0.7424 (m-10) REVERT: H 243 LEU cc_start: 0.8741 (mm) cc_final: 0.8501 (mm) REVERT: H 260 MET cc_start: 0.8957 (tmm) cc_final: 0.8517 (tmm) REVERT: H 262 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8214 (tt0) REVERT: H 291 LYS cc_start: 0.9016 (mmmt) cc_final: 0.8588 (mtmt) REVERT: I 206 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8383 (tm-30) REVERT: I 208 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8136 (t70) REVERT: P 210 GLU cc_start: 0.8628 (tp30) cc_final: 0.8045 (tp30) REVERT: P 214 LEU cc_start: 0.8828 (mm) cc_final: 0.8390 (mm) REVERT: Q 69 GLU cc_start: 0.8162 (tp30) cc_final: 0.7882 (tp30) REVERT: Q 87 MET cc_start: 0.8344 (mmt) cc_final: 0.7679 (mmm) REVERT: Q 139 GLU cc_start: 0.8268 (pp20) cc_final: 0.7962 (pp20) REVERT: Q 146 ASP cc_start: 0.7802 (p0) cc_final: 0.7216 (p0) REVERT: Q 148 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7540 (mm-30) REVERT: Q 160 TYR cc_start: 0.6882 (t80) cc_final: 0.6646 (t80) REVERT: Q 164 PHE cc_start: 0.7963 (m-80) cc_final: 0.7461 (m-80) REVERT: S 41 TYR cc_start: 0.8418 (t80) cc_final: 0.8072 (t80) REVERT: S 62 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8244 (pt0) REVERT: T 88 LYS cc_start: 0.8708 (mmmt) cc_final: 0.8358 (mmmt) REVERT: T 92 LYS cc_start: 0.7505 (pttm) cc_final: 0.7301 (pttm) REVERT: T 101 ASN cc_start: 0.9113 (p0) cc_final: 0.8145 (t0) REVERT: T 117 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8834 (pt0) REVERT: T 120 MET cc_start: 0.8835 (mtm) cc_final: 0.8508 (ttm) REVERT: T 147 TYR cc_start: 0.7727 (t80) cc_final: 0.7417 (t80) REVERT: W 45 GLU cc_start: 0.8485 (tp30) cc_final: 0.8210 (tp30) REVERT: W 48 ASN cc_start: 0.9346 (m110) cc_final: 0.9095 (m-40) REVERT: W 68 GLU cc_start: 0.8612 (tp30) cc_final: 0.8292 (tp30) REVERT: W 94 GLN cc_start: 0.8802 (mm110) cc_final: 0.8599 (mm-40) REVERT: W 98 LYS cc_start: 0.8540 (mtpt) cc_final: 0.8319 (mttp) REVERT: X 98 ARG cc_start: 0.9339 (tmm-80) cc_final: 0.8941 (tmm-80) REVERT: Z 50 MET cc_start: 0.8002 (tpp) cc_final: 0.7019 (tpp) REVERT: Z 54 ASN cc_start: 0.8861 (m-40) cc_final: 0.8295 (m110) REVERT: Z 64 ASP cc_start: 0.8551 (p0) cc_final: 0.8330 (p0) REVERT: Z 75 PHE cc_start: 0.8818 (m-80) cc_final: 0.8556 (m-80) REVERT: Z 79 LYS cc_start: 0.8769 (tppp) cc_final: 0.8164 (tppp) REVERT: Z 124 MET cc_start: 0.8493 (mmm) cc_final: 0.8194 (mmm) REVERT: a 16 LEU cc_start: 0.9420 (mp) cc_final: 0.9197 (mp) REVERT: a 46 TYR cc_start: 0.8411 (t80) cc_final: 0.8175 (t80) REVERT: q 8 LYS cc_start: 0.7850 (ttmt) cc_final: 0.7122 (mmtm) REVERT: q 46 ASN cc_start: 0.6651 (t0) cc_final: 0.6357 (t0) REVERT: q 81 MET cc_start: 0.7598 (mtt) cc_final: 0.7301 (mpp) REVERT: q 88 ARG cc_start: 0.6496 (ttm-80) cc_final: 0.6123 (ttm-80) REVERT: q 89 TRP cc_start: 0.8791 (t60) cc_final: 0.8282 (t60) REVERT: q 93 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7782 (mtp) REVERT: q 142 THR cc_start: 0.8779 (m) cc_final: 0.8449 (t) outliers start: 172 outliers final: 88 residues processed: 960 average time/residue: 0.2158 time to fit residues: 343.2492 Evaluate side-chains 878 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 782 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 284 GLU Chi-restraints excluded: chain G residue 408 ARG Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 511 LYS Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 648 GLU Chi-restraints excluded: chain G residue 696 MET Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 111 GLU Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 335 LEU Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 131 LYS Chi-restraints excluded: chain Q residue 167 ASN Chi-restraints excluded: chain S residue 62 GLN Chi-restraints excluded: chain S residue 93 ASN Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain W residue 19 SER Chi-restraints excluded: chain W residue 29 ASN Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain X residue 117 TRP Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain Z residue 97 ILE Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain q residue 93 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 306 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 321 optimal weight: 3.9990 chunk 279 optimal weight: 8.9990 chunk 163 optimal weight: 0.6980 chunk 202 optimal weight: 0.0870 chunk 334 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 223 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 376 optimal weight: 9.9990 overall best weight: 2.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN Q 85 ASN Q 88 GLN ** T 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 76 GLN a 58 ASN r 9 GLN ** s 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.101468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.080525 restraints weight = 107484.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.083196 restraints weight = 47848.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.084852 restraints weight = 28868.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.085901 restraints weight = 21182.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.086505 restraints weight = 17604.564| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.6334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 34591 Z= 0.207 Angle : 1.045 78.743 46938 Z= 0.382 Chirality : 0.047 0.309 5137 Planarity : 0.005 0.129 5964 Dihedral : 8.122 144.755 4718 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.85 % Favored : 96.12 % Rotamer: Outliers : 5.02 % Allowed : 22.71 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.13), residues: 4129 helix: 0.59 (0.12), residues: 1864 sheet: -1.10 (0.26), residues: 385 loop : -0.92 (0.15), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 207 TYR 0.042 0.002 TYR T 85 PHE 0.018 0.002 PHE A 62 TRP 0.031 0.002 TRP X 117 HIS 0.006 0.001 HIS D 431 Details of bonding type rmsd covalent geometry : bond 0.00469 (34551) covalent geometry : angle 0.75312 (46848) SS BOND : bond 0.00368 ( 3) SS BOND : angle 1.11711 ( 6) hydrogen bonds : bond 0.04444 ( 1430) hydrogen bonds : angle 5.24978 ( 4137) metal coordination : bond 0.02623 ( 37) metal coordination : angle 17.14082 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 824 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: A 88 MET cc_start: 0.8274 (ttp) cc_final: 0.8040 (ttp) REVERT: A 105 GLU cc_start: 0.9252 (tp30) cc_final: 0.8944 (tp30) REVERT: B 129 ASP cc_start: 0.8525 (m-30) cc_final: 0.7862 (m-30) REVERT: B 170 TYR cc_start: 0.9170 (t80) cc_final: 0.8634 (t80) REVERT: B 215 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8323 (tm-30) REVERT: C 114 THR cc_start: 0.8979 (m) cc_final: 0.8656 (p) REVERT: C 165 TYR cc_start: 0.9106 (m-80) cc_final: 0.8627 (m-80) REVERT: C 168 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8200 (tm-30) REVERT: C 209 LEU cc_start: 0.9320 (mp) cc_final: 0.9061 (mt) REVERT: C 227 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7500 (tt0) REVERT: D 82 LEU cc_start: 0.8789 (tt) cc_final: 0.8588 (tt) REVERT: D 294 ARG cc_start: 0.8407 (mtm-85) cc_final: 0.8159 (mtt-85) REVERT: D 300 TRP cc_start: 0.8758 (t-100) cc_final: 0.8477 (t-100) REVERT: D 356 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9136 (pp) REVERT: E 120 MET cc_start: 0.8753 (mpp) cc_final: 0.8531 (mpp) REVERT: E 132 GLN cc_start: 0.8029 (pm20) cc_final: 0.7756 (pm20) REVERT: E 167 LEU cc_start: 0.8501 (tp) cc_final: 