Starting phenix.real_space_refine on Sat Aug 8 13:45:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8glx_40222/08_2026/8glx_40222.cif Found real_map, /net/cci-nas-00/data/ceres_data/8glx_40222/08_2026/8glx_40222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8glx_40222/08_2026/8glx_40222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8glx_40222/08_2026/8glx_40222.map" model { file = "/net/cci-nas-00/data/ceres_data/8glx_40222/08_2026/8glx_40222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8glx_40222/08_2026/8glx_40222.cif" } resolution = 3.88 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= 0.000 sd= 1.000 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 Zn 2 6.06 5 P 114 5.49 5 Mg 6 5.21 5 S 98 5.16 5 C 17972 2.51 5 N 5162 2.21 5 O 5534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28888 Number of models: 1 Model: "" Number of chains: 18 Chain: "G" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3116 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 14, 'TRANS': 376} Chain breaks: 1 Chain: "X" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2523 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "H" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1029 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "I" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1021 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "E" Number of atoms: 3831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3831 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 19, 'TRANS': 458} Chain breaks: 1 Chain: "F" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3860 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 19, 'TRANS': 462} Chain: "C" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3116 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 14, 'TRANS': 376} Chain breaks: 1 Chain: "Y" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2523 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "A" Number of atoms: 3831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3831 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 19, 'TRANS': 458} Chain breaks: 1 Chain: "B" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3860 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 19, 'TRANS': 462} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4111 SG CYS X 124 22.200 66.436 86.653 1.00 6.09 S ATOM 4132 SG CYS X 127 20.617 69.860 86.021 1.00 23.79 S ATOM 4350 SG CYS X 152 19.915 67.936 89.303 1.00 26.87 S ATOM 19491 SG CYS Y 124 89.493 34.107 43.667 1.00 65.09 S ATOM 19512 SG CYS Y 127 92.309 34.224 46.420 1.00 61.21 S ATOM 19730 SG CYS Y 152 92.629 36.005 42.896 1.00 60.84 S Time building chain proxies: 6.45, per 1000 atoms: 0.22 Number of scatterers: 28888 At special positions: 0 Unit cell: (181.26, 152.19, 169.29, 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 2 29.99 S 98 16.00 P 114 15.00 Mg 6 11.99 O 5534 8.00 N 5162 7.00 C 17972 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 975.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN X 601 " pdb="ZN ZN X 601 " - pdb=" ND1 HIS X 155 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 124 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 152 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 127 " pdb=" ZN Y 601 " pdb="ZN ZN Y 601 " - pdb=" ND1 HIS Y 155 " pdb="ZN ZN Y 601 " - pdb=" SG CYS Y 124 " pdb="ZN ZN Y 601 " - pdb=" SG CYS Y 152 " pdb="ZN ZN Y 601 " - pdb=" SG CYS Y 127 " Number of angles added : 6 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6264 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 14 sheets defined 57.1% alpha, 4.9% beta 48 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'G' and resid 15 through 19 removed outlier: 3.719A pdb=" N ARG G 19 " --> pdb=" O GLU G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 41 removed outlier: 3.914A pdb=" N ALA G 37 " --> pdb=" O SER G 33 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ALA G 38 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 53 removed outlier: 3.798A pdb=" N GLN G 52 " --> pdb=" O SER G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 63 removed outlier: 3.576A pdb=" N ARG G 58 " --> pdb=" O SER G 54 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR G 61 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE G 62 " --> pdb=" O ARG G 58 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N CYS G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 69 Processing helix chain 'G' and resid 73 through 89 removed outlier: 4.023A pdb=" N LEU G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU G 78 " --> pdb=" O GLY G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 115 removed outlier: 3.679A pdb=" N ASN G 107 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY G 108 " --> pdb=" O HIS G 104 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU G 110 " --> pdb=" O GLN G 106 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL G 112 " --> pdb=" O GLY G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 150 Processing helix chain 'G' and resid 179 through 194 removed outlier: 4.416A pdb=" N ILE G 183 " --> pdb=" O SER G 179 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N CYS G 184 " --> pdb=" O LEU G 180 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE G 188 " --> pdb=" O CYS G 184 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP G 192 " --> pdb=" O PHE G 188 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA G 194 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 204 Processing helix chain 'G' and resid 210 through 224 removed outlier: 4.025A pdb=" N MET G 217 " --> pdb=" O MET G 213 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER G 218 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN G 222 " --> pdb=" O SER G 218 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS G 224 " --> pdb=" O ILE G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 240 removed outlier: 3.505A pdb=" N LEU G 237 " --> pdb=" O ILE G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 258 removed outlier: 4.098A pdb=" N MET G 248 " --> pdb=" O GLY G 244 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU G 249 " --> pdb=" O SER G 245 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL G 253 " --> pdb=" O LEU G 249 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL G 256 " --> pdb=" O PHE G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 273 removed outlier: 3.603A pdb=" N ARG G 272 " --> pdb=" O PRO G 269 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU G 273 " --> pdb=" O LYS G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 317 removed outlier: 4.173A pdb=" N GLN G 317 " --> pdb=" O ASP G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 341 Processing helix chain 'G' and resid 343 through 362 removed outlier: 3.853A pdb=" N VAL G 347 " --> pdb=" O VAL G 343 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL G 348 " --> pdb=" O MET G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 379 Processing helix chain 'G' and resid 382 through 392 Processing helix chain 'G' and resid 393 through 399 Processing helix chain 'X' and resid 12 through 24 removed outlier: 3.534A pdb=" N GLN X 24 " --> pdb=" O ALA X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 37 Processing helix chain 'X' and resid 53 through 58 removed outlier: 3.581A pdb=" N HIS X 58 " --> pdb=" O VAL X 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 74 Processing helix chain 'X' and resid 76 through 85 removed outlier: 4.097A pdb=" N TYR X 80 " --> pdb=" O LEU X 76 " (cutoff:3.500A) Proline residue: X 82 - end of helix removed outlier: 4.049A pdb=" N GLY X 85 " --> pdb=" O ALA X 81 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 96 Processing helix chain 'X' and resid 101 through 108 removed outlier: 4.045A pdb=" N HIS X 105 " --> pdb=" O GLN X 101 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU X 108 " --> pdb=" O VAL X 104 " (cutoff:3.500A) Processing helix chain 'X' and resid 126 through 135 Processing helix chain 'X' and resid 189 through 200 Processing helix chain 'X' and resid 201 through 204 removed outlier: 3.744A pdb=" N ASP X 204 " --> pdb=" O PRO X 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 201 through 204' Processing helix chain 'X' and resid 216 through 230 removed outlier: 3.920A pdb=" N LEU X 220 " --> pdb=" O GLU X 216 " (cutoff:3.500A) Processing helix chain 'X' and resid 240 through 248 Processing helix chain 'X' and resid 251 through 258 Processing helix chain 'X' and resid 269 through 276 Processing helix chain 'X' and resid 283 through 295 removed outlier: 3.525A pdb=" N HIS X 287 " --> pdb=" O SER X 283 " (cutoff:3.500A) Processing helix chain 'X' and resid 299 through 310 Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.586A pdb=" N ARG E 19 " --> pdb=" O GLU E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 26 Processing helix chain 'E' and resid 32 through 37 removed outlier: 3.989A pdb=" N ALA E 37 " --> pdb=" O SER E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 41 removed outlier: 4.067A pdb=" N LYS E 41 " --> pdb=" O ALA E 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 38 through 41' Processing helix chain 'E' and resid 54 through 63 Processing helix chain 'E' and resid 73 through 88 removed outlier: 4.171A pdb=" N LEU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU E 78 " --> pdb=" O GLY E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 113 Processing helix chain 'E' and resid 141 through 149 Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 179 through 196 removed outlier: 3.877A pdb=" N ILE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N CYS E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 224 removed outlier: 3.739A pdb=" N GLN E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 260 removed outlier: 3.592A pdb=" N ILE E 259 " --> pdb=" O MET E 255 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY E 260 " --> pdb=" O VAL E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 275 removed outlier: 3.936A pdb=" N ILE E 274 " --> pdb=" O LYS E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 281 removed outlier: 3.940A pdb=" N SER E 281 " --> pdb=" O ALA E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 317 removed outlier: 3.592A pdb=" N GLN E 317 " --> pdb=" O ASP E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 341 Processing helix chain 'E' and resid 343 through 362 removed outlier: 3.747A pdb=" N VAL E 348 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY E 362 " --> pdb=" O ALA E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 378 removed outlier: 3.611A pdb=" N GLN E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 381 No H-bonds generated for 'chain 'E' and resid 379 through 381' Processing helix chain 'E' and resid 382 through 392 Processing helix chain 'E' and resid 393 through 400 removed outlier: 3.540A pdb=" N TYR E 400 " --> pdb=" O ARG E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 419 removed outlier: 3.616A pdb=" N ILE E 419 " --> pdb=" O LEU E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 433 removed outlier: 3.657A pdb=" N LYS E 430 " --> pdb=" O THR E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 448 Processing helix chain 'E' and resid 452 through 467 Proline residue: E 458 - end of helix removed outlier: 3.506A pdb=" N ASN E 467 " --> pdb=" O ALA E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 483 Proline residue: E 477 - end of helix Processing helix chain 'F' and resid 15 through 19 removed outlier: 3.538A pdb=" N TYR F 18 " --> pdb=" O VAL F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 26 Processing helix chain 'F' and resid 32 through 37 Processing helix chain 'F' and resid 47 through 52 removed outlier: 3.802A pdb=" N LEU F 51 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN F 52 " --> pdb=" O SER F 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 47 through 52' Processing helix chain 'F' and resid 54 through 64 Processing helix chain 'F' and resid 65 through 69 removed outlier: 4.070A pdb=" N TYR F 69 " --> pdb=" O PRO F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 89 removed outlier: 3.568A pdb=" N LEU F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 113 removed outlier: 3.911A pdb=" N HIS F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 151 removed outlier: 3.953A pdb=" N ARG F 148 " --> pdb=" O THR F 144 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 195 removed outlier: 3.723A pdb=" N CYS F 184 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE F 188 " --> pdb=" O CYS F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 203 Processing helix chain 'F' and resid 209 through 224 removed outlier: 3.574A pdb=" N SER F 218 " --> pdb=" O LEU F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 244 through 254 Processing helix chain 'F' and resid 255 through 257 No H-bonds generated for 'chain 'F' and resid 255 through 257' Processing helix chain 'F' and resid 278 through 287 Processing helix chain 'F' and resid 305 through 318 removed outlier: 3.533A pdb=" N ILE F 309 " --> pdb=" O ASN F 305 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU F 318 " --> pdb=" O ASN F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 341 Processing helix chain 'F' and resid 343 through 362 removed outlier: 3.748A pdb=" N VAL F 348 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS F 349 " --> pdb=" O ASP F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 379 removed outlier: 3.714A pdb=" N LEU F 379 " --> pdb=" O TYR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 392 removed outlier: 3.707A pdb=" N SER F 391 " --> pdb=" O GLU F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 400 Processing helix chain 'F' and resid 407 through 424 removed outlier: 3.774A pdb=" N ASP F 418 " --> pdb=" O GLN F 414 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE F 419 " --> pdb=" O LEU F 415 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA F 420 " --> pdb=" O GLN F 416 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA F 421 " --> pdb=" O LEU F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 434 removed outlier: 3.830A pdb=" N GLN F 433 " --> pdb=" O GLU F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 446 removed outlier: 4.461A pdb=" N MET F 446 " --> pdb=" O HIS F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 467 removed outlier: 3.747A pdb=" N ALA F 463 " --> pdb=" O THR F 459 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE F 464 " --> pdb=" O ILE F 460 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER F 465 " --> pdb=" O LYS F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 485 Proline residue: F 477 - end of helix removed outlier: 3.617A pdb=" N GLN F 481 " --> pdb=" O PRO F 477 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TRP F 482 " --> pdb=" O LEU F 478 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N MET F 484 " --> pdb=" O LEU F 480 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU F 485 " --> pdb=" O GLN F 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 19 Processing helix chain 'C' and resid 21 through 26 removed outlier: 3.617A pdb=" N GLU C 25 " --> pdb=" O ASN C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 40 removed outlier: 4.190A pdb=" N ALA C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 53 removed outlier: 4.065A pdb=" N ASP C 50 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 52 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS C 53 " --> pdb=" O ASP C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 63 removed outlier: 3.508A pdb=" N THR C 61 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 69 Processing helix chain 'C' and resid 74 through 90 removed outlier: 4.329A pdb=" N LEU C 78 " --> pdb=" O GLY C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 107 removed outlier: 3.936A pdb=" N ASN C 107 " --> pdb=" O LYS C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 115 removed outlier: 3.928A pdb=" N ARG C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL C 112 " --> pdb=" O GLY C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 151 Processing helix chain 'C' and resid 179 through 192 removed outlier: 4.130A pdb=" N ILE C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N CYS C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 185 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP C 192 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 209 through 224 removed outlier: 4.215A pdb=" N SER C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 239 removed outlier: 3.958A pdb=" N HIS C 236 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 258 removed outlier: 3.669A pdb=" N MET C 248 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 272 Processing helix chain 'C' and resid 305 through 317 Processing helix chain 'C' and resid 329 through 341 Processing helix chain 'C' and resid 344 through 362 removed outlier: 4.095A pdb=" N VAL C 348 " --> pdb=" O MET C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 379 removed outlier: 3.796A pdb=" N LEU C 379 " --> pdb=" O TYR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 392 removed outlier: 3.745A pdb=" N LEU C 386 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 399 Processing helix chain 'Y' and resid 12 through 24 removed outlier: 3.702A pdb=" N GLN Y 24 " --> pdb=" O ALA Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 37 Processing helix chain 'Y' and resid 53 through 59 Processing helix chain 'Y' and resid 66 through 74 Processing helix chain 'Y' and resid 76 through 85 removed outlier: 3.667A pdb=" N TYR Y 80 " --> pdb=" O LEU Y 76 " (cutoff:3.500A) Proline residue: Y 82 - end of helix removed outlier: 3.904A pdb=" N GLY Y 85 " --> pdb=" O ALA Y 81 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 97 removed outlier: 3.875A pdb=" N GLU Y 97 " --> pdb=" O ILE Y 93 " (cutoff:3.500A) Processing helix chain 'Y' and resid 101 through 108 removed outlier: 3.711A pdb=" N LEU Y 108 " --> pdb=" O VAL Y 104 " (cutoff:3.500A) Processing helix chain 'Y' and resid 124 through 135 removed outlier: 4.184A pdb=" N ALA Y 129 " --> pdb=" O PRO Y 125 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU Y 130 " --> pdb=" O ASP Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 189 through 204 removed outlier: 3.521A pdb=" N THR Y 193 " --> pdb=" O LEU Y 189 " (cutoff:3.500A) Proline residue: Y 201 - end of helix removed outlier: 4.081A pdb=" N ASP Y 204 " --> pdb=" O ALA Y 200 " (cutoff:3.500A) Processing helix chain 'Y' and resid 205 through 210 removed outlier: 3.788A pdb=" N ALA Y 208 " --> pdb=" O ALA Y 205 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU Y 210 " --> pdb=" O ARG Y 207 " (cutoff:3.500A) Processing helix chain 'Y' and resid 214 through 230 Processing helix chain 'Y' and resid 240 through 250 Processing helix chain 'Y' and resid 251 through 258 Processing helix chain 'Y' and resid 269 through 276 Processing helix chain 'Y' and resid 283 through 295 removed outlier: 