Starting phenix.real_space_refine on Mon May 26 16:12:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8glx_40222/05_2025/8glx_40222.cif Found real_map, /net/cci-nas-00/data/ceres_data/8glx_40222/05_2025/8glx_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_40222/05_2025/8glx_40222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8glx_40222/05_2025/8glx_40222.map" model { file = "/net/cci-nas-00/data/ceres_data/8glx_40222/05_2025/8glx_40222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8glx_40222/05_2025/8glx_40222.cif" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 16.87, per 1000 atoms: 0.58 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: 6.55 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 9.72 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: 9.40 Time building geometry restraints manager: 7.76 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=" 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=" CG PRO A 304 " pdb=" CD PRO A 304 " ideal model delta sigma weight residual 1.503 1.417 0.086 3.40e-02 8.65e+02 6.41e+00 bond pdb=" CB PRO G 269 " pdb=" CG PRO G 269 " ideal model delta sigma weight residual 1.492 1.580 -0.088 5.00e-02 4.00e+02 3.10e+00 bond pdb=" C ILE E 457 " pdb=" N PRO E 458 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.30e-02 5.92e+03 2.10e+00 bond pdb=" CB PRO X 201 " pdb=" CG PRO X 201 " ideal model delta sigma weight residual 1.492 1.564 -0.072 5.00e-02 4.00e+02 2.06e+00 ... (remaining 29651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 40002 2.39 - 4.78: 483 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: 3475 0.044 - 0.089: 852 0.089 - 0.133: 209 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 485 or resid 601 through 602)) selection = (chain 'B' and (resid 4 through 124 or resid 130 through 485 or resid 601 throug \ h 602)) selection = (chain 'E' and (resid 4 through 485 or resid 601 through 602)) selection = (chain 'F' and (resid 4 through 124 or resid 130 through 485 or resid 601 throug \ h 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: 6.960 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: 1.260 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 71.060 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6097 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= 0.134 Angle : 0.695 11.962 40614 Z= 0.351 Chirality : 0.042 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.041 0.002 TRP Y 291 HIS 0.014 0.001 HIS G 383 PHE 0.018 0.001 PHE C 351 TYR 0.028 0.001 TYR B 375 ARG 0.010 0.000 ARG G 55 Details of bonding type rmsd hydrogen bonds : bond 0.17695 ( 1177) hydrogen bonds : angle 5.91617 ( 3317) metal coordination : bond 0.03271 ( 8) metal coordination : angle 2.87797 ( 6) covalent geometry : bond 0.00297 (29656) covalent geometry : angle 0.69396 (40608) *********************** 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 : 3.016 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: 0.7922 (mm) REVERT: Y 31 GLN cc_start: 0.6217 (tt0) cc_final: 0.5988 (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: 0.6336 (p0) REVERT: B 169 TYR cc_start: 0.8147 (p90) cc_final: 0.6756 (p90) REVERT: B 255 MET cc_start: 0.6945 (ppp) cc_final: 0.6381 (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: 0.6458 (t80) REVERT: B 389 LEU cc_start: 0.7159 (mm) cc_final: 0.6910 (mm) outliers start: 2 outliers final: 0 residues processed: 413 average time/residue: 0.4045 time to fit residues: 262.0230 Evaluate side-chains 324 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 8.9990 chunk 257 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 173 optimal weight: 8.9990 chunk 137 optimal weight: 1.9990 chunk 266 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 chunk 308 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 HIS E 147 HIS ** E 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 442 HIS ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 HIS C 198 ASN C 298 GLN ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN B 319 GLN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.243918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.223074 restraints weight = 38231.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.219882 restraints weight = 81209.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.217653 restraints weight = 41141.867| |-----------------------------------------------------------------------------| r_work (final): 0.4471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4469 r_free = 0.4469 target_work(ls_wunit_k1) = 0.215 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4469 r_free = 0.4469 target_work(ls_wunit_k1) = 0.215 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29664 Z= 0.147 Angle : 0.642 11.869 40614 Z= 0.322 Chirality : 0.041 0.176 4568 Planarity : 0.005 0.092 4854 Dihedral : 17.750 174.833 4882 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.21 % Allowed : 8.03 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3298 helix: -0.07 (0.13), residues: 1639 sheet: 0.39 (0.41), residues: 178 loop : -1.18 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 336 HIS 0.013 0.001 HIS C 383 PHE 0.018 0.001 PHE Y 275 TYR 0.033 0.001 TYR B 337 ARG 0.010 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 1177) hydrogen bonds : angle 4.55824 ( 3317) metal coordination : bond 0.01894 ( 8) metal coordination : angle 2.72522 ( 6) covalent geometry : bond 0.00332 (29656) covalent geometry : angle 0.64084 (40608) *********************** 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 393 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 358 time to evaluate : 2.