0.8132 (tp) REVERT: E 172 GLU cc_start: 0.8782 (pm20) cc_final: 0.8521 (mp0) REVERT: E 174 GLU cc_start: 0.8200 (mp0) cc_final: 0.7221 (mm-30) REVERT: F 214 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8756 (mm-30) REVERT: F 220 GLN cc_start: 0.7853 (pm20) cc_final: 0.7581 (pm20) REVERT: F 387 GLU cc_start: 0.8188 (mp0) cc_final: 0.7702 (mp0) REVERT: G 94 MET cc_start: 0.8688 (mmm) cc_final: 0.8474 (tpp) REVERT: G 126 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8481 (pp) REVERT: G 138 ASP cc_start: 0.9280 (OUTLIER) cc_final: 0.9022 (t0) REVERT: G 254 MET cc_start: 0.8423 (mtm) cc_final: 0.8152 (mtt) REVERT: G 255 ASP cc_start: 0.8218 (m-30) cc_final: 0.7970 (m-30) REVERT: G 283 GLU cc_start: 0.7867 (pm20) cc_final: 0.7655 (pm20) REVERT: G 410 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7456 (mt-10) REVERT: G 511 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8589 (mmtp) REVERT: G 598 ASN cc_start: 0.8708 (p0) cc_final: 0.8346 (p0) REVERT: H 31 MET cc_start: 0.9023 (mtt) cc_final: 0.8820 (mtp) REVERT: H 47 GLN cc_start: 0.9173 (tm-30) cc_final: 0.8374 (tm-30) REVERT: H 142 TYR cc_start: 0.8688 (m-80) cc_final: 0.8466 (m-10) REVERT: H 152 SER cc_start: 0.9353 (OUTLIER) cc_final: 0.8924 (t) REVERT: H 156 MET cc_start: 0.8430 (ptm) cc_final: 0.8043 (ptt) REVERT: H 172 MET cc_start: 0.7465 (ppp) cc_final: 0.7218 (ppp) REVERT: H 260 MET cc_start: 0.8976 (tmm) cc_final: 0.8481 (tmm) REVERT: H 262 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8381 (tt0) REVERT: H 291 LYS cc_start: 0.9122 (mmmt) cc_final: 0.8556 (mtmt) REVERT: I 98 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7228 (mtt-85) REVERT: I 165 ASP cc_start: 0.9075 (OUTLIER) cc_final: 0.8873 (m-30) REVERT: I 206 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8438 (tm-30) REVERT: I 208 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8040 (t70) REVERT: P 89 TYR cc_start: 0.8184 (t80) cc_final: 0.7839 (t80) REVERT: P 210 GLU cc_start: 0.8685 (tp30) cc_final: 0.8161 (tp30) REVERT: Q 146 ASP cc_start: 0.7885 (p0) cc_final: 0.7239 (p0) REVERT: Q 148 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7605 (mm-30) REVERT: Q 160 TYR cc_start: 0.6602 (t80) cc_final: 0.6159 (t80) REVERT: Q 164 PHE cc_start: 0.7945 (m-80) cc_final: 0.7222 (m-80) REVERT: S 41 TYR cc_start: 0.8480 (t80) cc_final: 0.8256 (t80) REVERT: S 62 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8332 (pt0) REVERT: T 88 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8393 (mmmt) REVERT: T 98 LEU cc_start: 0.8022 (tp) cc_final: 0.7764 (tt) REVERT: T 101 ASN cc_start: 0.9125 (p0) cc_final: 0.8185 (t0) REVERT: T 120 MET cc_start: 0.8748 (mtm) cc_final: 0.8437 (ttm) REVERT: T 147 TYR cc_start: 0.7808 (t80) cc_final: 0.7463 (t80) REVERT: W 45 GLU cc_start: 0.8654 (tp30) cc_final: 0.8277 (tp30) REVERT: W 48 ASN cc_start: 0.9342 (m110) cc_final: 0.9087 (m-40) REVERT: W 73 ASN cc_start: 0.8422 (m-40) cc_final: 0.8168 (t0) REVERT: W 94 GLN cc_start: 0.8817 (mm110) cc_final: 0.8323 (tt0) REVERT: W 98 LYS cc_start: 0.8490 (mtpt) cc_final: 0.8224 (mttp) REVERT: X 44 MET cc_start: 0.8932 (mtt) cc_final: 0.8628 (mtt) REVERT: X 98 ARG cc_start: 0.9376 (tmm-80) cc_final: 0.8868 (tmm-80) REVERT: Z 50 MET cc_start: 0.7998 (tpp) cc_final: 0.7039 (tpp) REVERT: Z 54 ASN cc_start: 0.8894 (m-40) cc_final: 0.8292 (m110) REVERT: Z 75 PHE cc_start: 0.8868 (m-80) cc_final: 0.8655 (m-80) REVERT: Z 79 LYS cc_start: 0.8692 (tppp) cc_final: 0.8031 (tppp) REVERT: Z 124 MET cc_start: 0.8556 (mmm) cc_final: 0.8127 (mmm) REVERT: a 46 TYR cc_start: 0.8515 (t80) cc_final: 0.8083 (t80) REVERT: q 8 LYS cc_start: 0.7807 (ttmt) cc_final: 0.7114 (mmtm) REVERT: q 71 LYS cc_start: 0.5082 (tptm) cc_final: 0.4817 (mtpp) REVERT: q 81 MET cc_start: 0.7693 (mtt) cc_final: 0.7416 (mtt) REVERT: q 86 TRP cc_start: 0.7679 (m100) cc_final: 0.7227 (m100) REVERT: q 89 TRP cc_start: 0.8809 (t60) cc_final: 0.8309 (t60) REVERT: q 93 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.8047 (mtp) REVERT: q 142 THR cc_start: 0.8864 (m) cc_final: 0.8526 (t) outliers start: 182 outliers final: 118 residues processed: 918 average time/residue: 0.2052 time to fit residues: 313.0313 Evaluate side-chains 903 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 774 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 277 MET Chi-restraints excluded: chain G residue 284 GLU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 310 GLU Chi-restraints excluded: chain G residue 365 ASN Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 511 LYS Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 648 GLU Chi-restraints excluded: chain G residue 696 MET Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain H residue 301 CYS Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 111 GLU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 165 ASP Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 253 THR Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 335 LEU Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 167 ASN Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain S residue 62 GLN Chi-restraints excluded: chain S residue 93 ASN Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain V residue 18 ASP Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain X residue 117 TRP Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 71 LEU Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 55 VAL 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 93 MET Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 148 optimal weight: 2.9990 chunk 246 optimal weight: 0.7980 chunk 243 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 277 optimal weight: 9.9990 chunk 221 optimal weight: 7.9990 chunk 366 optimal weight: 20.0000 chunk 384 optimal weight: 1.9990 chunk 326 optimal weight: 9.9990 chunk 121 optimal weight: 0.0570 chunk 159 optimal weight: 7.9990 overall best weight: 2.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 HIS ** F 418 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** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN Q 123 ASN ** T 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 76 GLN ** s 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.101753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.080949 restraints weight = 106727.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.083630 restraints weight = 47742.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.085269 restraints weight = 28711.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.086303 restraints weight = 21059.