3.756A pdb=" N HIS Y 287 " --> pdb=" O SER Y 283 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL Y 290 " --> pdb=" O GLN Y 286 " (cutoff:3.500A) Processing helix chain 'Y' and resid 299 through 310 removed outlier: 3.569A pdb=" N LEU Y 310 " --> pdb=" O GLN Y 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 19 removed outlier: 3.527A pdb=" N TYR A 18 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 19 " --> pdb=" O GLU A 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 15 through 19' Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 36 through 41 removed outlier: 3.751A pdb=" N LYS A 41 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.946A pdb=" N LEU A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 47 through 52' Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 64 through 69 Processing helix chain 'A' and resid 73 through 89 removed outlier: 3.547A pdb=" N LEU A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU A 78 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 100 through 113 Processing helix chain 'A' and resid 142 through 150 Processing helix chain 'A' and resid 179 through 196 removed outlier: 3.626A pdb=" N ILE A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE A 188 " --> pdb=" O CYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 224 removed outlier: 3.594A pdb=" N GLN A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 238 through 243 removed outlier: 3.803A pdb=" N SER A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 260 removed outlier: 3.705A pdb=" N PHE A 252 " --> pdb=" O MET A 248 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 259 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 removed outlier: 3.619A pdb=" N ARG A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 273 " --> pdb=" O PRO A 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 268 through 273' Processing helix chain 'A' and resid 274 through 277 removed outlier: 4.479A pdb=" N ALA A 277 " --> pdb=" O ILE A 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 274 through 277' Processing helix chain 'A' and resid 305 through 318 removed outlier: 3.828A pdb=" N LEU A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 340 removed outlier: 3.792A pdb=" N TRP A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 361 removed outlier: 4.266A pdb=" N VAL A 348 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 378 removed outlier: 4.079A pdb=" N LEU A 371 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 392 Processing helix chain 'A' and resid 393 through 400 Processing helix chain 'A' and resid 407 through 419 removed outlier: 4.010A pdb=" N ILE A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 441 through 447 Processing helix chain 'A' and resid 452 through 466 Proline residue: A 458 - end of helix removed outlier: 3.759A pdb=" N GLN A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 485 removed outlier: 4.073A pdb=" N VAL A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 485 " --> pdb=" O GLN A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 19 removed outlier: 3.843A pdb=" N TYR B 18 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 19 " --> pdb=" O GLU B 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 15 through 19' Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.549A pdb=" N LEU B 51 " --> pdb=" O SER B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 69 Proline residue: B 66 - end of helix Processing helix chain 'B' and resid 75 through 88 removed outlier: 3.752A pdb=" N LEU B 79 " --> pdb=" O THR B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 114 removed outlier: 3.824A pdb=" N HIS B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 113 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 151 removed outlier: 4.458A pdb=" N ILE B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 195 removed outlier: 3.610A pdb=" N PHE B 188 " --> pdb=" O CYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 209 through 224 removed outlier: 3.663A pdb=" N SER B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 246 through 253 Processing helix chain 'B' and resid 268 through 273 removed outlier: 3.558A pdb=" N ARG B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU B 273 " --> pdb=" O PRO B 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 268 through 273' Processing helix chain 'B' and resid 278 through 286 removed outlier: 3.866A pdb=" N ALA B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 318 removed outlier: 3.634A pdb=" N ILE B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.644A pdb=" N ARG B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 362 removed outlier: 3.676A pdb=" N VAL B 348 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 359 " --> pdb=" O GLN B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 379 removed outlier: 3.648A pdb=" N LEU B 379 " --> pdb=" O TYR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 392 Processing helix chain 'B' and resid 393 through 400 Processing helix chain 'B' and resid 407 through 424 removed outlier: 4.561A pdb=" N GLU B 424 " --> pdb=" O ALA B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 434 removed outlier: 3.857A pdb=" N ALA B 431 " --> pdb=" O PRO B 427 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 432 " --> pdb=" O GLU B 428 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU B 434 " --> pdb=" O LYS B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 449 removed outlier: 3.537A pdb=" N LYS B 448 " --> pdb=" O TYR B 444 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 467 removed outlier: 3.991A pdb=" N LYS B 461 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS B 462 " --> pdb=" O PRO B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 484 Processing sheet with id=AA1, first strand: chain 'G' and resid 169 through 173 removed outlier: 6.171A pdb=" N LEU G 170 " --> pdb=" O VAL G 230 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ASP G 232 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE G 172 " --> pdb=" O ASP G 232 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU G 229 " --> pdb=" O MET G 264 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE G 266 " --> pdb=" O LEU G 229 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE G 231 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU G 132 " --> pdb=" O VAL G 263 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY G 136 " --> pdb=" O GLY G 267 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY G 289 " --> pdb=" O SER G 131 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU G 133 " --> pdb=" O GLY G 289 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 156 through 158 Processing sheet with id=AA3, first strand: chain 'E' and resid 6 through 7 removed outlier: 6.340A pdb=" N ILE E 6 " --> pdb=" O TYR E 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 169 through 173 removed outlier: 6.384A pdb=" N LEU E 170 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASP E 232 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE E 172 " --> pdb=" O ASP E 232 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU E 229 " --> pdb=" O MET E 264 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE E 266 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE E 231 " --> pdb=" O ILE E 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 299 through 300 Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 7 removed outlier: 6.787A pdb=" N ILE F 6 " --> pdb=" O TYR F 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 169 through 173 removed outlier: 3.561A pdb=" N MET F 264 " --> pdb=" O LEU F 229 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE F 291 " --> pdb=" O LEU F 133 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE F 135 " --> pdb=" O ILE F 291 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 6 through 7 removed outlier: 6.403A pdb=" N ILE C 6 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 169 through 173 removed outlier: 3.616A pdb=" N MET C 264 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 132 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 133 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE C 291 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE C 135 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Y' and resid 120 through 123 removed outlier: 4.970A pdb=" N PHE Y 121 " --> pdb=" O PHE Y 161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE Y 161 " --> pdb=" O PHE Y 121 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 5 through 7 removed outlier: 6.295A pdb=" N ILE A 6 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU A 226 " --> pdb=" O GLN A 166 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL A 168 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 291 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A 135 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP A 293 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AB4, first strand: chain 'B' and resid 5 through 7 removed outlier: 6.259A pdb=" N ILE B 6 " --> pdb=" O TYR B 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 170 through 173 removed outlier: 6.586A pdb=" N LEU B 170 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASP B 232 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE B 172 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N ILE B 291 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU B 133 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N TRP B 293 