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 203 TYR cc_start: 0.7368 (m-80) cc_final: 0.6949 (m-10) REVERT: G 235 GLN cc_start: 0.4689 (OUTLIER) cc_final: 0.4367 (pt0) REVERT: X 99 GLN cc_start: 0.7291 (pt0) cc_final: 0.6440 (tm-30) REVERT: X 122 ARG cc_start: 0.8327 (mpp80) cc_final: 0.7569 (mtt90) REVERT: E 219 GLN cc_start: 0.6992 (tm-30) cc_final: 0.6423 (tp-100) REVERT: F 55 ARG cc_start: 0.7341 (mtm180) cc_final: 0.7133 (ttp-170) REVERT: F 70 PHE cc_start: 0.7525 (t80) cc_final: 0.7312 (t80) REVERT: C 67 ASP cc_start: 0.5501 (t0) cc_final: 0.5049 (t0) REVERT: C 351 PHE cc_start: 0.8218 (t80) cc_final: 0.7404 (t80) REVERT: C 377 ASP cc_start: 0.5976 (m-30) cc_final: 0.5555 (m-30) REVERT: Y 26 ILE cc_start: 0.8166 (mm) cc_final: 0.7913 (mm) REVERT: B 95 ASN cc_start: 0.7804 (t0) cc_final: 0.6552 (p0) REVERT: B 169 TYR cc_start: 0.8138 (p90) cc_final: 0.6808 (p90) REVERT: B 344 MET cc_start: 0.7327 (tpt) cc_final: 0.6587 (tpt) outliers start: 35 outliers final: 26 residues processed: 378 average time/residue: 0.3992 time to fit residues: 241.5454 Evaluate side-chains 336 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 309 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 VAL 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 4 THR 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 361 LEU Chi-restraints excluded: chain F residue 401 SER 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 164 VAL Chi-restraints excluded: chain B residue 238 SER 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 14 optimal weight: 0.9980 chunk 316 optimal weight: 1.9990 chunk 336 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 276 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 189 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 295 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** E 442 HIS ** 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 305 ASN ** 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 71 GLN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.242881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.222598 restraints weight = 38230.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.218258 restraints weight = 56013.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.216458 restraints weight = 50208.779| |-----------------------------------------------------------------------------| r_work (final): 0.4482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4486 r_free = 0.4486 target_work(ls_wunit_k1) = 0.217 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4486 r_free = 0.4486 target_work(ls_wunit_k1) = 0.217 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29664 Z= 0.133 Angle : 0.607 12.994 40614 Z= 0.303 Chirality : 0.039 0.159 4568 Planarity : 0.004 0.070 4854 Dihedral : 17.654 162.317 4882 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.00 % Favored : 94.97 % Rotamer: Outliers : 1.49 % Allowed : 11.80 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3298 helix: 0.01 (0.13), residues: 1652 sheet: 0.42 (0.40), residues: 170 loop : -1.21 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 291 HIS 0.011 0.001 HIS G 383 PHE 0.019 0.001 PHE Y 172 TYR 0.032 0.001 TYR B 337 ARG 0.009 0.000 ARG X 40 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 1177) hydrogen bonds : angle 4.35720 ( 3317) metal coordination : bond 0.01490 ( 8) metal coordination : angle 2.41034 ( 6) covalent geometry : bond 0.00303 (29656) covalent geometry : angle 0.60614 (40608) *********************** 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 371 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 328 time to evaluate : 3.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 101 LEU cc_start: 0.6313 (OUTLIER) cc_final: 0.6004 (tp) REVERT: G 203 TYR cc_start: 0.7539 (m-80) cc_final: 0.6923 (m-10) REVERT: G 316 TRP cc_start: 0.5900 (t-100) cc_final: 0.5668 (t-100) REVERT: X 99 GLN cc_start: 0.7295 (pt0) cc_final: 0.6384 (tm-30) REVERT: X 122 ARG cc_start: 0.8244 (mpp80) cc_final: 0.7600 (mtt90) REVERT: E 219 GLN cc_start: 0.7027 (tm-30) cc_final: 0.6438 (tp-100) REVERT: F 213 MET cc_start: 0.7002 (mtm) cc_final: 0.6739 (mtm) REVERT: F 248 MET cc_start: 0.5613 (mmt) cc_final: 0.5307 (mmt) REVERT: F 470 MET cc_start: 0.0060 (ttp) cc_final: -0.0323 (pmm) REVERT: C 67 ASP cc_start: 0.5467 (t0) cc_final: 0.5017 (t0) REVERT: C 351 PHE cc_start: 0.7972 (t80) cc_final: 0.7311 (t80) REVERT: C 377 ASP cc_start: 0.5912 (m-30) cc_final: 0.5596 (m-30) REVERT: Y 26 ILE cc_start: 0.8298 (mm) cc_final: 0.8042 (mm) REVERT: A 184 CYS cc_start: 0.6886 (OUTLIER) cc_final: 0.6639 (t) REVERT: A 202 ARG cc_start: 0.7302 (ptt-90) cc_final: 0.5778 (ttm170) REVERT: B 95 ASN cc_start: 0.7709 (t0) cc_final: 0.7432 (t0) REVERT: B 169 TYR cc_start: 0.8150 (p90) cc_final: 0.6856 (p90) REVERT: B 255 MET cc_start: 0.7004 (ppp) cc_final: 0.5673 (ptp) REVERT: B 344 MET cc_start: 0.7173 (tpt) cc_final: 0.6493 (tpt) outliers start: 43 outliers final: 24 residues processed: 359 average time/residue: 0.4143 time to fit residues: 233.4369 Evaluate side-chains 330 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 304 time to evaluate : 3.053 ------------------------------------------------------------------------------- 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 220 ILE Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 346 ILE Chi-restraints excluded: chain X residue 300 VAL 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 265 LEU Chi-restraints excluded: chain F residue 