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.086926 restraints weight = 17517.371| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.6597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 34591 Z= 0.190 Angle : 1.029 79.183 46938 Z= 0.375 Chirality : 0.046 0.304 5137 Planarity : 0.005 0.130 5964 Dihedral : 8.102 144.186 4718 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 4.96 % Allowed : 23.90 % Favored : 71.14 % 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: -0.38 (0.13), residues: 4129 helix: 0.65 (0.12), residues: 1865 sheet: -1.24 (0.26), residues: 396 loop : -0.89 (0.15), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG q 88 TYR 0.038 0.002 TYR T 85 PHE 0.018 0.002 PHE s 45 TRP 0.039 0.002 TRP V 97 HIS 0.008 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00439 (34551) covalent geometry : angle 0.73937 (46848) SS BOND : bond 0.00389 ( 3) SS BOND : angle 1.12430 ( 6) hydrogen bonds : bond 0.04296 ( 1430) hydrogen bonds : angle 5.19007 ( 4137) metal coordination : bond 0.02322 ( 37) metal coordination : angle 16.93867 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 817 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.9328 (tp30) cc_final: 0.9031 (tp30) REVERT: B 117 PHE cc_start: 0.9190 (m-10) cc_final: 0.8987 (m-10) REVERT: B 145 LEU cc_start: 0.9660 (OUTLIER) cc_final: 0.9345 (tp) REVERT: B 170 TYR cc_start: 0.9169 (t80) cc_final: 0.8633 (t80) REVERT: B 190 TYR cc_start: 0.9406 (m-80) cc_final: 0.9194 (m-80) REVERT: C 114 THR cc_start: 0.8972 (m) cc_final: 0.8643 (p) REVERT: C 165 TYR cc_start: 0.9144 (m-80) cc_final: 0.8691 (m-80) REVERT: C 168 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8257 (tm-30) REVERT: C 209 LEU cc_start: 0.9324 (mp) cc_final: 0.9029 (mt) REVERT: C 214 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8754 (pt0) REVERT: C 227 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: D 82 LEU cc_start: 0.8777 (tt) cc_final: 0.8557 (tt) REVERT: D 185 MET cc_start: 0.9197 (tpt) cc_final: 0.8876 (tpp) REVERT: D 300 TRP cc_start: 0.8736 (t-100) cc_final: 0.8396 (t-100) REVERT: E 118 TYR cc_start: 0.8177 (m-80) cc_final: 0.7898 (m-80) REVERT: E 167 LEU cc_start: 0.8585 (tp) cc_final: 0.8186 (tp) REVERT: E 174 GLU cc_start: 0.8250 (mp0) cc_final: 0.7366 (mm-30) REVERT: F 214 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8463 (mm-30) REVERT: F 220 GLN cc_start: 0.7974 (pm20) cc_final: 0.7644 (pm20) REVERT: F 387 GLU cc_start: 0.8180 (mp0) cc_final: 0.7735 (mp0) REVERT: G 94 MET cc_start: 0.8717 (mmm) cc_final: 0.8498 (tpp) REVERT: G 126 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8523 (pp) REVERT: G 138 ASP cc_start: 0.9341 (OUTLIER) cc_final: 0.9017 (t0) REVERT: G 254 MET cc_start: 0.8436 (mtm) cc_final: 0.8164 (mtt) REVERT: G 255 ASP cc_start: 0.8258 (m-30) cc_final: 0.8002 (m-30) REVERT: G 598 ASN cc_start: 0.8807 (p0) cc_final: 0.8544 (p0) REVERT: H 47 GLN cc_start: 0.9205 (tm-30) cc_final: 0.8370 (tm-30) REVERT: H 142 TYR cc_start: 0.8809 (m-80) cc_final: 0.8505 (m-10) REVERT: H 152 SER cc_start: 0.9348 (m) cc_final: 0.8910 (t) REVERT: H 156 MET cc_start: 0.8430 (ptm) cc_final: 0.8134 (ptt) REVERT: H 172 MET cc_start: 0.7535 (ppp) cc_final: 0.7318 (ppp) REVERT: H 173 TRP cc_start: 0.8580 (m-10) cc_final: 0.7605 (m-10) REVERT: H 202 GLU cc_start: 0.7234 (mm-30) cc_final: 0.7000 (mm-30) REVERT: H 260 MET cc_start: 0.9019 (tmm) cc_final: 0.8524 (tmm) REVERT: H 262 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8379 (tt0) REVERT: H 291 LYS cc_start: 0.9039 (mmmt) cc_final: 0.8536 (mtmt) REVERT: I 206 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8532 (tm-30) REVERT: I 208 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.8143 (t70) REVERT: P 210 GLU cc_start: 0.8552 (tp30) cc_final: 0.7989 (tp30) REVERT: Q 69 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7923 (tp30) REVERT: Q 146 ASP cc_start: 0.7903 (p0) cc_final: 0.7246 (p0) REVERT: Q 148 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7765 (mm-30) REVERT: Q 164 PHE cc_start: 0.7897 (m-80) cc_final: 0.7644 (m-80) REVERT: S 62 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8333 (pt0) REVERT: T 101 ASN cc_start: 0.9149 (p0) cc_final: 0.8242 (t0) REVERT: T 120 MET cc_start: 0.8829 (mtm) cc_final: 0.8615 (mtt) REVERT: T 147 TYR cc_start: 0.7809 (t80) cc_final: 0.7496 (t80) REVERT: W 27 ASP cc_start: 0.8385 (t70) cc_final: 0.8132 (t70) REVERT: W 45 GLU cc_start: 0.8718 (tp30) cc_final: 0.8268 (tp30) REVERT: W 48 ASN cc_start: 0.9401 (m110) cc_final: 0.9104 (m-40) REVERT: W 68 GLU cc_start: 0.8637 (tp30) cc_final: 0.8380 (tp30) REVERT: W 94 GLN cc_start: 0.8866 (mm110) cc_final: 0.8375 (tt0) REVERT: W 98 LYS cc_start: 0.8440 (mtpt) cc_final: 0.8168 (mttp) REVERT: X 44 MET cc_start: 0.8854 (mtt) cc_final: 0.8485 (mtt) REVERT: X 98 ARG cc_start: 0.9388 (tmm-80) cc_final: 0.8973 (tmm-80) REVERT: Z 50 MET cc_start: 0.8102 (tpp) cc_final: 0.7226 (tpp) REVERT: Z 54 ASN cc_start: 0.8913 (m-40) cc_final: 0.8290 (m110) REVERT: Z 79 LYS cc_start: 0.8818 (tppp) cc_final: 0.8140 (tppp) REVERT: Z 124 MET cc_start: 0.8594 (mmm) cc_final: 0.8088 (mmm) REVERT: a 35 GLU cc_start: 0.5569 (tp30) cc_final: 0.5257 (tp30) REVERT: a 46 TYR cc_start: 0.8579 (t80) cc_final: 0.8035 (t80) REVERT: b 16 GLU cc_start: 0.7823 (pt0) cc_final: 0.7623 (pt0) REVERT: q 8 LYS cc_start: 0.7843 (ttmt) cc_final: 0.7151 (mmtm) REVERT: q 71 LYS cc_start: 0.5003 (tptm) cc_final: 0.4738 (mtpp) REVERT: q 89 TRP cc_start: 0.8818 (t60) cc_final: 0.8199 (t60) REVERT: q 142 THR cc_start: 0.8912 (m) cc_final: 0.8580 (t) outliers start: 180 outliers final: 118 residues processed: 912 average time/residue: 0.2052 time to fit residues: 309.7695 Evaluate side-chains 897 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 773 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 277 MET Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 310 GLU Chi-restraints excluded: chain G residue 365 ASN Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 648 GLU Chi-restraints excluded: chain G residue 696 MET Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain H residue 301 CYS Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain P residue 43 HIS Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 272 LEU Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 335 LEU Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 167 ASN Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain S residue 62 GLN Chi-restraints excluded: chain S residue 93 ASN Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain V residue 18 ASP Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain W residue 19 SER Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 69 MET Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain X residue 117 TRP Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain Z residue 71 LEU Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 55 VAL 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 r residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 55 optimal weight: 0.6980 chunk 260 optimal weight: 0.9980 chunk 250 optimal weight: 2.9990 chunk 363 optimal weight: 0.0270 chunk 129 optimal weight: 30.0000 chunk 213 optimal weight: 3.9990 chunk 265 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 300 optimal weight: 0.1980 chunk 226 optimal weight: 2.9990 chunk 359 optimal weight: 4.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 HIS ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 ASN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 ASN ** G 260 ASN ** 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 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 76 GLN ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 49 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.102975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.081384 restraints weight = 104832.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.084119 restraints weight = 47708.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.085856 restraints weight = 29060.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.086943 restraints weight = 21401.