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE B 135 " --> pdb=" O TRP B 293 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 3075 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 5.96 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7208 1.33 - 1.46: 6922 1.46 - 1.58: 15143 1.58 - 1.71: 219 1.71 - 1.83: 164 Bond restraints: 29656 Sorted by residual: bond pdb=" C3' DT I 26 " pdb=" C2' DT I 26 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DG I 39 " pdb=" C2' DG I 39 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.77e+00 bond pdb=" C3' DC I 23 " pdb=" C2' DC I 23 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.56e+00 bond pdb=" CB PRO A 304 " pdb=" CG PRO A 304 " ideal model delta sigma weight residual 1.492 1.630 -0.138 5.00e-02 4.00e+02 7.58e+00 bond pdb=" C3' DA I 28 " pdb=" C2' DA I 28 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.10e+00 ... (remaining 29651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 39929 2.39 - 4.78: 556 4.78 - 7.18: 103 7.18 - 9.57: 14 9.57 - 11.96: 6 Bond angle restraints: 40608 Sorted by residual: angle pdb=" CA PRO A 304 " pdb=" N PRO A 304 " pdb=" CD PRO A 304 " ideal model delta sigma weight residual 112.00 101.97 10.03 1.40e+00 5.10e-01 5.13e+01 angle pdb=" CA PRO X 201 " pdb=" N PRO X 201 " pdb=" CD PRO X 201 " ideal model delta sigma weight residual 112.00 103.94 8.06 1.40e+00 5.10e-01 3.31e+01 angle pdb=" CA PRO G 269 " pdb=" N PRO G 269 " pdb=" CD PRO G 269 " ideal model delta sigma weight residual 112.00 104.30 7.70 1.40e+00 5.10e-01 3.02e+01 angle pdb=" N PRO A 304 " pdb=" CD PRO A 304 " pdb=" CG PRO A 304 " ideal model delta sigma weight residual 103.20 95.42 7.78 1.50e+00 4.44e-01 2.69e+01 angle pdb=" N GLN B 373 " pdb=" CA GLN B 373 " pdb=" CB GLN B 373 " ideal model delta sigma weight residual 110.28 117.59 -7.31 1.55e+00 4.16e-01 2.22e+01 ... (remaining 40603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.77: 16822 33.77 - 67.54: 866 67.54 - 101.31: 49 101.31 - 135.08: 3 135.08 - 168.85: 2 Dihedral angle restraints: 17742 sinusoidal: 8050 harmonic: 9692 Sorted by residual: dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 108.85 -168.85 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O2A ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PA ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 91.18 -151.18 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" O1B ADP F 601 " pdb=" O3A ADP F 601 " pdb=" PB ADP F 601 " pdb=" PA ADP F 601 " ideal model delta sinusoidal sigma weight residual 300.00 170.05 129.95 1 2.00e+01 2.50e-03 3.94e+01 ... (remaining 17739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3381 0.044 - 0.089: 929 0.089 - 0.133: 226 0.133 - 0.178: 25 0.178 - 0.222: 7 Chirality restraints: 4568 Sorted by residual: chirality pdb=" CB ILE A 457 " pdb=" CA ILE A 457 " pdb=" CG1 ILE A 457 " pdb=" CG2 ILE A 457 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB THR E 437 " pdb=" CA THR E 437 " pdb=" OG1 THR E 437 " pdb=" CG2 THR E 437 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA GLN C 355 " pdb=" N GLN C 355 " pdb=" C GLN C 355 " pdb=" CB GLN C 355 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.57e-01 ... (remaining 4565 not shown) Planarity restraints: 4854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA X 200 " -0.099 5.00e-02 4.00e+02 1.45e-01 3.38e+01 pdb=" N PRO X 201 " 0.251 5.00e-02 4.00e+02 pdb=" CA PRO X 201 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO X 201 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 268 " -0.092 5.00e-02 4.00e+02 1.35e-01 2.91e+01 pdb=" N PRO G 269 " 0.233 5.00e-02 4.00e+02 pdb=" CA PRO G 269 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO G 269 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 303 " 0.068 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO A 304 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 304 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 304 " 0.053 5.00e-02 4.00e+02 ... (remaining 4851 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 209 2.58 - 3.16: 22520 3.16 - 3.74: 44681 3.74 - 4.32: 57773 4.32 - 4.90: 94216 Nonbonded interactions: 219399 Sorted by model distance: nonbonded pdb=" O3G ATP C 601 " pdb="MG MG C 602 " model vdw 1.996 2.170 nonbonded pdb=" OG1 THR G 143 " pdb="MG MG G 602 " model vdw 2.083 2.170 nonbonded pdb=" O3G ATP G 601 " pdb="MG MG G 602 " model vdw 2.088 2.170 nonbonded pdb=" O1B ADP B 601 " pdb="MG MG B 602 " model vdw 2.111 2.170 nonbonded pdb=" OG1 THR X 299 " pdb=" OE1 GLU X 302 " model vdw 2.136 3.040 ... (remaining 219394 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 602) selection = (chain 'B' and (resid 4 through 124 or resid 130 through 602)) selection = (chain 'E' and resid 4 through 602) selection = (chain 'F' and (resid 4 through 124 or resid 130 through 602)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'X' selection = chain 'Y' } 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=0.61 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 32.770 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 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 : 0.003 0.138 29664 Z= 0.229 Angle : 0.721 11.962 40614 Z= 0.418 Chirality : 0.043 0.222 4568 Planarity : 0.006 0.145 4854 Dihedral : 18.080 168.849 11478 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.37 % Favored : 95.60 % Rotamer: Outliers : 0.07 % Allowed : 0.38 % Favored : 99.55 % 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: -1.04 (0.14), residues: 3298 helix: -0.20 (0.13), residues: 1569 sheet: 0.21 (0.40), residues: 186 loop : -1.26 (0.15), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 55 TYR 0.028 0.001 TYR B 375 PHE 0.018 0.001 PHE C 351 TRP 0.041 0.002 TRP Y 291 HIS 0.014 0.001 HIS G 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.23 (29656) covalent geometry : angle 0.72034 / 0.42 (40608) hydrogen bonds : bond 0.17695 / 11.78 ( 1177) hydrogen bonds : angle 5.91617 / 4.10 ( 3317) metal coordination : bond 0.03271 / 1.46 ( 8) metal coordination : angle 2.87797 / 1.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 412 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 99 GLN cc_start: 0.7334 (pt0) cc_final: 0.6528 (tm-30) REVERT: X 122 ARG cc_start: 0.8166 (mpp80) cc_final: 0.7504 (mtt90) REVERT: E 219 GLN cc_start: 0.6943 (tm-30) cc_final: 0.6322 (tp-100) REVERT: E 344 MET cc_start: 0.7025 (tpt) cc_final: 0.6327 (tpt) REVERT: F 55 ARG cc_start: 0.7366 (mtm180) cc_final: 0.7089 (ttp-170) REVERT: F 315 LEU cc_start: 0.8127 (tp) cc_final: 0.7916 (tp) REVERT: Y 26 ILE cc_start: 0.8213 (mm) cc_final: 0.7926 (mm) REVERT: Y 31 GLN cc_start: 0.6218 (tt0) cc_final: 0.5991 (tt0) REVERT: A 40 LEU cc_start: 0.6017 (mm) cc_final: 0.5747 (mp) REVERT: A 202 ARG cc_start: 0.7586 (ptt-90) cc_final: 0.5954 (ttm170) REVERT: A 470 MET cc_start: 0.5635 (mmp) cc_final: 0.4547 (mmm) REVERT: B 95 ASN cc_start: 0.7586 (t0) cc_final: 0.6337 (p0) REVERT: B 169 TYR cc_start: 0.8147 (p90) cc_final: 0.6757 (p90) REVERT: B 255 MET cc_start: 0.6945 (ppp) cc_final: 0.6380 (ptm) REVERT: B 344 MET cc_start: 0.7136 (tpt) cc_final: 0.6201 (tpt) REVERT: B 375 TYR cc_start: 0.6829 (t80) cc_final: 0.6457 (t80) REVERT: B 389 LEU cc_start: 0.7159 (mm) cc_final: 0.6909 (mm) outliers start: 2 outliers final: 0 residues processed: 413 average time/residue: 0.2035 time to fit residues: 133.5416 Evaluate side-chains 325 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 319 GLN ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 HIS E 147 HIS E 414 GLN E 442 HIS F 236 HIS ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 HIS C 60 HIS C 198 ASN C 298 GLN ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 68 GLN ** Y 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.238929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.219219 restraints weight = 38489.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.213310 restraints weight = 53759.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.211431 restraints weight = 58682.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.211064 restraints weight = 51025.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.209075 restraints weight = 48450.371| |-----------------------------------------------------------------------------| r_work (final): 0.4406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4404 r_free = 0.4404 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4403 r_free = 0.4403 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.4403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 29664 Z= 0.244 Angle : 0.761 13.070 40614 Z= 0.385 Chirality : 0.046 0.190 4568 Planarity : 0.006 0.093 4854 Dihedral : 18.024 174.756 4882 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.03 % Favored : 93.94 % Rotamer: Outliers : 1.52 % Allowed : 9.45 % Favored : 89.03 % 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: -1.20 (0.14), residues: 3298 helix: -0.34 (0.13), residues: 1635 sheet: 0.05 (0.39), residues: 176 loop : -1.34 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 372 TYR 0.032 0.002 TYR B 337 PHE 0.023 0.002 PHE X 161 TRP 0.027 0.002 TRP A 336 HIS 0.009 0.001 HIS G 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.24 (29656) covalent geometry : angle 0.76006 / 0.39 (40608) hydrogen bonds : bond 0.05426 / 3.64 ( 1177) hydrogen bonds : angle 4.85588 / 3.34 ( 3317) metal coordination : bond 0.01949 / 0.95 ( 8) metal coordination : angle 3.40872 / 1.