401 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 293 TRP 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 184 CYS Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 348 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 108 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 283 optimal weight: 3.9990 chunk 309 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 160 optimal weight: 0.6980 chunk 306 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 324 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 235 GLN E 442 HIS F 52 GLN ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 341 GLN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 HIS C 60 HIS C 198 ASN Y 31 GLN Y 68 GLN ** Y 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 HIS B 166 GLN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.244547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.223113 restraints weight = 38524.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.220057 restraints weight = 81786.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.217474 restraints weight = 40617.404| |-----------------------------------------------------------------------------| r_work (final): 0.4476 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4470 r_free = 0.4470 target_work(ls_wunit_k1) = 0.215 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4470 r_free = 0.4470 target_work(ls_wunit_k1) = 0.215 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.1653 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= 0.122 Angle : 0.586 13.348 40614 Z= 0.293 Chirality : 0.039 0.221 4568 Planarity : 0.004 0.064 4854 Dihedral : 17.553 147.957 4882 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.94 % Favored : 95.03 % Rotamer: Outliers : 1.70 % Allowed : 14.05 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 3298 helix: 0.18 (0.13), residues: 1626 sheet: 0.45 (0.40), residues: 174 loop : -1.15 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 316 HIS 0.006 0.001 HIS G 383 PHE 0.041 0.001 PHE Y 275 TYR 0.045 0.001 TYR B 375 ARG 0.005 0.000 ARG X 94 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 1177) hydrogen bonds : angle 4.22397 ( 3317) metal coordination : bond 0.01224 ( 8) metal coordination : angle 2.12208 ( 6) covalent geometry : bond 0.00275 (29656) covalent geometry : angle 0.58530 (40608) *********************** 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 369 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 320 time to evaluate : 3.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 203 TYR cc_start: 0.7743 (m-80) cc_final: 0.7020 (m-10) REVERT: X 40 ARG cc_start: 0.7500 (tpp80) cc_final: 0.6815 (mpt-90) REVERT: X 99 GLN cc_start: 0.7339 (pt0) cc_final: 0.6392 (tm-30) REVERT: X 122 ARG cc_start: 0.8361 (mpp80) cc_final: 0.7632 (mtt90) REVERT: E 87 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7129 (mt) REVERT: E 219 GLN cc_start: 0.6971 (tm-30) cc_final: 0.6726 (tm-30) REVERT: F 213 MET cc_start: 0.6880 (mtm) cc_final: 0.6655 (mtm) REVERT: F 248 MET cc_start: 0.5842 (mmt) cc_final: 0.5540 (mmt) REVERT: C 67 ASP cc_start: 0.5453 (t0) cc_final: 0.4974 (t0) REVERT: C 351 PHE cc_start: 0.7927 (t80) cc_final: 0.7303 (t80) REVERT: C 377 ASP cc_start: 0.6172 (m-30) cc_final: 0.5784 (m-30) REVERT: C 385 MET cc_start: 0.3841 (mmp) cc_final: 0.3613 (mmp) REVERT: Y 26 ILE cc_start: 0.8311 (mm) cc_final: 0.8003 (mm) REVERT: A 385 MET cc_start: 0.6414 (ttm) cc_final: 0.6104 (ttp) REVERT: B 123 GLU cc_start: 0.7332 (tp30) cc_final: 0.6667 (tp30) REVERT: B 169 TYR cc_start: 0.8109 (p90) cc_final: 0.6779 (p90) REVERT: B 255 MET cc_start: 0.7025 (ppp) cc_final: 0.5940 (ptp) REVERT: B 344 MET cc_start: 0.6887 (tpt) cc_final: 0.6358 (tpt) outliers start: 49 outliers final: 33 residues processed: 357 average time/residue: 0.4227 time to fit residues: 236.4642 Evaluate side-chains 335 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 301 time to evaluate : 3.033 ------------------------------------------------------------------------------- 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 220 ILE Chi-restraints excluded: chain G residue 346 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 184 CYS Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 268 THR 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 F residue 419 ILE 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 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 181 LEU Chi-restraints excluded: chain A residue 185 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 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 257 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 332 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 306 optimal weight: 0.5980 chunk 206 optimal weight: 6.9990 chunk 283 optimal weight: 9.9990 chunk 218 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 71 optimal weight: 20.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 442 HIS F 208 HIS F 236 HIS F 246 GLN ** 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 68 GLN ** Y 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN A 76 HIS ** A 235 GLN ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.241520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.220242 restraints weight = 38244.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.214130 restraints weight = 51860.