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.087595 restraints weight = 17852.965| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.6822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 34591 Z= 0.151 Angle : 1.000 77.175 46938 Z= 0.373 Chirality : 0.046 0.294 5137 Planarity : 0.005 0.129 5964 Dihedral : 8.051 141.126 4718 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.85 % Favored : 96.12 % Rotamer: Outliers : 3.97 % Allowed : 25.47 % Favored : 70.56 % 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: -0.29 (0.13), residues: 4129 helix: 0.71 (0.12), residues: 1868 sheet: -1.12 (0.27), residues: 366 loop : -0.85 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG q 34 TYR 0.038 0.002 TYR T 85 PHE 0.019 0.001 PHE D 458 TRP 0.063 0.002 TRP V 97 HIS 0.008 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00348 (34551) covalent geometry : angle 0.75029 (46848) SS BOND : bond 0.00438 ( 3) SS BOND : angle 1.18536 ( 6) hydrogen bonds : bond 0.04099 ( 1430) hydrogen bonds : angle 5.09128 ( 4137) metal coordination : bond 0.01937 ( 37) metal coordination : angle 15.64163 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 854 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.7666 (t80) REVERT: A 68 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8376 (mm-30) REVERT: A 93 ILE cc_start: 0.8075 (mm) cc_final: 0.7745 (tp) REVERT: A 105 GLU cc_start: 0.9363 (tp30) cc_final: 0.9118 (tp30) REVERT: B 77 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7779 (ptpt) REVERT: B 117 PHE cc_start: 0.9157 (m-10) cc_final: 0.8939 (m-10) REVERT: B 129 ASP cc_start: 0.8518 (m-30) cc_final: 0.7789 (m-30) REVERT: B 145 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9364 (tp) REVERT: B 170 TYR cc_start: 0.9126 (t80) cc_final: 0.8595 (t80) REVERT: B 215 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8573 (tm-30) REVERT: C 114 THR cc_start: 0.8974 (m) cc_final: 0.8617 (p) REVERT: C 165 TYR cc_start: 0.9156 (m-80) cc_final: 0.8682 (m-80) REVERT: C 168 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8225 (tm-30) REVERT: C 214 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8748 (pt0) REVERT: D 82 LEU cc_start: 0.8728 (tt) cc_final: 0.8499 (tt) REVERT: D 158 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9118 (mm) REVERT: D 185 MET cc_start: 0.9100 (tpt) cc_final: 0.8785 (tpp) REVERT: D 300 TRP cc_start: 0.8659 (t-100) cc_final: 0.8438 (t-100) REVERT: D 460 GLU cc_start: 0.8220 (pt0) cc_final: 0.7435 (pt0) REVERT: E 74 GLN cc_start: 0.8068 (mt0) cc_final: 0.7283 (tt0) REVERT: E 91 TRP cc_start: 0.6348 (t-100) cc_final: 0.6137 (t-100) REVERT: E 118 TYR cc_start: 0.7979 (m-80) cc_final: 0.7714 (m-80) REVERT: E 167 LEU cc_start: 0.8596 (tp) cc_final: 0.8229 (tp) REVERT: E 173 VAL cc_start: 0.8975 (p) cc_final: 0.8599 (p) REVERT: E 174 GLU cc_start: 0.8268 (mp0) cc_final: 0.7530 (mm-30) REVERT: F 214 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8522 (mm-30) REVERT: F 220 GLN cc_start: 0.8047 (pm20) cc_final: 0.7741 (pm20) REVERT: F 387 GLU cc_start: 0.8136 (mp0) cc_final: 0.7726 (mp0) REVERT: F 436 GLN cc_start: 0.8706 (mt0) cc_final: 0.8481 (mp10) REVERT: F 450 MET cc_start: 0.8929 (ttm) cc_final: 0.8680 (ttp) REVERT: G 126 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8491 (pp) REVERT: G 138 ASP cc_start: 0.9254 (OUTLIER) cc_final: 0.9004 (t0) REVERT: G 254 MET cc_start: 0.8274 (mtm) cc_final: 0.8050 (mtt) REVERT: G 283 GLU cc_start: 0.7890 (pm20) cc_final: 0.7449 (pt0) REVERT: G 410 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6896 (mt-10) REVERT: G 598 ASN cc_start: 0.8760 (p0) cc_final: 0.8512 (p0) REVERT: H 47 GLN cc_start: 0.9168 (tm-30) cc_final: 0.8343 (tm-30) REVERT: H 142 TYR cc_start: 0.8806 (m-80) cc_final: 0.8478 (m-10) REVERT: H 152 SER cc_start: 0.9395 (m) cc_final: 0.8961 (t) REVERT: H 156 MET cc_start: 0.8410 (ptm) cc_final: 0.8083 (ptt) REVERT: H 172 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.7286 (ppp) REVERT: H 173 TRP cc_start: 0.8620 (m-10) cc_final: 0.7527 (m-10) REVERT: H 202 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7028 (mm-30) REVERT: H 260 MET cc_start: 0.9034 (tmm) cc_final: 0.8631 (tmm) REVERT: H 261 MET cc_start: 0.8269 (mtm) cc_final: 0.7655 (mtm) REVERT: H 262 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8335 (tt0) REVERT: H 291 LYS cc_start: 0.8964 (mmmt) cc_final: 0.8461 (mtmt) REVERT: I 59 ARG cc_start: 0.7526 (mpt180) cc_final: 0.7283 (mmt180) REVERT: I 206 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8491 (tm-30) REVERT: I 208 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8051 (t70) REVERT: P 210 GLU cc_start: 0.8474 (tp30) cc_final: 0.7943 (tp30) REVERT: Q 69 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7848 (tp30) REVERT: Q 146 ASP cc_start: 0.7838 (p0) cc_final: 0.7545 (p0) REVERT: Q 148 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8011 (mm-30) REVERT: Q 164 PHE cc_start: 0.7918 (m-80) cc_final: 0.7255 (m-80) REVERT: S 62 GLN cc_start: 0.8604 (pt0) cc_final: 0.8359 (pt0) REVERT: T 101 ASN cc_start: 0.9235 (p0) cc_final: 0.8317 (t0) REVERT: T 147 TYR cc_start: 0.7845 (t80) cc_final: 0.7504 (t80) REVERT: W 27 ASP cc_start: 0.8366 (t70) cc_final: 0.7875 (t70) REVERT: W 45 GLU cc_start: 0.8742 (tp30) cc_final: 0.8189 (tp30) REVERT: W 48 ASN cc_start: 0.9381 (m110) cc_final: 0.9048 (m-40) REVERT: W 68 GLU cc_start: 0.8664 (tp30) cc_final: 0.8333 (tp30) REVERT: W 94 GLN cc_start: 0.8890 (mm110) cc_final: 0.8438 (tt0) REVERT: W 98 LYS cc_start: 0.8240 (mtpt) cc_final: 0.7994 (mttp) REVERT: X 44 MET cc_start: 0.8846 (mtt) cc_final: 0.8440 (mtt) REVERT: X 98 ARG cc_start: 0.9409 (tmm-80) cc_final: 0.8969 (tmm-80) REVERT: Z 50 MET cc_start: 0.8194 (tpp) cc_final: 0.7477 (tpp) REVERT: Z 54 ASN cc_start: 0.8765 (m-40) cc_final: 0.8066 (m110) REVERT: Z 64 ASP cc_start: 0.8447 (p0) cc_final: 0.8234 (p0) REVERT: Z 72 MET cc_start: 0.8437 (mmm) cc_final: 0.8100 (mmm) REVERT: Z 75 PHE cc_start: 0.8960 (m-80) cc_final: 0.8654 (m-80) REVERT: Z 76 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8885 (tp-100) REVERT: Z 79 LYS cc_start: 0.8614 (tppp) cc_final: 0.8050 (tppp) REVERT: Z 80 ASP cc_start: 0.8679 (p0) cc_final: 0.8349 (p0) REVERT: Z 111 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.6251 (m-80) REVERT: Z 124 MET cc_start: 0.8542 (mmm) cc_final: 0.8034 (mmm) REVERT: a 46 TYR cc_start: 0.8594 (t80) cc_final: 0.7936 (t80) REVERT: q 8 LYS cc_start: 0.7850 (ttmt) cc_final: 0.7148 (mmtm) REVERT: q 58 ARG cc_start: 0.7694 (mtm180) cc_final: 0.7405 (mtm180) REVERT: q 71 LYS cc_start: 0.4839 (tptm) cc_final: 0.4620 (mtpp) REVERT: q 81 MET cc_start: 0.7517 (mtt) cc_final: 0.7312 (mpp) REVERT: q 142 THR cc_start: 0.8899 (m) cc_final: 0.8580 (t) outliers start: 144 outliers final: 99 residues processed: 918 average time/residue: 0.2031 time to fit residues: 309.3657 Evaluate side-chains 883 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 775 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 310 GLU Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 648 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain H residue 301 CYS Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain P residue 272 LEU Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 335 LEU Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 167 ASN Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain S residue 93 ASN Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain V residue 18 ASP Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain W residue 19 SER Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain X residue 117 TRP Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 71 LEU Chi-restraints excluded: chain Z residue 76 GLN Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain Z residue 111 PHE Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 395 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 230 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 193 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 390 optimal weight: 10.0000 chunk 253 optimal weight: 6.9990 chunk 333 optimal weight: 3.9990 chunk 309 optimal weight: 20.0000 chunk 239 optimal weight: 0.3980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 GLN E 98 ASN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** 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 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 216 HIS ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.102319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.080818 restraints weight = 103999.