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 352 time to evaluate : 1.146 Fit side-chains REVERT: G 101 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6399 (tt) REVERT: G 203 TYR cc_start: 0.7751 (m-80) cc_final: 0.7181 (m-10) REVERT: G 235 GLN cc_start: 0.4925 (OUTLIER) cc_final: 0.4630 (pt0) REVERT: X 14 TYR cc_start: 0.8037 (t80) cc_final: 0.7823 (t80) REVERT: X 99 GLN cc_start: 0.7252 (pt0) cc_final: 0.6402 (tm-30) REVERT: X 122 ARG cc_start: 0.8598 (mpp80) cc_final: 0.7796 (mtt90) REVERT: E 205 LEU cc_start: 0.6696 (mt) cc_final: 0.6290 (mt) REVERT: E 219 GLN cc_start: 0.7040 (tm-30) cc_final: 0.6472 (tp-100) REVERT: E 344 MET cc_start: 0.7231 (tpt) cc_final: 0.6603 (tpt) REVERT: C 67 ASP cc_start: 0.5538 (t0) cc_final: 0.5104 (t0) REVERT: C 373 GLN cc_start: 0.6248 (tm-30) cc_final: 0.5895 (tm-30) REVERT: Y 26 ILE cc_start: 0.8227 (mm) cc_final: 0.7979 (mm) REVERT: B 95 ASN cc_start: 0.7743 (t0) cc_final: 0.6651 (p0) REVERT: B 169 TYR cc_start: 0.8042 (p90) cc_final: 0.6725 (p90) REVERT: B 344 MET cc_start: 0.7468 (tpt) cc_final: 0.6779 (tpt) outliers start: 44 outliers final: 31 residues processed: 375 average time/residue: 0.1925 time to fit residues: 116.3602 Evaluate side-chains 338 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 305 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 192 ASP Chi-restraints excluded: chain G residue 235 GLN Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 377 ASP Chi-restraints excluded: chain X residue 105 HIS Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain E residue 444 TYR Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 401 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain Y residue 6 VAL Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 250 PHE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 348 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 328 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 75 optimal weight: 50.0000 chunk 183 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 231 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 335 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 319 GLN ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 HIS E 147 HIS E 442 HIS ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 HIS ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN ** Y 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 HIS ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.241202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.219140 restraints weight = 38148.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.213566 restraints weight = 52835.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.210555 restraints weight = 52867.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.209935 restraints weight = 50121.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.208056 restraints weight = 46721.903| |-----------------------------------------------------------------------------| r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4403 r_free = 0.4403 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4403 r_free = 0.4403 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29664 Z= 0.136 Angle : 0.632 13.236 40614 Z= 0.318 Chirality : 0.041 0.169 4568 Planarity : 0.005 0.071 4854 Dihedral : 17.909 166.280 4882 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.18 % Favored : 94.78 % Rotamer: Outliers : 1.70 % Allowed : 13.11 % Favored : 85.19 % 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: -0.96 (0.14), residues: 3298 helix: -0.12 (0.13), residues: 1635 sheet: 0.26 (0.40), residues: 166 loop : -1.26 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG X 40 TYR 0.032 0.001 TYR B 337 PHE 0.017 0.001 PHE F 70 TRP 0.009 0.001 TRP C 336 HIS 0.013 0.001 HIS G 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (29656) covalent geometry : angle 0.63165 / 0.32 (40608) hydrogen bonds : bond 0.04336 / 2.89 ( 1177) hydrogen bonds : angle 4.52801 / 3.13 ( 3317) metal coordination : bond 0.01486 / 0.78 ( 8) metal coordination : angle 2.57638 / 1.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 323 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 203 TYR cc_start: 0.7745 (m-80) cc_final: 0.7189 (m-10) REVERT: X 35 GLU cc_start: 0.5817 (mm-30) cc_final: 0.5613 (mm-30) REVERT: X 99 GLN cc_start: 0.7130 (pt0) cc_final: 0.6349 (tm-30) REVERT: X 122 ARG cc_start: 0.8476 (mpp80) cc_final: 0.7577 (mtt90) REVERT: F 213 MET cc_start: 0.7037 (mtm) cc_final: 0.6769 (mtm) REVERT: F 357 ARG cc_start: 0.6327 (mtp180) cc_final: 0.6042 (mtp180) REVERT: C 67 ASP cc_start: 0.5503 (t0) cc_final: 0.5066 (t0) REVERT: C 198 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8319 (m-40) REVERT: C 351 PHE cc_start: 0.8055 (t80) cc_final: 0.7398 (t80) REVERT: Y 26 ILE cc_start: 0.8238 (mm) cc_final: 0.7951 (mm) REVERT: Y 31 GLN cc_start: 0.6241 (tt0) cc_final: 0.6029 (tt0) REVERT: B 95 ASN cc_start: 0.7754 (t0) cc_final: 0.7460 (t0) REVERT: B 169 TYR cc_start: 0.8029 (p90) cc_final: 0.6820 (p90) REVERT: B 255 MET cc_start: 0.7161 (ppp) cc_final: 0.5842 (ptp) REVERT: B 344 MET cc_start: 0.7046 (tpt) cc_final: 0.6404 (tpt) outliers start: 49 outliers final: 30 residues processed: 357 average time/residue: 0.1985 time to fit residues: 113.6979 Evaluate side-chains 338 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 307 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 105 HIS Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain E residue 444 TYR Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 401 SER Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain Y residue 6 VAL Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 250 PHE Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 291 optimal weight: 30.0000 chunk 234 optimal weight: 0.0470 chunk 304 optimal weight: 0.9980 chunk 274 optimal weight: 7.9990 chunk 79 optimal weight: 50.0000 chunk 184 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 318 optimal weight: 0.9980 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 HIS E 147 HIS ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN C 305 ASN ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN A 76 HIS A 355 GLN A 442 HIS B 71 GLN B 166 GLN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.242638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.220223 restraints weight = 38388.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.214837 restraints weight = 52202.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.211598 restraints weight = 50366.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.211247 restraints weight = 47304.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.210380 restraints weight = 42533.422| |-----------------------------------------------------------------------------| r_work (final): 0.4424 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4416 r_free = 0.4416 target_work(ls_wunit_k1) = 0.209 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4416 r_free = 0.4416 target_work(ls_wunit_k1) = 0.209 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29664 Z= 0.125 Angle : 0.609 14.067 40614 Z= 0.305 Chirality : 0.040 0.222 4568 Planarity : 0.004 0.065 4854 Dihedral : 17.823 153.474 4882 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.43 % Favored : 94.54 % Rotamer: Outliers : 1.87 % Allowed : 15.29 % Favored : 82.84 % 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: -0.80 (0.14), residues: 3298 helix: 0.04 (0.13), residues: 1628 sheet: 0.39 (0.40), residues: 173 loop : -1.22 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 94 TYR 0.046 0.001 TYR B 375 PHE 0.039 0.001 PHE Y 275 TRP 0.023 0.001 TRP B 316 HIS 0.011 0.001 HIS G 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (29656) covalent geometry : angle 0.60877 / 0.30 (40608) hydrogen bonds : bond 0.03864 / 2.58 ( 1177) hydrogen bonds : angle 4.32680 / 2.97 ( 3317) metal coordination : bond 0.01133 / 0.63 ( 8) metal coordination : angle 2.24504 / 1.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 321 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 203 TYR cc_start: 0.7683 (m-80) cc_final: 0.6876 (m-10) REVERT: X 99 GLN cc_start: 0.7190 (pt0) cc_final: 0.6364 (tm-30) REVERT: X 122 ARG cc_start: 0.8448 (mpp80) cc_final: 0.7728 (mtt180) REVERT: E 87 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7160 (mt) REVERT: F 213 MET cc_start: 0.6987 (mtm) cc_final: 0.6732 (mtm) REVERT: F 417 LEU cc_start: 0.8731 (mt) cc_final: 0.8481 (tt) REVERT: C 67 ASP cc_start: 0.5511 (t0) cc_final: 0.5033 (t0) REVERT: C 351 PHE cc_start: 0.7952 (t80) cc_final: 0.7316 (t80) REVERT: Y 26 ILE cc_start: 0.8295 (mm) cc_final: 0.7954 (mm) REVERT: Y 31 GLN cc_start: 0.6247 (tt0) cc_final: 0.6039 (tt0) REVERT: A 184 CYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6696 (t) REVERT: A 385 MET cc_start: 0.6413 (ttm) cc_final: 0.6137 (ttp) REVERT: B 169 TYR cc_start: 0.8019 (p90) cc_final: 0.6825 (p90) REVERT: B 255 MET cc_start: 0.7149 (ppp) cc_final: 0.5996 (ptp) REVERT: B 344 MET cc_start: 0.6877 (tpt) cc_final: 0.6437 (tpt) outliers start: 54 outliers final: 39 residues processed: 360 average time/residue: 0.2051 time to fit residues: 117.1049 Evaluate side-chains 343 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 302 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 104 HIS Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 105 HIS Chi-restraints excluded: chain X residue 106 LEU Chi-restraints excluded: chain X residue 300 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain E residue 444 TYR Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 401 SER Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 179 optimal weight: 0.0470 chunk 317 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 216 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 111 optimal weight: 0.0870 chunk 312 optimal weight: 5.9990 chunk 220 optimal weight: 8.9990 chunk 238 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 77 optimal weight: 30.0000 overall best weight: 1.1658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 HIS E 147 HIS ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 HIS C 102 GLN ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 68 GLN ** Y 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.242831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.221325 restraints weight = 38216.