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.211614 restraints weight = 53855.400| |-----------------------------------------------------------------------------| r_work (final): 0.4440 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4440 r_free = 0.4440 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4440 r_free = 0.4440 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29664 Z= 0.181 Angle : 0.656 14.237 40614 Z= 0.327 Chirality : 0.041 0.170 4568 Planarity : 0.005 0.066 4854 Dihedral : 17.580 136.620 4882 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.18 % Rotamer: Outliers : 2.21 % Allowed : 15.74 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3298 helix: 0.07 (0.13), residues: 1627 sheet: 0.20 (0.38), residues: 183 loop : -1.23 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 316 HIS 0.009 0.001 HIS E 147 PHE 0.023 0.002 PHE F 70 TYR 0.051 0.002 TYR B 375 ARG 0.015 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 1177) hydrogen bonds : angle 4.35535 ( 3317) metal coordination : bond 0.01283 ( 8) metal coordination : angle 2.29508 ( 6) covalent geometry : bond 0.00433 (29656) covalent geometry : angle 0.65535 (40608) *********************** 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 384 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 320 time to evaluate : 3.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 101 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6469 (tt) REVERT: G 150 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7313 (tp) REVERT: G 268 THR cc_start: 0.7533 (OUTLIER) cc_final: 0.7165 (m) REVERT: X 99 GLN cc_start: 0.7350 (pt0) cc_final: 0.6408 (tm-30) REVERT: X 122 ARG cc_start: 0.8571 (mpp80) cc_final: 0.8020 (mtt90) REVERT: E 70 PHE cc_start: 0.7147 (t80) cc_final: 0.6906 (t80) REVERT: E 147 HIS cc_start: 0.6607 (OUTLIER) cc_final: 0.5889 (t-90) REVERT: E 161 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7516 (pp20) REVERT: E 205 LEU cc_start: 0.6539 (mt) cc_final: 0.6153 (mt) REVERT: F 95 ASN cc_start: 0.8537 (t0) cc_final: 0.8230 (t0) REVERT: F 248 MET cc_start: 0.5828 (mmt) cc_final: 0.5381 (mmt) REVERT: F 249 LEU cc_start: 0.7267 (tt) cc_final: 0.6984 (tp) REVERT: F 470 MET cc_start: 0.0018 (ttt) cc_final: -0.0257 (pmm) REVERT: C 67 ASP cc_start: 0.5398 (t0) cc_final: 0.4966 (t0) REVERT: C 351 PHE cc_start: 0.7976 (t80) cc_final: 0.7430 (t80) REVERT: C 377 ASP cc_start: 0.6246 (m-30) cc_final: 0.5909 (m-30) REVERT: Y 26 ILE cc_start: 0.8350 (mm) cc_final: 0.8084 (mm) REVERT: A 217 MET cc_start: 0.5457 (ttt) cc_final: 0.5096 (ttt) REVERT: A 385 MET cc_start: 0.6366 (ttm) cc_final: 0.6109 (ttp) REVERT: B 253 VAL cc_start: 0.8652 (m) cc_final: 0.8311 (t) REVERT: B 255 MET cc_start: 0.7149 (ppp) cc_final: 0.6297 (ptp) outliers start: 64 outliers final: 39 residues processed: 369 average time/residue: 0.4174 time to fit residues: 243.2643 Evaluate side-chains 346 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 302 time to evaluate : 3.322 ------------------------------------------------------------------------------- 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 104 HIS 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 346 ILE 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 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 348 VAL 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 117 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 293 TRP 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 A residue 224 HIS 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 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 164 VAL 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 200 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 128 optimal weight: 0.7980 chunk 288 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 237 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 338 optimal weight: 0.7980 chunk 247 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 442 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 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 GLN A 383 HIS ** B 341 GLN ** 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 = 0.4733 r_free = 0.4733 target = 0.244929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.222924 restraints weight = 38301.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.219995 restraints weight = 81089.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.218686 restraints weight = 39715.902| |-----------------------------------------------------------------------------| r_work (final): 0.4466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4471 r_free = 0.4471 target_work(ls_wunit_k1) = 0.215 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4471 r_free = 0.4471 target_work(ls_wunit_k1) = 0.215 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.2061 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= 0.115 Angle : 0.597 14.116 40614 Z= 0.295 Chirality : 0.038 0.159 4568 Planarity : 0.004 0.064 4854 Dihedral : 17.462 133.242 4882 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.91 % Favored : 95.06 % Rotamer: Outliers : 1.80 % Allowed : 16.85 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 3298 helix: 0.30 (0.13), residues: 1625 sheet: 0.48 (0.40), residues: 173 loop : -1.14 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 293 HIS 0.014 0.001 HIS G 383 PHE 0.023 0.001 PHE C 23 TYR 0.018 0.001 TYR B 337 ARG 0.012 0.000 ARG B 333 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 1177) hydrogen bonds : angle 4.15141 ( 3317) metal coordination : bond 0.00910 ( 8) metal coordination : angle 1.89131 ( 6) covalent geometry : bond 0.00256 (29656) covalent geometry : angle 0.59645 (40608) *********************** 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 363 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 311 time to evaluate : 2.