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.083512 restraints weight = 47454.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.085245 restraints weight = 29088.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.086334 restraints weight = 21466.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.086894 restraints weight = 17884.213| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.6960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 34591 Z= 0.155 Angle : 0.995 77.511 46938 Z= 0.375 Chirality : 0.046 0.271 5137 Planarity : 0.005 0.129 5964 Dihedral : 7.962 139.359 4718 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.78 % Favored : 96.20 % Rotamer: Outliers : 3.80 % Allowed : 25.55 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.26 (0.13), residues: 4129 helix: 0.72 (0.12), residues: 1863 sheet: -1.11 (0.27), residues: 364 loop : -0.81 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 96 TYR 0.045 0.002 TYR E 112 PHE 0.026 0.001 PHE A 62 TRP 0.029 0.002 TRP X 117 HIS 0.010 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00363 (34551) covalent geometry : angle 0.74899 (46848) SS BOND : bond 0.00395 ( 3) SS BOND : angle 1.17149 ( 6) hydrogen bonds : bond 0.04066 ( 1430) hydrogen bonds : angle 5.04888 ( 4137) metal coordination : bond 0.01982 ( 37) metal coordination : angle 15.50026 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 820 time to evaluate : 1.457 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 4 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.7821 (t80) REVERT: A 68 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8418 (mt-10) REVERT: A 93 ILE cc_start: 0.8067 (mm) cc_final: 0.7754 (tp) REVERT: A 105 GLU cc_start: 0.9393 (tp30) cc_final: 0.9131 (tp30) REVERT: B 77 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7779 (ptmt) REVERT: B 106 HIS cc_start: 0.8725 (m170) cc_final: 0.8493 (m-70) REVERT: B 117 PHE cc_start: 0.9195 (m-10) cc_final: 0.8965 (m-10) REVERT: B 145 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9386 (tp) REVERT: B 156 ARG cc_start: 0.8367 (ptt180) cc_final: 0.7429 (ptt180) REVERT: B 170 TYR cc_start: 0.9106 (t80) cc_final: 0.8596 (t80) REVERT: C 114 THR cc_start: 0.8970 (m) cc_final: 0.8620 (p) REVERT: C 165 TYR cc_start: 0.9169 (m-80) cc_final: 0.8924 (m-80) REVERT: C 168 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8232 (tm-30) REVERT: C 214 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8734 (pt0) REVERT: C 239 GLU cc_start: 0.8246 (pm20) cc_final: 0.8019 (pm20) REVERT: D 158 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9154 (mm) REVERT: D 185 MET cc_start: 0.9057 (tpt) cc_final: 0.8769 (tpp) REVERT: D 274 ASP cc_start: 0.9060 (t0) cc_final: 0.8796 (t0) REVERT: D 300 TRP cc_start: 0.8699 (t-100) cc_final: 0.8451 (t-100) REVERT: D 460 GLU cc_start: 0.8150 (pt0) cc_final: 0.7373 (pt0) REVERT: E 74 GLN cc_start: 0.8127 (mt0) cc_final: 0.7351 (tt0) REVERT: E 167 LEU cc_start: 0.8606 (tp) cc_final: 0.8228 (tp) REVERT: E 172 GLU cc_start: 0.8764 (pm20) cc_final: 0.8561 (mp0) REVERT: E 173 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8760 (p) REVERT: E 174 GLU cc_start: 0.8359 (mp0) cc_final: 0.7649 (mm-30) REVERT: F 149 MET cc_start: 0.8405 (mtm) cc_final: 0.8149 (ptp) REVERT: F 214 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8524 (mm-30) REVERT: F 220 GLN cc_start: 0.8136 (pm20) cc_final: 0.7835 (pm20) REVERT: F 387 GLU cc_start: 0.8140 (mp0) cc_final: 0.7740 (mp0) REVERT: F 420 GLU cc_start: 0.8497 (tm-30) cc_final: 0.7707 (pt0) REVERT: F 436 GLN cc_start: 0.8662 (mt0) cc_final: 0.8453 (mp10) REVERT: F 450 MET cc_start: 0.8877 (ttm) cc_final: 0.8622 (ttp) REVERT: G 94 MET cc_start: 0.8944 (tpp) cc_final: 0.8706 (mmm) REVERT: G 126 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8438 (pp) REVERT: G 138 ASP cc_start: 0.9255 (OUTLIER) cc_final: 0.8997 (t0) REVERT: G 254 MET cc_start: 0.8336 (mtm) cc_final: 0.7838 (mtm) REVERT: G 283 GLU cc_start: 0.7791 (pm20) cc_final: 0.7514 (pm20) REVERT: G 410 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6945 (mt-10) REVERT: G 598 ASN cc_start: 0.8768 (p0) cc_final: 0.8538 (p0) REVERT: H 47 GLN cc_start: 0.9210 (tm-30) cc_final: 0.8329 (tm-30) REVERT: H 142 TYR cc_start: 0.8827 (m-80) cc_final: 0.8551 (m-80) REVERT: H 152 SER cc_start: 0.9400 (m) cc_final: 0.8973 (t) REVERT: H 156 MET cc_start: 0.8377 (ptm) cc_final: 0.8044 (ptt) REVERT: H 172 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7294 (ppp) REVERT: H 173 TRP cc_start: 0.8633 (m-10) cc_final: 0.7559 (m-10) REVERT: H 202 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7101 (mm-30) REVERT: H 260 MET cc_start: 0.9015 (tmm) cc_final: 0.8616 (tmm) REVERT: H 262 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8388 (tt0) REVERT: H 291 LYS cc_start: 0.9034 (mmmt) cc_final: 0.8490 (mtmt) REVERT: I 59 ARG cc_start: 0.7560 (mpt180) cc_final: 0.7336 (mmt180) REVERT: I 206 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8570 (tm-30) REVERT: I 208 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8042 (t70) REVERT: P 89 TYR cc_start: 0.8161 (t80) cc_final: 0.7803 (t80) REVERT: P 210 GLU cc_start: 0.8523 (tp30) cc_final: 0.7982 (tp30) REVERT: Q 69 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7881 (tp30) REVERT: Q 146 ASP cc_start: 0.7867 (p0) cc_final: 0.7555 (p0) REVERT: Q 148 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8073 (mm-30) REVERT: Q 164 PHE cc_start: 0.7932 (m-80) cc_final: 0.7286 (m-80) REVERT: S 62 GLN cc_start: 0.8624 (pt0) cc_final: 0.8385 (pt0) REVERT: T 101 ASN cc_start: 0.9221 (p0) cc_final: 0.8344 (t0) REVERT: T 120 MET cc_start: 0.8817 (mtm) cc_final: 0.8461 (ttm) REVERT: T 147 TYR cc_start: 0.7846 (t80) cc_final: 0.7548 (t80) REVERT: W 27 ASP cc_start: 0.8636 (t70) cc_final: 0.8155 (t70) REVERT: W 45 GLU cc_start: 0.8749 (tp30) cc_final: 0.8178 (tp30) REVERT: W 48 ASN cc_start: 0.9385 (m110) cc_final: 0.9019 (m-40) REVERT: W 68 GLU cc_start: 0.8685 (tp30) cc_final: 0.8367 (tp30) REVERT: W 92 GLU cc_start: 0.9021 (tp30) cc_final: 0.8618 (tp30) REVERT: W 94 GLN cc_start: 0.8867 (mm110) cc_final: 0.8566 (tt0) REVERT: X 55 ARG cc_start: 0.8504 (mmm-85) cc_final: 0.8292 (mmm-85) REVERT: X 98 ARG cc_start: 0.9423 (tmm-80) cc_final: 0.8971 (tmm-80) REVERT: Z 50 MET cc_start: 0.8164 (tpp) cc_final: 0.7444 (tpp) REVERT: Z 54 ASN cc_start: 0.8766 (m-40) cc_final: 0.8051 (m110) REVERT: Z 64 ASP cc_start: 0.8467 (p0) cc_final: 0.8264 (p0) REVERT: Z 75 PHE cc_start: 0.8914 (m-80) cc_final: 0.8618 (m-80) REVERT: Z 79 LYS cc_start: 0.8649 (tppp) cc_final: 0.8181 (tppp) REVERT: Z 111 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.6250 (m-80) REVERT: Z 124 MET cc_start: 0.8547 (mmm) cc_final: 0.8049 (mmm) REVERT: Z 140 PHE cc_start: 0.9139 (t80) cc_final: 0.8650 (t80) REVERT: a 46 TYR cc_start: 0.8564 (t80) cc_final: 0.7905 (t80) REVERT: q 8 LYS cc_start: 0.7789 (ttmt) cc_final: 0.7110 (mmtm) REVERT: q 58 ARG cc_start: 0.7693 (mtm180) cc_final: 0.7409 (mtm180) REVERT: q 71 LYS cc_start: 0.4794 (tptm) cc_final: 0.4562 (mtpp) REVERT: q 81 MET cc_start: 0.7586 (mtt) cc_final: 0.7296 (mpp) REVERT: q 89 TRP cc_start: 0.8759 (t60) cc_final: 0.8546 (t60) REVERT: q 142 THR cc_start: 0.8925 (m) cc_final: 0.8614 (t) outliers start: 138 outliers final: 107 residues processed: 884 average time/residue: 0.2037 time to fit residues: 298.6602 Evaluate side-chains 898 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 782 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 234 GLN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 310 GLU Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 648 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 301 CYS Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 272 LEU Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 300 TRP Chi-restraints excluded: chain P residue 335 LEU Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 167 ASN Chi-restraints excluded: chain S residue 93 ASN Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 18 ASP Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain W residue 19 SER Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain X residue 117 TRP Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain Z residue 71 LEU Chi-restraints excluded: chain Z residue 76 GLN Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 111 PHE Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 61 TYR Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 85 optimal weight: 2.9990 chunk 366 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 340 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 236 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 266 optimal weight: 5.9990 chunk 369 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** 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 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 GLN Z 76 GLN ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 46 ASN ** s 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.100767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.079569 restraints weight = 103001.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.082191 restraints weight = 46934.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.083880 restraints weight = 28825.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.084926 restraints weight = 21326.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.085561 restraints weight = 17855.867| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.7113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 34591 Z= 0.149 Angle : 0.993 76.312 46938 Z= 0.379 Chirality : 0.046 0.274 5137 Planarity : 0.005 0.127 5964 Dihedral : 7.889 137.958 4718 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.78 % Favored : 96.20 % Rotamer: Outliers : 3.61 % Allowed : 26.07 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.23 (0.13), residues: 4129 helix: 0.75 (0.12), residues: 1863 sheet: -1.08 (0.27), residues: 362 loop : -0.81 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 26 TYR 0.031 0.002 TYR T 85 PHE 0.028 0.001 PHE A 62 TRP 0.045 0.002 TRP q 86 HIS 0.018 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00352 (34551) covalent geometry : angle 0.76059 (46848) SS BOND : bond 0.00394 ( 3) SS BOND : angle 1.20188 ( 6) hydrogen bonds : bond 0.03954 ( 1430) hydrogen bonds : angle 5.03225 ( 4137) metal coordination : bond 0.01854 ( 37) metal coordination : angle 15.10784 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 831 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.7789 (t80) REVERT: A 68 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8393 (mt-10) REVERT: A 93 ILE cc_start: 0.8054 (mm) cc_final: 0.7673 (tp) REVERT: B 77 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7739 (ptmt) REVERT: B 117 PHE cc_start: 0.9110 (m-10) cc_final: 0.8882 (m-10) REVERT: B 170 TYR cc_start: 0.9058 (OUTLIER) cc_final: 0.8592 (t80) REVERT: C 114 THR cc_start: 0.8932 (m) cc_final: 0.8593 (p) REVERT: C 165 TYR cc_start: 0.9140 (m-80) cc_final: 0.8779 (m-80) REVERT: C 168 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8184 (tm-30) REVERT: D 158 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9120 (mm) REVERT: D 185 MET cc_start: 0.8982 (tpt) cc_final: 0.8726 (tpp) REVERT: D 274 ASP cc_start: 0.8976 (t0) cc_final: 0.8768 (t0) REVERT: D 300 TRP cc_start: 0.8679 (t-100) cc_final: 0.8457 (t-100) REVERT: E 74 GLN cc_start: 0.8061 (mt0) cc_final: 0.7355 (tt0) REVERT: E 167 LEU cc_start: 0.8607 (tp) cc_final: 0.8255 (tp) REVERT: E 173 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8938 (p) REVERT: E 174 GLU cc_start: 0.8252 (mp0) cc_final: 0.7621 (mm-30) REVERT: F 149 MET cc_start: 0.8424 (mtm) cc_final: 0.8149 (ptp) REVERT: F 157 TYR cc_start: 0.7573 (t80) cc_final: 0.7287 (t80) REVERT: F 214 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8478 (mm-30) REVERT: F 387 GLU cc_start: 0.8071 (mp0) cc_final: 0.7718 (mp0) REVERT: F 420 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7611 (pt0) REVERT: F 450 MET cc_start: 0.8858 (ttm) cc_final: 0.8576 (ttp) REVERT: G 94 MET cc_start: 0.8906 (tpp) cc_final: 0.8693 (mmm) REVERT: G 126 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8496 (pp) REVERT: G 138 ASP cc_start: 0.9237 (OUTLIER) cc_final: 0.8998 (t0) REVERT: G 410 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6867 (mt-10) REVERT: G 598 ASN cc_start: 0.8748 (p0) cc_final: 0.8541 (p0) REVERT: G 696 MET cc_start: 0.8625 (tpp) cc_final: 0.8407 (mmm) REVERT: H 47 GLN cc_start: 0.9179 (tm-30) cc_final: 0.8287 (tm-30) REVERT: H 51 ASP cc_start: 0.8693 (p0) cc_final: 0.8425 (p0) REVERT: H 78 SER cc_start: 0.9392 (m) cc_final: 0.8865 (p) REVERT: H 142 TYR cc_start: 0.8739 (m-80) cc_final: 0.8440 (m-80) REVERT: H 152 SER cc_start: 0.9330 (m) cc_final: 0.8943 (t) REVERT: H 156 MET cc_start: 0.8330 (ptm) cc_final: 0.8103 (ptt) REVERT: H 172 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7275 (ppp) REVERT: H 173 TRP cc_start: 0.8627 (m-10) cc_final: 0.7604 (m-10) REVERT: H 202 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7064 (mm-30) REVERT: H 260 MET cc_start: 0.8971 (tmm) cc_final: 0.8614 (tmm) REVERT: H 261 MET cc_start: 0.8240 (mtm) cc_final: 0.7654 (mtm) REVERT: H 262 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8303 (tt0) REVERT: H 291 LYS cc_start: 0.8891 (mmmt) cc_final: 0.8437 (mtmt) REVERT: I 206 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8599 (tm-30) REVERT: I 208 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.8110 (t70) REVERT: P 210 GLU cc_start: 0.8445 (tp30) cc_final: 0.7953 (tp30) REVERT: Q 69 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7823 (tp30) REVERT: Q 146 ASP cc_start: 0.7834 (p0) cc_final: 0.7556 (p0) REVERT: Q 164 PHE cc_start: 0.7895 (m-80) cc_final: 0.7250 (m-80) REVERT: R 112 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7869 (tptp) REVERT: S 91 MET cc_start: 0.8580 (ptt) cc_final: 0.7972 (ppp) REVERT: T 90 TYR cc_start: 0.6009 (t80) cc_final: 0.5568 (m-10) REVERT: T 101 ASN cc_start: 0.9227 (p0) cc_final: 0.8428 (t0) REVERT: T 120 MET cc_start: 0.8804 (mtm) cc_final: 0.8462 (ttm) REVERT: T 147 TYR cc_start: 0.7803 (t80) cc_final: 0.7504 (t80) REVERT: W 27 ASP cc_start: 0.8477 (t70) cc_final: 0.8175 (t70) REVERT: W 45 GLU cc_start: 0.8707 (tp30) cc_final: 0.8113 (tp30) REVERT: W 48 ASN cc_start: 0.9396 (m110) cc_final: 0.9002 (m-40) REVERT: W 68 GLU cc_start: 0.8620 (tp30) cc_final: 0.8353 (tp30) REVERT: W 92 GLU cc_start: 0.9002 (tp30) cc_final: 0.8567 (tp30) REVERT: W 94 GLN cc_start: 0.8855 (mm110) cc_final: 0.8487 (tt0) REVERT: W 98 LYS cc_start: 0.8057 (mtpt) cc_final: 0.7752 (mttp) REVERT: W 100 TRP cc_start: 0.8381 (m-10) cc_final: 0.7958 (m-10) REVERT: X 98 ARG cc_start: 0.9382 (tmm-80) cc_final: 0.8939 (tmm-80) REVERT: Z 50 MET cc_start: 0.8037 (tpp) cc_final: 0.7452 (tpp) REVERT: Z 54 ASN cc_start: 0.8719 (m-40) cc_final: 0.8194 (m110) REVERT: Z 64 ASP cc_start: 0.8335 (p0) cc_final: 0.8133 (p0) REVERT: Z 75 PHE cc_start: 0.8838 (m-80) cc_final: 0.8590 (m-80) REVERT: Z 76 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8710 (tp-100) REVERT: Z 79 LYS cc_start: 0.8468 (tppp) cc_final: 0.8116 (tppp) REVERT: Z 80 ASP cc_start: 0.8728 (p0) cc_final: 0.8186 (p0) REVERT: Z 124 MET cc_start: 0.8467 (mmm) cc_final: 0.7993 (mmm) REVERT: Z 140 PHE cc_start: 0.9131 (t80) cc_final: 0.8730 (t80) REVERT: a 17 VAL cc_start: 0.9200 (OUTLIER) cc_final: 0.8938 (p) REVERT: a 46 TYR cc_start: 0.8471 (t80) cc_final: 0.7992 (t80) REVERT: b 40 LYS cc_start: 0.8705 (pttm) cc_final: 0.8499 (ttmm) REVERT: b 41 TYR cc_start: 0.7672 (m-10) cc_final: 0.7397 (m-10) REVERT: b 78 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8583 (pp) REVERT: b 81 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9131 (mt) REVERT: q 8 LYS cc_start: 0.7848 (ttmt) cc_final: 0.7292 (mmtm) REVERT: q 58 ARG cc_start: 0.7735 (mtm180) cc_final: 0.7327 (mtm180) REVERT: q 59 HIS cc_start: 0.5870 (p90) cc_final: 0.5460 (p90) REVERT: q 71 LYS cc_start: 0.4936 (tptm) cc_final: 0.4703 (mtpp) REVERT: q 81 MET cc_start: 0.7665 (mtt) cc_final: 0.7340 (mpp) REVERT: q 88 ARG cc_start: 0.6591 (ttm-80) cc_final: 0.5984 (ttm-80) REVERT: q 89 TRP cc_start: 0.8790 (t60) cc_final: 0.8361 (t60) REVERT: q 142 THR cc_start: 0.8939 (m) cc_final: 0.8660 (t) outliers start: 131 outliers final: 91 residues processed: 887 average time/residue: 0.2046 time to fit residues: 301.4312 Evaluate side-chains 884 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 780 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 234 GLN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 310 GLU Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 648 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 208 ASP Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 272 LEU Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 335 LEU Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain R residue 112 LYS Chi-restraints excluded: chain S residue 93 ASN Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain W residue 19 SER Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain X residue 117 TRP Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain Z residue 71 LEU Chi-restraints excluded: chain Z residue 76 GLN Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 61 TYR Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 46 ASN Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 74 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 211 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 165 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 121 optimal weight: 0.0010 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** 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 235 ASN H 287 HIS ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 99 HIS ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 46 ASN ** s 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.101610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.080410 restraints weight = 103412.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.083050 restraints weight = 47396.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.084729 restraints weight = 29050.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.085785 restraints weight = 21516.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.086435 restraints weight = 17977.742| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.7254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 34591 Z= 0.148 Angle : 1.007 75.401 46938 Z= 0.393 Chirality : 0.046 0.317 5137 Planarity : 0.005 0.127 5964 Dihedral : 7.833 137.241 4718 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.83 % Favored : 96.15 % Rotamer: Outliers : 3.09 % Allowed : 27.21 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.29 (0.13), residues: 4129 helix: 0.66 (0.12), residues: 1874 sheet: -1.05 (0.27), residues: 362 loop : -0.81 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 26 TYR 0.029 0.002 TYR T 85 PHE 0.041 0.001 PHE B 121 TRP 0.048 0.002 TRP q 86 HIS 0.012 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00345 (34551) covalent geometry : angle 0.79501 (46848) SS BOND : bond 0.00434 ( 3) SS BOND : angle 1.23334 ( 6) hydrogen bonds : bond 0.04001 ( 1430) hydrogen bonds : angle 5.02265 ( 4137) metal coordination : bond 0.01683 ( 37) metal coordination : angle 14.62560 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 830 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.7790 (t80) REVERT: A 68 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8422 (mt-10) REVERT: A 93 ILE cc_start: 0.7932 (mm) cc_final: 0.7576 (tp) REVERT: B 77 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7748 (ptmt) REVERT: B 117 PHE cc_start: 0.9090 (m-10) cc_final: 0.8887 (m-10) REVERT: B 129 ASP cc_start: 0.8543 (m-30) cc_final: 0.7848 (m-30) REVERT: B 170 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.8505 (t80) REVERT: C 114 THR cc_start: 0.8881 (m) cc_final: 0.8433 (p) REVERT: C 145 TYR cc_start: 0.9011 (p90) cc_final: 0.8628 (p90) REVERT: C 165 TYR cc_start: 0.9134 (m-80) cc_final: 0.8811 (m-80) REVERT: C 168 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8232 (tm-30) REVERT: D 82 LEU cc_start: 0.8837 (tt) cc_final: 0.8576 (pp) REVERT: D 158 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9135 (mm) REVERT: D 185 MET cc_start: 0.8931 (tpt) cc_final: 0.8677 (tpp) REVERT: D 270 ASN cc_start: 0.8571 (m-40) cc_final: 0.8345 (m-40) REVERT: D 279 THR cc_start: 0.9190 (m) cc_final: 0.8989 (m) REVERT: D 300 TRP cc_start: 0.8636 (t-100) cc_final: 0.8421 (t-100) REVERT: E 39 VAL cc_start: 0.8653 (t) cc_final: 0.8445 (p) REVERT: E 74 GLN cc_start: 0.8056 (mt0) cc_final: 0.7343 (tt0) REVERT: E 167 LEU cc_start: 0.8622 (tp) cc_final: 0.8256 (tp) REVERT: E 174 GLU cc_start: 0.8303 (mp0) cc_final: 0.7676 (mm-30) REVERT: F 149 MET cc_start: 0.8399 (mtm) cc_final: 0.8140 (ptp) REVERT: F 157 TYR cc_start: 0.7406 (t80) cc_final: 0.7188 (t80) REVERT: F 214 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8478 (mm-30) REVERT: F 387 GLU cc_start: 0.8027 (mp0) cc_final: 0.7683 (mp0) REVERT: F 420 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7651 (pt0) REVERT: F 450 