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.218187 restraints weight = 81926.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.215145 restraints weight = 41214.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.215268 restraints weight = 52962.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.215954 restraints weight = 26713.329| |-----------------------------------------------------------------------------| r_work (final): 0.4456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4457 r_free = 0.4457 target_work(ls_wunit_k1) = 0.214 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4457 r_free = 0.4457 target_work(ls_wunit_k1) = 0.214 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29664 Z= 0.136 Angle : 0.614 14.516 40614 Z= 0.307 Chirality : 0.040 0.214 4568 Planarity : 0.004 0.065 4854 Dihedral : 17.791 145.012 4882 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.22 % Favored : 94.75 % Rotamer: Outliers : 2.66 % Allowed : 16.16 % Favored : 81.18 % 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: -0.74 (0.14), residues: 3298 helix: 0.11 (0.13), residues: 1627 sheet: 0.35 (0.39), residues: 173 loop : -1.22 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 357 TYR 0.049 0.001 TYR B 375 PHE 0.029 0.001 PHE C 23 TRP 0.020 0.001 TRP B 316 HIS 0.010 0.001 HIS G 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (29656) covalent geometry : angle 0.61376 / 0.31 (40608) hydrogen bonds : bond 0.03792 / 2.54 ( 1177) hydrogen bonds : angle 4.30560 / 2.96 ( 3317) metal coordination : bond 0.00912 / 0.53 ( 8) metal coordination : angle 2.14810 / 1.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 321 time to evaluate : 1.107 Fit side-chains REVERT: G 101 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6316 (tp) REVERT: G 150 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7275 (tp) REVERT: G 195 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6890 (tp) REVERT: G 268 THR cc_start: 0.7535 (OUTLIER) cc_final: 0.7251 (m) REVERT: X 99 GLN cc_start: 0.7070 (pt0) cc_final: 0.6345 (tm-30) REVERT: X 122 ARG cc_start: 0.8396 (mpp80) cc_final: 0.7609 (mtt90) REVERT: E 87 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7216 (mt) REVERT: E 161 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7588 (pp20) REVERT: F 249 LEU cc_start: 0.7410 (tt) cc_final: 0.7156 (tp) REVERT: F 417 LEU cc_start: 0.8743 (mt) cc_final: 0.8528 (tt) REVERT: C 67 ASP cc_start: 0.5453 (t0) cc_final: 0.5030 (t0) REVERT: C 377 ASP cc_start: 0.6228 (m-30) cc_final: 0.5945 (m-30) REVERT: Y 26 ILE cc_start: 0.8295 (mm) cc_final: 0.7995 (mm) REVERT: Y 31 GLN cc_start: 0.6231 (tt0) cc_final: 0.6029 (tt0) REVERT: A 385 MET cc_start: 0.6384 (ttm) cc_final: 0.6077 (ttp) REVERT: B 155 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.6572 (tt0) REVERT: B 169 TYR cc_start: 0.8041 (p90) cc_final: 0.6802 (p90) REVERT: B 255 MET cc_start: 0.7139 (ppp) cc_final: 0.6212 (ptp) REVERT: B 344 MET cc_start: 0.6758 (tpt) cc_final: 0.6555 (tpt) outliers start: 77 outliers final: 45 residues processed: 377 average time/residue: 0.1942 time to fit residues: 116.7483 Evaluate side-chains 352 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 300 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 104 HIS Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 106 LEU Chi-restraints excluded: chain X residue 300 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 442 HIS Chi-restraints excluded: chain E residue 444 TYR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 401 SER Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 293 TRP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 299 THR Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 286 optimal weight: 0.4980 chunk 197 optimal weight: 3.9990 chunk 78 optimal weight: 40.0000 chunk 20 optimal weight: 0.0980 chunk 23 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 277 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 314 ASN ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 HIS E 147 HIS ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 HIS C 355 GLN ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS B 341 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.245039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.222737 restraints weight = 38325.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.216721 restraints weight = 51179.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.214166 restraints weight = 54945.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.214040 restraints weight = 51785.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.213163 restraints weight = 39700.676| |-----------------------------------------------------------------------------| r_work (final): 0.4445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4447 r_free = 0.4447 target_work(ls_wunit_k1) = 0.212 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4447 r_free = 0.4447 target_work(ls_wunit_k1) = 0.212 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 29664 Z= 0.114 Angle : 0.602 14.715 40614 Z= 0.299 Chirality : 0.039 0.183 4568 Planarity : 0.004 0.065 4854 Dihedral : 17.732 134.407 4882 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.03 % Favored : 94.94 % Rotamer: Outliers : 2.15 % Allowed : 17.51 % Favored : 80.35 % 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: -0.63 (0.15), residues: 3298 helix: 0.21 (0.13), residues: 1637 sheet: 0.43 (0.40), residues: 173 loop : -1.19 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 372 TYR 0.023 0.001 TYR C 375 PHE 0.035 0.001 PHE E 70 TRP 0.011 0.001 TRP G 316 HIS 0.012 0.001 HIS E 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (29656) covalent geometry : angle 0.60189 / 0.30 (40608) hydrogen bonds : bond 0.03557 / 2.37 ( 1177) hydrogen bonds : angle 4.21464 / 2.90 ( 3317) metal coordination : bond 0.00789 / 0.47 ( 8) metal coordination : angle 1.99210 / 1.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 313 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: G 150 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7377 (tp) REVERT: X 99 GLN cc_start: 0.7178 (pt0) cc_final: 0.6281 (tm-30) REVERT: X 122 ARG cc_start: 0.8423 (mpp80) cc_final: 0.7626 (mtt180) REVERT: E 87 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7021 (mt) REVERT: E 161 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7658 (pp20) REVERT: F 417 LEU cc_start: 0.8710 (mt) cc_final: 0.8493 (tt) REVERT: C 67 ASP cc_start: 0.5384 (t0) cc_final: 0.4964 (t0) REVERT: C 264 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7493 (ttm) REVERT: C 351 PHE cc_start: 0.7953 (t80) cc_final: 0.7376 (t80) REVERT: C 377 ASP cc_start: 0.6352 (m-30) cc_final: 0.6106 (m-30) REVERT: Y 26 ILE cc_start: 0.8284 (mm) cc_final: 0.8031 (mm) REVERT: A 385 MET cc_start: 0.6349 (ttm) cc_final: 0.6077 (ttp) REVERT: B 169 TYR cc_start: 0.7998 (p90) cc_final: 0.6775 (p90) REVERT: B 255 MET cc_start: 0.7003 (ppp) cc_final: 0.6065 (ptp) REVERT: B 484 MET cc_start: 0.1865 (tmm) cc_final: 0.1555 (tmm) outliers start: 62 outliers final: 42 residues processed: 360 average time/residue: 0.1928 time to fit residues: 111.9017 Evaluate side-chains 348 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 302 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 104 HIS Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 93 ILE Chi-restraints excluded: chain X residue 106 LEU Chi-restraints excluded: chain X residue 300 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 442 HIS Chi-restraints excluded: chain E residue 444 TYR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 299 THR Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 277 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 289 optimal weight: 8.9990 chunk 323 optimal weight: 7.9990 chunk 50 optimal weight: 0.0060 chunk 185 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 241 optimal weight: 0.9980 chunk 175 optimal weight: 8.9990 chunk 137 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 314 ASN ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 HIS ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS F 246 GLN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 HIS C 355 GLN ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN ** Y 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 HIS A 383 HIS B 130 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.243702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.222513 restraints weight = 38286.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.219235 restraints weight = 81675.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.217338 restraints weight = 41256.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.216199 restraints weight = 46437.