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 101 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.6217 (tp) REVERT: G 268 THR cc_start: 0.7341 (OUTLIER) cc_final: 0.7050 (m) REVERT: X 99 GLN cc_start: 0.7175 (pt0) cc_final: 0.6276 (tm-30) REVERT: X 122 ARG cc_start: 0.8362 (mpp80) cc_final: 0.7598 (mtt180) REVERT: E 70 PHE cc_start: 0.6956 (t80) cc_final: 0.6752 (t80) REVERT: E 87 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7019 (mt) REVERT: E 147 HIS cc_start: 0.6500 (OUTLIER) cc_final: 0.5953 (t-90) REVERT: E 219 GLN cc_start: 0.6984 (tm-30) cc_final: 0.6394 (tt0) REVERT: F 95 ASN cc_start: 0.8430 (t0) cc_final: 0.8070 (t0) REVERT: F 248 MET cc_start: 0.5887 (mmt) cc_final: 0.5561 (mmt) REVERT: F 470 MET cc_start: 0.0369 (ttt) cc_final: -0.0004 (pmm) REVERT: C 67 ASP cc_start: 0.5448 (t0) cc_final: 0.5042 (t0) REVERT: C 377 ASP cc_start: 0.6419 (m-30) cc_final: 0.6039 (m-30) REVERT: Y 26 ILE cc_start: 0.8325 (mm) cc_final: 0.8031 (mm) REVERT: A 385 MET cc_start: 0.6547 (ttm) cc_final: 0.6260 (ttp) REVERT: B 253 VAL cc_start: 0.8599 (m) cc_final: 0.8253 (t) REVERT: B 255 MET cc_start: 0.7142 (ppp) cc_final: 0.5904 (ptp) outliers start: 52 outliers final: 30 residues processed: 354 average time/residue: 0.4100 time to fit residues: 229.7790 Evaluate side-chains 332 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 298 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 LEU 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 268 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 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 C residue 164 VAL Chi-restraints excluded: chain C residue 220 ILE 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 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 370 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 319 optimal weight: 0.9980 chunk 307 optimal weight: 2.9990 chunk 301 optimal weight: 0.0670 chunk 254 optimal weight: 8.9990 chunk 135 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 283 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 chunk 121 optimal weight: 8.9990 chunk 79 optimal weight: 20.0000 overall best weight: 1.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 314 ASN 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 ** 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 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS B 130 GLN ** 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 = 0.4699 r_free = 0.4699 target = 0.240916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.217029 restraints weight = 38119.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.210163 restraints weight = 59625.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.208160 restraints weight = 55524.241| |-----------------------------------------------------------------------------| r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4399 r_free = 0.4399 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4399 r_free = 0.4399 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29664 Z= 0.178 Angle : 0.663 14.852 40614 Z= 0.327 Chirality : 0.041 0.179 4568 Planarity : 0.005 0.066 4854 Dihedral : 17.496 134.597 4882 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.70 % Favored : 94.27 % Rotamer: Outliers : 2.49 % Allowed : 17.02 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.15), residues: 3298 helix: 0.21 (0.13), residues: 1618 sheet: 0.17 (0.38), residues: 183 loop : -1.21 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 316 HIS 0.008 0.001 HIS E 147 PHE 0.022 0.002 PHE C 23 TYR 0.018 0.001 TYR F 169 ARG 0.010 0.000 ARG G 202 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 1177) hydrogen bonds : angle 4.29791 ( 3317) metal coordination : bond 0.02296 ( 8) metal coordination : angle 2.42115 ( 6) covalent geometry : bond 0.00421 (29656) covalent geometry : angle 0.66253 (40608) *********************** 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 374 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 302 time to evaluate : 3.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 101 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6648 (tt) REVERT: G 195 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6849 (tp) REVERT: G 239 ARG cc_start: 0.7054 (mmt-90) cc_final: 0.6672 (mpt180) REVERT: G 268 THR cc_start: 0.7523 (OUTLIER) cc_final: 0.7129 (m) REVERT: X 99 GLN cc_start: 0.7298 (pt0) cc_final: 0.6274 (tm-30) REVERT: X 122 ARG cc_start: 0.8308 (mpp80) cc_final: 0.7840 (mtt90) REVERT: E 70 PHE cc_start: 0.7268 (t80) cc_final: 0.6977 (t80) REVERT: E 147 HIS cc_start: 0.6541 (OUTLIER) cc_final: 0.5893 (t-90) REVERT: E 161 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8055 (pt0) REVERT: F 95 ASN cc_start: 0.8517 (t0) cc_final: 0.8186 (t0) REVERT: F 248 MET cc_start: 0.5877 (mmt) cc_final: 0.5379 (mmt) REVERT: F 470 MET cc_start: 0.0383 (ttt) cc_final: -0.0087 (pmm) REVERT: C 67 ASP cc_start: 0.5409 (t0) cc_final: 0.4971 (t0) REVERT: C 377 ASP cc_start: 0.6541 (m-30) cc_final: 0.6205 (m-30) REVERT: Y 26 ILE cc_start: 0.8371 (mm) cc_final: 0.8087 (mm) REVERT: A 202 ARG cc_start: 0.7584 (ptt-90) cc_final: 0.5680 (ttm170) REVERT: A 203 TYR cc_start: 0.6218 (m-80) cc_final: 0.5712 (m-80) REVERT: A 217 MET cc_start: 0.5692 (ttt) cc_final: 0.5026 (ttt) REVERT: A 344 MET cc_start: 0.8058 (mmt) cc_final: 0.7653 (mmt) REVERT: A 385 MET cc_start: 0.6460 (ttm) cc_final: 0.6200 (ttp) REVERT: B 253 VAL cc_start: 0.8755 (m) cc_final: 0.8453 (t) REVERT: B 255 MET cc_start: 