MET cc_start: 0.8840 (ttm) cc_final: 0.8560 (ttp) REVERT: G 126 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8388 (pp) REVERT: G 138 ASP cc_start: 0.9226 (OUTLIER) cc_final: 0.9019 (t0) REVERT: G 598 ASN cc_start: 0.8766 (p0) cc_final: 0.8559 (p0) REVERT: G 696 MET cc_start: 0.8612 (tpp) cc_final: 0.8337 (mmm) REVERT: H 47 GLN cc_start: 0.9165 (tm-30) cc_final: 0.8589 (tm-30) REVERT: H 51 ASP cc_start: 0.8719 (p0) cc_final: 0.8490 (p0) REVERT: H 78 SER cc_start: 0.9390 (m) cc_final: 0.8870 (p) REVERT: H 142 TYR cc_start: 0.8701 (m-80) cc_final: 0.8323 (m-10) REVERT: H 152 SER cc_start: 0.9356 (m) cc_final: 0.8934 (t) REVERT: H 156 MET cc_start: 0.8296 (ptm) cc_final: 0.8087 (ptt) REVERT: H 172 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.7289 (ppp) REVERT: H 173 TRP cc_start: 0.8551 (m-10) cc_final: 0.7531 (m-10) REVERT: H 202 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7079 (mm-30) REVERT: H 257 THR cc_start: 0.9349 (m) cc_final: 0.9085 (p) REVERT: H 260 MET cc_start: 0.8962 (tmm) cc_final: 0.8549 (tmm) REVERT: H 261 MET cc_start: 0.8210 (mtm) cc_final: 0.7623 (mtm) REVERT: H 262 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8320 (tt0) REVERT: H 291 LYS cc_start: 0.9015 (mmmt) cc_final: 0.8566 (mtmt) REVERT: I 206 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8533 (tm-30) REVERT: P 210 GLU cc_start: 0.8446 (tp30) cc_final: 0.7945 (tp30) REVERT: P 219 ASN cc_start: 0.8782 (m-40) cc_final: 0.8124 (t0) REVERT: Q 69 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7790 (tp30) REVERT: Q 146 ASP cc_start: 0.7547 (p0) cc_final: 0.7262 (p0) REVERT: Q 164 PHE cc_start: 0.7923 (m-80) cc_final: 0.7420 (m-80) REVERT: S 41 TYR cc_start: 0.8453 (t80) cc_final: 0.8232 (t80) REVERT: T 90 TYR cc_start: 0.5870 (t80) cc_final: 0.5464 (m-10) REVERT: T 101 ASN cc_start: 0.9231 (p0) cc_final: 0.8415 (t0) REVERT: T 120 MET cc_start: 0.8783 (mtm) cc_final: 0.8423 (ttm) REVERT: T 147 TYR cc_start: 0.7809 (t80) cc_final: 0.7573 (t80) REVERT: V 83 GLN cc_start: 0.8386 (tp40) cc_final: 0.8050 (tp-100) REVERT: W 27 ASP cc_start: 0.8312 (t70) cc_final: 0.8019 (t70) REVERT: W 37 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8640 (mm-30) REVERT: W 45 GLU cc_start: 0.8746 (tp30) cc_final: 0.8176 (tp30) REVERT: W 48 ASN cc_start: 0.9387 (m110) cc_final: 0.9025 (m-40) REVERT: W 68 GLU cc_start: 0.8715 (tp30) cc_final: 0.8451 (tp30) REVERT: W 92 GLU cc_start: 0.8999 (tp30) cc_final: 0.8549 (tp30) REVERT: W 94 GLN cc_start: 0.8864 (mm110) cc_final: 0.8532 (tt0) REVERT: W 98 LYS cc_start: 0.7993 (mtpt) cc_final: 0.7699 (mttp) REVERT: W 100 TRP cc_start: 0.8332 (m-10) cc_final: 0.7894 (m-10) REVERT: W 114 GLU cc_start: 0.5451 (pm20) cc_final: 0.5110 (pm20) REVERT: W 129 HIS cc_start: 0.8217 (m90) cc_final: 0.8009 (m90) REVERT: X 98 ARG cc_start: 0.9384 (tmm-80) cc_final: 0.9007 (ptt90) REVERT: Z 50 MET cc_start: 0.8016 (tpp) cc_final: 0.7417 (tpp) REVERT: Z 51 MET cc_start: 0.8684 (tmm) cc_final: 0.7763 (tmm) REVERT: Z 54 ASN cc_start: 0.8713 (m-40) cc_final: 0.8199 (m110) REVERT: Z 64 ASP cc_start: 0.8424 (p0) cc_final: 0.8215 (p0) REVERT: Z 76 GLN cc_start: 0.9339 (OUTLIER) cc_final: 0.8955 (tp-100) REVERT: Z 80 ASP cc_start: 0.8672 (p0) cc_final: 0.8122 (p0) REVERT: Z 124 MET cc_start: 0.8463 (mmm) cc_final: 0.7947 (mmm) REVERT: Z 140 PHE cc_start: 0.9122 (t80) cc_final: 0.8791 (t80) REVERT: a 17 VAL cc_start: 0.9162 (OUTLIER) cc_final: 0.8892 (p) REVERT: b 40 LYS cc_start: 0.8710 (pttm) cc_final: 0.8496 (ttmm) REVERT: b 41 TYR cc_start: 0.7647 (m-10) cc_final: 0.7380 (m-10) REVERT: b 78 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8620 (pp) REVERT: b 81 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9144 (mt) REVERT: q 8 LYS cc_start: 0.7850 (ttmt) cc_final: 0.7377 (mmtm) REVERT: q 58 ARG cc_start: 0.7751 (mtm180) cc_final: 0.7483 (mtm180) REVERT: q 59 HIS cc_start: 0.5899 (p90) cc_final: 0.5599 (p90) REVERT: q 71 LYS cc_start: 0.4953 (tptm) cc_final: 0.4718 (mtpp) REVERT: q 81 MET cc_start: 0.7665 (mtt) cc_final: 0.7327 (mpp) REVERT: q 88 ARG cc_start: 0.6551 (ttm-80) cc_final: 0.5998 (ttm-80) REVERT: q 89 TRP cc_start: 0.8782 (t60) cc_final: 0.8427 (t60) REVERT: q 142 THR cc_start: 0.8973 (m) cc_final: 0.8688 (t) outliers start: 112 outliers final: 90 residues processed: 876 average time/residue: 0.1991 time to fit residues: 290.0542 Evaluate side-chains 890 residues out of total 3628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 790 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 234 GLN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 310 GLU Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain G residue 583 ILE Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 648 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 235 ASN Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 335 LEU Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain S residue 93 ASN Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain X residue 117 TRP Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain Z residue 71 LEU Chi-restraints excluded: chain Z residue 76 GLN Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 46 ASN Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 307 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 356 optimal weight: 6.9990 chunk 398 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 373 optimal weight: 9.9990 chunk 198 optimal weight: 2.9990 chunk 405 optimal weight: 0.0060 chunk 168 optimal weight: 2.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 ASN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** 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 235 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN Q 141 ASN ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 46 ASN ** s 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.099678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.078269 restraints weight = 103739.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.080837 restraints weight = 48165.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.082484 restraints weight = 29887.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.083515 restraints weight = 22311.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.084041 restraints weight = 18730.871| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.7313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 34591 Z= 0.191 Angle : 1.069 78.572 46938 Z= 0.404 Chirality : 0.047 0.311 5137 Planarity : 0.006 0.210 5964 Dihedral : 7.818 138.205 4718 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.97 % Favored : 96.00 % Rotamer: Outliers : 3.17 % Allowed : 27.40 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.26 (0.13), residues: 4129 helix: 0.71 (0.12), residues: 1863 sheet: -1.08 (0.26), residues: 361 loop : -0.81 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 26 TYR 0.029 0.002 TYR T 85 PHE 0.029 0.002 PHE A 62 TRP 0.037 0.002 TRP q 86 HIS 0.013 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00447 (34551) covalent geometry : angle 0.82378 (46848) SS BOND : bond 0.00345 ( 3) SS BOND : angle 1.18966 ( 6) hydrogen bonds : bond 0.04068 ( 1430) hydrogen bonds : angle 5.10120 ( 4137) metal coordination : bond 0.02432 ( 37) metal coordination : angle 16.12498 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8547.91 seconds wall clock time: 147 minutes 52.17 seconds (8872.17 seconds total)