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.216870 restraints weight = 22829.504| |-----------------------------------------------------------------------------| r_work (final): 0.4449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4450 r_free = 0.4450 target_work(ls_wunit_k1) = 0.213 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4450 r_free = 0.4450 target_work(ls_wunit_k1) = 0.213 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29664 Z= 0.136 Angle : 0.626 15.138 40614 Z= 0.309 Chirality : 0.040 0.213 4568 Planarity : 0.004 0.065 4854 Dihedral : 17.714 133.595 4882 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.43 % Favored : 94.54 % Rotamer: Outliers : 2.42 % Allowed : 17.51 % Favored : 80.07 % 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: -0.65 (0.15), residues: 3298 helix: 0.20 (0.13), residues: 1632 sheet: 0.40 (0.40), residues: 173 loop : -1.20 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 372 TYR 0.017 0.001 TYR B 337 PHE 0.022 0.001 PHE E 70 TRP 0.012 0.001 TRP G 316 HIS 0.006 0.001 HIS C 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (29656) covalent geometry : angle 0.62576 / 0.31 (40608) hydrogen bonds : bond 0.03671 / 2.46 ( 1177) hydrogen bonds : angle 4.24506 / 2.92 ( 3317) metal coordination : bond 0.02471 / 1.07 ( 8) metal coordination : angle 2.41104 / 1.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 309 time to evaluate : 1.063 Fit side-chains REVERT: G 101 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.6402 (tp) REVERT: G 150 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7355 (tp) REVERT: G 268 THR cc_start: 0.7533 (OUTLIER) cc_final: 0.7204 (m) REVERT: X 99 GLN cc_start: 0.7058 (pt0) cc_final: 0.6364 (tm-30) REVERT: X 122 ARG cc_start: 0.8404 (mpp80) cc_final: 0.7685 (mtt90) REVERT: E 87 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7199 (mt) REVERT: E 161 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7627 (pp20) REVERT: F 95 ASN cc_start: 0.8388 (t0) cc_final: 0.8050 (t0) REVERT: C 67 ASP cc_start: 0.5312 (t0) cc_final: 0.4954 (t0) REVERT: C 264 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7451 (ttm) REVERT: C 377 ASP cc_start: 0.6396 (m-30) cc_final: 0.6140 (m-30) REVERT: Y 26 ILE cc_start: 0.8296 (mm) cc_final: 0.8015 (mm) REVERT: A 385 MET cc_start: 0.6291 (ttm) cc_final: 0.6044 (ttp) REVERT: B 102 GLN cc_start: 0.5162 (mm-40) cc_final: 0.4911 (mm-40) REVERT: B 155 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.6457 (tt0) REVERT: B 255 MET cc_start: 0.7023 (ppp) cc_final: 0.6055 (ptp) outliers start: 70 outliers final: 48 residues processed: 363 average time/residue: 0.1820 time to fit residues: 106.8251 Evaluate side-chains 359 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 304 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 104 HIS Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 341 GLN Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 93 ILE Chi-restraints excluded: chain X residue 106 LEU Chi-restraints excluded: chain X residue 300 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 442 HIS Chi-restraints excluded: chain E residue 444 TYR Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 401 SER Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 293 TRP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain Y residue 6 VAL Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain Y residue 299 THR Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 212 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 299 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 chunk 187 optimal weight: 0.2980 chunk 236 optimal weight: 30.0000 chunk 245 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 280 optimal weight: 20.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 HIS ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 HIS ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN ** Y 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 HIS A 383 HIS ** B 442 HIS ** 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 = 0.4706 r_free = 0.4706 target = 0.242022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.220415 restraints weight = 38160.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.217417 restraints weight = 81529.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.214603 restraints weight = 40975.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.214964 restraints weight = 47239.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.215426 restraints weight = 25468.041| |-----------------------------------------------------------------------------| r_work (final): 0.4445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4453 r_free = 0.4453 target_work(ls_wunit_k1) = 0.213 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4453 r_free = 0.4453 target_work(ls_wunit_k1) = 0.213 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29664 Z= 0.140 Angle : 0.629 15.280 40614 Z= 0.311 Chirality : 0.040 0.170 4568 Planarity : 0.004 0.065 4854 Dihedral : 17.682 133.689 4882 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.52 % Favored : 94.45 % Rotamer: Outliers : 2.32 % Allowed : 17.89 % Favored : 79.79 % 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: -0.63 (0.15), residues: 3298 helix: 0.22 (0.13), residues: 1633 sheet: 0.36 (0.39), residues: 173 loop : -1.19 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 372 TYR 0.017 0.001 TYR B 337 PHE 0.022 0.001 PHE C 23 TRP 0.015 0.001 TRP G 316 HIS 0.006 0.001 HIS C 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (29656) covalent geometry : angle 0.62825 / 0.31 (40608) hydrogen bonds : bond 0.03687 / 2.47 ( 1177) hydrogen bonds : angle 4.25456 / 2.93 ( 3317) metal coordination : bond 0.02047 / 1.03 ( 8) metal coordination : angle 2.22242 / 1.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 317 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: G 101 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6335 (tp) REVERT: G 150 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7351 (tp) REVERT: G 268 THR cc_start: 0.7534 (OUTLIER) cc_final: 0.7204 (m) REVERT: X 99 GLN cc_start: 0.7067 (pt0) cc_final: 0.6312 (tm-30) REVERT: X 122 ARG cc_start: 0.8407 (mpp80) cc_final: 0.7614 (mtt90) REVERT: E 87 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7197 (mt) REVERT: E 161 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7691 (pp20) REVERT: F 95 ASN cc_start: 0.8418 (t0) cc_final: 0.8089 (t0) REVERT: F 357 ARG cc_start: 0.6127 (mtp-110) cc_final: 0.5866 (mtp180) REVERT: C 67 ASP cc_start: 0.5345 (t0) cc_final: 0.4947 (t0) REVERT: C 264 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7394 (ttm) REVERT: C 351 PHE cc_start: 0.7940 (t80) cc_final: 0.7525 (t80) REVERT: C 377 ASP cc_start: 0.6463 (m-30) cc_final: 0.6238 (m-30) REVERT: Y 26 ILE cc_start: 0.8328 (mm) cc_final: 0.8035 (mm) REVERT: A 385 MET cc_start: 0.6355 (ttm) cc_final: 0.6106 (ttp) REVERT: B 102 GLN cc_start: 0.5219 (mm-40) cc_final: 0.4952 (mm-40) REVERT: B 155 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.6431 (tt0) REVERT: B 169 TYR cc_start: 0.8132 (p90) cc_final: 0.7870 (p90) REVERT: B 255 MET cc_start: 0.7003 (ppp) cc_final: 0.6210 (ptp) outliers start: 67 outliers final: 49 residues processed: 369 average time/residue: 0.1986 time to fit residues: 117.2878 Evaluate side-chains 359 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 303 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 104 HIS Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 93 ILE Chi-restraints excluded: chain X residue 106 LEU Chi-restraints excluded: chain X residue 300 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 444 TYR Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 401 SER Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 293 TRP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 223 GLN Chi-restraints excluded: chain Y residue 299 THR Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 293 TRP Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 265 optimal weight: 9.9990 chunk 315 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 285 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 312 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 236 optimal weight: 30.0000 chunk 264 optimal weight: 0.5980 chunk 168 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 HIS F 322 GLN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN ** Y 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 HIS ** 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 = 0.4693 r_free = 0.4693 target = 0.240368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.218564 restraints weight = 38092.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.213515 restraints weight = 59228.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.210995 restraints weight = 55974.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.210954 restraints weight = 53842.