0.7238 (ppp) cc_final: 0.6018 (ptp) outliers start: 72 outliers final: 48 residues processed: 358 average time/residue: 0.4272 time to fit residues: 243.3284 Evaluate side-chains 348 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 295 time to evaluate : 2.875 ------------------------------------------------------------------------------- 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 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 G residue 321 LEU 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 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 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 C residue 65 ILE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 293 TRP Chi-restraints excluded: chain C residue 332 VAL 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 213 MET Chi-restraints excluded: chain A residue 224 HIS 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 164 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 309 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 330 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 226 optimal weight: 7.9990 chunk 210 optimal weight: 7.9990 chunk 323 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 414 GLN C 60 HIS C 176 HIS Y 31 GLN ** Y 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN A 383 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 = 0.4661 r_free = 0.4661 target = 0.236436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.213569 restraints weight = 38280.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.206787 restraints weight = 60422.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.203699 restraints weight = 63441.238| |-----------------------------------------------------------------------------| r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4360 r_free = 0.4360 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4360 r_free = 0.4360 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 29664 Z= 0.266 Angle : 0.781 16.033 40614 Z= 0.389 Chirality : 0.045 0.210 4568 Planarity : 0.006 0.067 4854 Dihedral : 17.674 141.133 4882 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.76 % Favored : 93.21 % Rotamer: Outliers : 2.73 % Allowed : 17.72 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3298 helix: -0.09 (0.13), residues: 1609 sheet: -0.22 (0.38), residues: 183 loop : -1.47 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 316 HIS 0.011 0.001 HIS E 147 PHE 0.033 0.002 PHE F 70 TYR 0.037 0.002 TYR B 69 ARG 0.010 0.001 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.04827 ( 1177) hydrogen bonds : angle 4.69545 ( 3317) metal coordination : bond 0.02778 ( 8) metal coordination : angle 2.67571 ( 6) covalent geometry : bond 0.00648 (29656) covalent geometry : angle 0.77997 (40608) *********************** 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 386 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 307 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 101 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6511 (tt) REVERT: G 195 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7071 (tp) REVERT: G 203 TYR cc_start: 0.8076 (m-80) cc_final: 0.7650 (m-10) REVERT: G 239 ARG cc_start: 0.7113 (mmt-90) cc_final: 0.6667 (mpt180) REVERT: X 14 TYR cc_start: 0.7939 (t80) cc_final: 0.7697 (t80) REVERT: X 35 GLU cc_start: 0.6064 (mm-30) cc_final: 0.5629 (mm-30) REVERT: X 99 GLN cc_start: 0.7209 (pt0) cc_final: 0.6238 (tm-30) REVERT: X 122 ARG cc_start: 0.8608 (mpp80) cc_final: 0.7865 (mtt90) REVERT: E 70 PHE cc_start: 0.7474 (t80) cc_final: 0.7026 (t80) REVERT: E 147 HIS cc_start: 0.6801 (OUTLIER) cc_final: 0.6162 (t-90) REVERT: E 161 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7723 (pp20) REVERT: E 219 GLN cc_start: 0.7087 (tm-30) cc_final: 0.6485 (tt0) REVERT: E 336 TRP cc_start: 0.6177 (OUTLIER) cc_final: 0.5336 (t60) REVERT: F 248 MET cc_start: 0.5868 (mmt) cc_final: 0.5284 (mmt) REVERT: F 470 MET cc_start: 0.0333 (ttt) cc_final: -0.0197 (pmm) REVERT: C 67 ASP cc_start: 0.5480 (t0) cc_final: 0.5120 (t0) REVERT: Y 26 ILE cc_start: 0.8316 (mm) cc_final: 0.8059 (mm) REVERT: A 87 ILE cc_start: 0.6807 (mt) cc_final: 0.5830 (pt) REVERT: A 217 MET cc_start: 0.5731 (ttt) cc_final: 0.5122 (ttt) REVERT: A 344 MET cc_start: 0.8229 (mmt) cc_final: 0.7717 (mmt) REVERT: A 385 MET cc_start: 0.6497 (ttm) cc_final: 0.6252 (ttp) REVERT: B 155 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.6816 (tt0) REVERT: B 253 VAL cc_start: 0.8821 (m) cc_final: 0.8576 (t) REVERT: B 255 MET cc_start: 0.7486 (ppp) cc_final: 0.6124 (ptp) REVERT: B 446 MET cc_start: 0.5077 (mtt) cc_final: 0.4427 (mtt) outliers start: 79 outliers final: 56 residues processed: 364 average time/residue: 0.4037 time to fit residues: 233.0762 Evaluate side-chains 354 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 292 time to evaluate : 3.040 ------------------------------------------------------------------------------- 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 156 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 192 ASP Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 346 ILE Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 43 VAL Chi-restraints excluded: chain X residue 105 HIS Chi-restraints excluded: chain X residue 106 LEU Chi-restraints excluded: chain E residue 4 THR 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 336 TRP 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 117 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 220 ILE 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 181 LEU Chi-restraints