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.210323 restraints weight = 40850.364| |-----------------------------------------------------------------------------| r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4426 r_free = 0.4426 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4426 r_free = 0.4426 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29664 Z= 0.169 Angle : 0.677 15.808 40614 Z= 0.334 Chirality : 0.042 0.222 4568 Planarity : 0.005 0.066 4854 Dihedral : 17.702 134.508 4882 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.97 % Favored : 94.00 % Rotamer: Outliers : 2.18 % Allowed : 18.34 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.15), residues: 3298 helix: 0.17 (0.13), residues: 1635 sheet: 0.17 (0.39), residues: 173 loop : -1.21 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 372 TYR 0.029 0.001 TYR B 69 PHE 0.023 0.002 PHE F 70 TRP 0.018 0.001 TRP B 316 HIS 0.007 0.001 HIS C 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (29656) covalent geometry : angle 0.67628 / 0.33 (40608) hydrogen bonds : bond 0.03937 / 2.65 ( 1177) hydrogen bonds : angle 4.35078 / 3.00 ( 3317) metal coordination : bond 0.02055 / 1.01 ( 8) metal coordination : angle 2.25943 / 1.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 305 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: G 101 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6508 (tp) REVERT: G 150 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7366 (tp) REVERT: G 268 THR cc_start: 0.7594 (OUTLIER) cc_final: 0.7242 (m) REVERT: X 99 GLN cc_start: 0.7128 (pt0) cc_final: 0.6310 (tm-30) REVERT: X 122 ARG cc_start: 0.8372 (mpp80) cc_final: 0.7682 (mtt90) REVERT: E 161 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7728 (pp20) REVERT: E 205 LEU cc_start: 0.6632 (mt) cc_final: 0.6309 (mt) REVERT: C 67 ASP cc_start: 0.5373 (t0) cc_final: 0.4957 (t0) REVERT: C 264 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7520 (ttm) REVERT: C 351 PHE cc_start: 0.7967 (t80) cc_final: 0.7569 (t80) REVERT: Y 26 ILE cc_start: 0.8327 (mm) cc_final: 0.8050 (mm) REVERT: A 202 ARG cc_start: 0.7797 (ptt-90) cc_final: 0.5798 (ttm170) REVERT: A 385 MET cc_start: 0.6354 (ttm) cc_final: 0.6114 (ttp) REVERT: B 102 GLN cc_start: 0.5243 (mm-40) cc_final: 0.4954 (mm-40) REVERT: B 155 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.6613 (tt0) REVERT: B 169 TYR cc_start: 0.8071 (p90) cc_final: 0.7824 (p90) REVERT: B 255 MET cc_start: 0.7044 (ppp) cc_final: 0.6038 (ptp) REVERT: B 484 MET cc_start: 0.2182 (tmm) cc_final: 0.1784 (tmm) outliers start: 63 outliers final: 50 residues processed: 351 average time/residue: 0.1955 time to fit residues: 110.3970 Evaluate side-chains 351 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 295 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 104 HIS Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 93 ILE Chi-restraints excluded: chain X residue 106 LEU Chi-restraints excluded: chain X residue 300 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 444 TYR Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 401 SER Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 293 TRP Chi-restraints excluded: chain C residue 308 TRP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain Y residue 223 GLN Chi-restraints excluded: chain Y residue 299 THR Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 293 TRP Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 264 optimal weight: 0.0000 chunk 332 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 336 optimal weight: 0.6980 chunk 204 optimal weight: 2.9990 chunk 292 optimal weight: 0.9990 chunk 309 optimal weight: 9.9990 chunk 217 optimal weight: 6.9990 chunk 102 optimal weight: 0.0000 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 HIS ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN ** Y 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 HIS ** 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 = 0.4714 r_free = 0.4714 target = 0.242992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.221713 restraints weight = 37985.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.218279 restraints weight = 82388.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.216445 restraints weight = 41490.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.215908 restraints weight = 50588.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.216769 restraints weight = 25204.198| |-----------------------------------------------------------------------------| r_work (final): 0.4463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4457 r_free = 0.4457 target_work(ls_wunit_k1) = 0.214 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4457 r_free = 0.4457 target_work(ls_wunit_k1) = 0.214 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29664 Z= 0.121 Angle : 0.642 15.011 40614 Z= 0.314 Chirality : 0.040 0.172 4568 Planarity : 0.004 0.065 4854 Dihedral : 17.621 133.709 4882 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.15 % Favored : 94.78 % Rotamer: Outliers : 1.83 % Allowed : 18.89 % Favored : 79.27 % 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: -0.59 (0.15), residues: 3298 helix: 0.25 (0.13), residues: 1644 sheet: 0.25 (0.39), residues: 173 loop : -1.16 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 372 TYR 0.025 0.001 TYR B 69 PHE 0.026 0.001 PHE C 23 TRP 0.020 0.001 TRP B 316 HIS 0.005 0.001 HIS F 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (29656) covalent geometry : angle 0.64124 / 0.31 (40608) hydrogen bonds : bond 0.03536 / 2.37 ( 1177) hydrogen bonds : angle 4.26845 / 2.94 ( 3317) metal coordination : bond 0.02003 / 0.99 ( 8) metal coordination : angle 1.99920 / 1.15 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 303 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: G 101 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6396 (tp) REVERT: G 150 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7376 (tp) REVERT: G 268 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.7175 (m) REVERT: X 99 GLN cc_start: 0.7005 (pt0) cc_final: 0.6335 (tm-30) REVERT: X 122 ARG cc_start: 0.8333 (mpp80) cc_final: 0.7578 (mtt90) REVERT: E 161 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7681 (pp20) REVERT: F 291 ILE cc_start: 0.7591 (mm) cc_final: 0.7371 (mt) REVERT: F 357 ARG cc_start: 0.6162 (mtp-110) cc_final: 0.5937 (mtp180) REVERT: C 67 ASP cc_start: 0.5394 (t0) cc_final: 0.4984 (t0) REVERT: C 264 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7342 (ttm) REVERT: C 351 PHE cc_start: 0.7887 (t80) cc_final: 0.7412 (t80) REVERT: Y 26 ILE cc_start: 0.8309 (mm) cc_final: 0.8005 (mm) REVERT: A 202 ARG cc_start: 0.7644 (ptt-90) cc_final: 0.5812 (ttm170) REVERT: A 385 MET cc_start: 0.6383 (ttm) cc_final: 0.6125 (ttp) REVERT: B 102 GLN cc_start: 0.5219 (mm-40) cc_final: 0.4969 (mm-40) REVERT: B 155 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.6458 (tt0) REVERT: B 169 TYR cc_start: 0.8137 (p90) cc_final: 0.7891 (p90) REVERT: B 255 MET cc_start: 0.6951 (ppp) cc_final: 0.5920 (ptp) REVERT: B 484 MET cc_start: 0.1775 (tmm) cc_final: 0.1573 (tmm) outliers start: 53 outliers final: 44 residues processed: 341 average time/residue: 0.1801 time to fit residues: 98.7206 Evaluate side-chains 342 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 292 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 104 HIS Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 93 ILE Chi-restraints excluded: chain X residue 300 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 444 TYR Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 223 GLN Chi-restraints excluded: chain Y residue 299 THR Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 293 TRP Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 124 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 45 optimal weight: 0.1980 chunk 217 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 337 optimal weight: 0.0070 chunk 168 optimal weight: 3.9990 chunk 39 optimal weight: 0.0980 chunk 191 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 HIS E 246 GLN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN ** Y 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 HIS ** 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 = 0.4736 r_free = 0.4736 target = 0.245427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.224606 restraints weight = 38339.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.221446 restraints weight = 80976.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.219621 restraints weight = 39943.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.218973 restraints weight = 51169.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.219761 restraints weight = 25628.741| |-----------------------------------------------------------------------------| r_work (final): 0.4483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4483 r_free = 0.4483 target_work(ls_wunit_k1) = 0.217 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4483 r_free = 0.4483 target_work(ls_wunit_k1) = 0.217 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 29664 Z= 0.111 Angle : 0.638 14.935 40614 Z= 0.310 Chirality : 0.040 0.256 4568 Planarity : 0.004 0.065 4854 Dihedral : 17.538 131.642 4882 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.15 % Favored : 94.78 % Rotamer: Outliers : 1.66 % Allowed : 19.20 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.15), residues: 3298 helix: 0.37 (0.13), residues: 1642 sheet: 0.31 (0.38), residues: 179 loop : -1.05 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 372 TYR 0.041 0.001 TYR B 375 PHE 0.024 0.001 PHE A 187 TRP 0.022 0.001 TRP B 316 HIS 0.005 0.001 HIS F 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (29656) covalent geometry : angle 0.63751 / 0.31 (40608) hydrogen bonds : bond 0.03344 / 2.24 ( 1177) hydrogen bonds : angle 4.17684 / 2.87 ( 3317) metal coordination : bond 0.01820 / 0.91 ( 8) metal coordination : angle 1.95043 / 1.12 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4539.85 seconds wall clock time: 79 minutes 34.91 seconds (4774.91 seconds total)