excluded: chain Y residue 223 GLN Chi-restraints excluded: chain Y residue 250 PHE 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 224 HIS 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 133 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain B residue 164 VAL 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 389 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 480 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 130 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 chunk 300 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 268 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 442 HIS F 102 GLN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN ** 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.242867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.221501 restraints weight = 38171.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.217902 restraints weight = 78454.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.216124 restraints weight = 39197.993| |-----------------------------------------------------------------------------| r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4444 r_free = 0.4444 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 = 0.4444 r_free = 0.4444 target_work(ls_wunit_k1) = 0.212 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 29664 Z= 0.126 Angle : 0.645 14.352 40614 Z= 0.316 Chirality : 0.040 0.228 4568 Planarity : 0.004 0.066 4854 Dihedral : 17.462 139.638 4882 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.76 % Favored : 95.18 % Rotamer: Outliers : 1.94 % Allowed : 18.75 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 3298 helix: 0.17 (0.13), residues: 1639 sheet: -0.00 (0.38), residues: 183 loop : -1.27 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 316 HIS 0.004 0.001 HIS B 442 PHE 0.017 0.001 PHE C 23 TYR 0.044 0.001 TYR B 375 ARG 0.007 0.000 ARG B 333 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 1177) hydrogen bonds : angle 4.33996 ( 3317) metal coordination : bond 0.02060 ( 8) metal coordination : angle 2.01670 ( 6) covalent geometry : bond 0.00280 (29656) covalent geometry : angle 0.64428 (40608) *********************** 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: 56 poor density : 312 time to evaluate : 3.094 Fit side-chains revert: symmetry clash REVERT: G 239 ARG cc_start: 0.7023 (mmt-90) cc_final: 0.6609 (mpt180) REVERT: X 99 GLN cc_start: 0.7154 (pt0) cc_final: 0.6299 (tm-30) REVERT: X 122 ARG cc_start: 0.8365 (mpp80) cc_final: 0.7738 (mtt90) REVERT: E 70 PHE cc_start: 0.7199 (t80) cc_final: 0.6817 (t80) REVERT: E 147 HIS cc_start: 0.6674 (OUTLIER) cc_final: 0.6256 (t-90) REVERT: E 161 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8022 (pt0) REVERT: E 219 GLN cc_start: 0.6991 (tm-30) cc_final: 0.6376 (tt0) REVERT: E 470 MET cc_start: 0.0526 (mmt) cc_final: 0.0250 (mmm) REVERT: F 248 MET cc_start: 0.5940 (mmt) cc_final: 0.5484 (mmt) REVERT: F 380 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7422 (ptpp) REVERT: F 470 MET cc_start: 0.0462 (ttt) cc_final: -0.0119 (pmm) REVERT: C 67 ASP cc_start: 0.5375 (t0) cc_final: 0.4941 (t0) REVERT: C 264 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7548 (ttm) REVERT: C 375 TYR cc_start: 0.7433 (t80) cc_final: 0.7183 (t80) REVERT: Y 26 ILE cc_start: 0.8382 (mm) cc_final: 0.8076 (mm) REVERT: A 217 MET cc_start: 0.6010 (ttt) cc_final: 0.5601 (ttt) REVERT: A 385 MET cc_start: 0.6564 (ttm) cc_final: 0.6285 (ttp) REVERT: A 440 GLN cc_start: 0.4412 (mm-40) cc_final: 0.4163 (mm-40) REVERT: B 253 VAL cc_start: 0.8677 (m) cc_final: 0.8388 (t) REVERT: B 255 MET cc_start: 0.7284 (ppp) cc_final: 0.5881 (ptp) REVERT: B 446 MET cc_start: 0.5045 (mtt) cc_final: 0.4410 (mtt) outliers start: 56 outliers final: 38 residues processed: 350 average time/residue: 0.4090 time to fit residues: 226.4312 Evaluate side-chains 339 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 297 time to evaluate : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 104 HIS Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain E residue 4 THR 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 444 TYR Chi-restraints excluded: chain F residue 46 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 380 LYS 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 223 GLN Chi-restraints excluded: chain Y residue 299 THR Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 366 ILE 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 133 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 336 TRP 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 329 optimal weight: 2.9990 chunk 318 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 273 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 185 optimal weight: 0.8980 chunk 313 optimal weight: 5.9990 chunk 2 optimal weight: 0.0470 chunk 243 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 314 ASN G 341 GLN ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 223 GLN ** 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.241315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.219750 restraints weight = 37987.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.216806 restraints weight = 78887.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.213707 restraints weight = 40253.109| |-----------------------------------------------------------------------------| r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4438 r_free = 0.4438 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4438 r_free = 0.4438 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 29664 Z= 0.191 Angle : 0.753 59.199 40614 Z= 0.396 Chirality : 0.041 0.508 4568 Planarity : 0.005 0.103 4854 Dihedral : 17.460 139.607 4882 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.88 % Favored : 95.06 % Rotamer: Outliers : 1.76 % Allowed : 19.24 % Favored : 79.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.15), residues: 3298 helix: 0.16 (0.13), residues: 1639 sheet: 0.00 (0.38), residues: 183 loop : -1.26 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 316 HIS 0.007 0.001 HIS G 383 PHE 0.017 0.001 PHE C 23 TYR 0.047 0.002 TYR C 337 ARG 0.097 0.001 ARG G 202 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 1177) hydrogen bonds : angle 4.36102 ( 3317) metal coordination : bond 0.02031 ( 8) metal coordination : angle 2.02584 ( 6) covalent geometry : bond 0.00430 (29656) covalent geometry : angle 0.75304 (40608) ********************** 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 349 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 298 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 101 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6327 (tp) REVERT: G 203 TYR cc_start: 0.7906 (m-80) cc_final: 0.7383 (m-10) REVERT: G 239 ARG cc_start: 0.7052 (mmt-90) cc_final: 0.6621 (mpt180) REVERT: X 99 GLN cc_start: 0.7126 (pt0) cc_final: 0.6270 (tm-30) REVERT: X 122 ARG cc_start: 0.8307 (mpp80) cc_final: 0.7702 (mtt90) REVERT: E 70 PHE cc_start: 0.7139 (t80) cc_final: 0.6776 (t80) REVERT: E 147 HIS cc_start: 0.6659 (OUTLIER) cc_final: 0.6261 (t-90) REVERT: E 161 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7994 (pt0) REVERT: E 219 GLN cc_start: 0.6919 (tm-30) cc_final: 0.6300 (tt0) REVERT: E 470 MET cc_start: 0.0521 (mmt) cc_final: 0.0259 (mmm) REVERT: F 248 MET cc_start: 0.6011 (mmt) cc_final: 0.5590 (mmt) REVERT: F 380 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7414 (ptpp) REVERT: F 470 MET cc_start: 0.0401 (ttt) cc_final: -0.0146 (pmm) REVERT: C 67 ASP cc_start: 0.5311 (t0) cc_final: 0.4887 (t0) REVERT: C 264 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7517 (ttm) REVERT: C 375 TYR cc_start: 0.7332 (t80) cc_final: 0.7116 (t80) REVERT: Y 26 ILE cc_start: 0.8366 (mm) cc_final: 0.8076 (mm) REVERT: A 217 MET cc_start: 0.6003 (ttt) cc_final: 0.5554 (ttt) REVERT: A 385 MET cc_start: 0.6481 (ttm) cc_final: 0.6206 (ttp) REVERT: A 440 GLN cc_start: 0.4401 (mm-40) cc_final: 0.4166 (mm-40) REVERT: B 253 VAL cc_start: 0.8621 (m) cc_final: 0.8345 (t) REVERT: B 255 MET cc_start: 0.7338 (ppp) cc_final: 0.5942 (ptp) REVERT: B 446 MET cc_start: 0.5063 (mtt) cc_final: 0.4390 (mtt) outliers start: 51 outliers final: 41 residues processed: 335 average time/residue: 0.3935 time to fit residues: 210.2528 Evaluate side-chains 341 residues out of total 2890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 295 time to evaluate : 3.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 156 VAL Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain E residue 4 THR 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 444 TYR Chi-restraints excluded: chain F residue 46 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 328 LEU Chi-restraints excluded: chain F residue 380 LYS Chi-restraints excluded: chain F residue 401 SER Chi-restraints excluded: chain F residue 415 LEU 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 291 TRP 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 366 ILE 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 133 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 336 TRP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 291 optimal weight: 40.0000 chunk 199 optimal weight: 0.9990 chunk 241 optimal weight: 9.9990 chunk 330 optimal weight: 2.9990 chunk 243 optimal weight: 7.9990 chunk 312 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 336 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 314 ASN G 341 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 ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.241263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.219655 restraints weight = 38172.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.216754 restraints weight = 77991.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.213366 restraints weight = 40040.038| |-----------------------------------------------------------------------------| r_work (final): 0.4441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4441 r_free = 0.4441 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 = 0.4441 r_free = 0.4441 target_work(ls_wunit_k1) = 0.212 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 29664 Z= 0.191 Angle : 0.753 59.199 40614 Z= 0.396 Chirality : 0.041 0.508 4568 Planarity : 0.005 0.103 4854 Dihedral : 17.460 139.607 4882 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.88 % Favored : 95.06 % Rotamer: Outliers : 1.63 % Allowed : 19.31 % Favored : 79.07 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.15), residues: 3298 helix: 0.16 (0.13), residues: 1639 sheet: 0.00 (0.38), residues: 183 loop : -1.26 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 316 HIS 0.007 0.001 HIS G 383 PHE 0.017 0.001 PHE C 23 TYR 0.047 0.002 TYR C 337 ARG 0.097 0.001 ARG G 202 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 1177) hydrogen bonds : angle 4.36102 ( 3317) metal coordination : bond 0.02031 ( 8) metal coordination : angle 2.02584 ( 6) covalent geometry : bond 0.00430 (29656) covalent geometry : angle 0.75304 (40608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8297.23 seconds wall clock time: 146 minutes 58.97 seconds (8818.97 seconds total)