Starting phenix.real_space_refine on Sun Jun 7 01:18:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9umt_64312/06_2026/9umt_64312.cif Found real_map, /net/cci-nas-00/data/ceres_data/9umt_64312/06_2026/9umt_64312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9umt_64312/06_2026/9umt_64312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9umt_64312/06_2026/9umt_64312.map" model { file = "/net/cci-nas-00/data/ceres_data/9umt_64312/06_2026/9umt_64312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9umt_64312/06_2026/9umt_64312.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 sd= 0.588 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: 8 Type Number sf(0) Gaussians Al 8 5.89 5 P 16 5.49 5 Mg 8 5.21 5 S 196 5.16 5 C 20247 2.51 5 N 5643 2.21 5 O 6269 1.98 5 F 24 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 164 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32411 Number of models: 1 Model: "" Number of chains: 24 Chain: "F" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "A" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "C" Number of atoms: 4085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4085 Classifications: {'peptide': 525} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 507} Chain: "B" Number of atoms: 3907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3907 Classifications: {'peptide': 517} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 502} Chain: "G" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4095 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 18, 'TRANS': 512} Chain: "H" Number of atoms: 4023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4023 Classifications: {'peptide': 525} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "D" Number of atoms: 4014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4014 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 15, 'TRANS': 507} Chain: "E" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4030 Classifications: {'peptide': 529} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.83, per 1000 atoms: 0.24 Number of scatterers: 32411 At special positions: 0 Unit cell: (171.39, 111.36, 176.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 196 16.00 P 16 15.00 Al 8 13.00 Mg 8 11.99 F 24 9.00 O 6269 8.00 N 5643 7.00 C 20247 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 Atom "HETATM32201 O3A ADP A 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM32233 O3A ADP C 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM32297 O3A ADP G 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM32169 O3A ADP F 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.4 seconds 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7850 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 50 sheets defined 53.1% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'F' and resid 14 through 33 removed outlier: 4.190A pdb=" N ARG F 18 " --> pdb=" O GLY F 14 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE F 31 " --> pdb=" O SER F 27 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL F 32 " --> pdb=" O ILE F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 64 Processing helix chain 'F' and resid 69 through 86 Processing helix chain 'F' and resid 89 through 109 removed outlier: 3.609A pdb=" N VAL F 93 " --> pdb=" O GLY F 89 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE F 95 " --> pdb=" O THR F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 136 removed outlier: 3.671A pdb=" N VAL F 117 " --> pdb=" O HIS F 113 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU F 134 " --> pdb=" O ARG F 130 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU F 136 " --> pdb=" O ILE F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 157 removed outlier: 4.019A pdb=" N LEU F 148 " --> pdb=" O GLY F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 179 removed outlier: 3.656A pdb=" N ASN F 170 " --> pdb=" O ASP F 166 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE F 179 " --> pdb=" O ALA F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 195 removed outlier: 3.790A pdb=" N VAL F 195 " --> pdb=" O VAL F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 280 removed outlier: 4.154A pdb=" N SER F 268 " --> pdb=" O ARG F 264 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 304 Processing helix chain 'F' and resid 312 through 323 Processing helix chain 'F' and resid 381 through 405 Processing helix chain 'F' and resid 413 through 427 removed outlier: 3.697A pdb=" N GLU F 424 " --> pdb=" O SER F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 445 removed outlier: 4.355A pdb=" N ALA F 437 " --> pdb=" O ARG F 433 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE F 438 " --> pdb=" O GLU F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 456 Processing helix chain 'F' and resid 462 through 477 removed outlier: 3.570A pdb=" N ASN F 477 " --> pdb=" O GLU F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 484 removed outlier: 3.832A pdb=" N LYS F 484 " --> pdb=" O LYS F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 502 Processing helix chain 'F' and resid 507 through 526 Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.838A pdb=" N ARG A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 43 No H-bonds generated for 'chain 'A' and resid 41 through 43' Processing helix chain 'A' and resid 66 through 72 Processing helix chain 'A' and resid 78 through 95 removed outlier: 3.854A pdb=" N LYS A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 83 " --> pdb=" O PRO A 79 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 119 removed outlier: 3.583A pdb=" N THR A 103 " --> pdb=" O THR A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 144 removed outlier: 3.633A pdb=" N ILE A 126 " --> pdb=" O HIS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 168 removed outlier: 3.797A pdb=" N PHE A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 189 removed outlier: 3.993A pdb=" N LYS A 181 " --> pdb=" O ASP A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 284 Processing helix chain 'A' and resid 297 through 307 removed outlier: 3.784A pdb=" N ALA A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.718A pdb=" N VAL A 341 " --> pdb=" O PRO A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 402 removed outlier: 3.794A pdb=" N LYS A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 Processing helix chain 'A' and resid 431 through 454 removed outlier: 4.262A pdb=" N ALA A 435 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Proline residue: A 447 - end of helix removed outlier: 3.757A pdb=" N ALA A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 469 removed outlier: 3.849A pdb=" N LEU A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 497 through 516 Processing helix chain 'C' and resid 19 through 37 removed outlier: 3.581A pdb=" N ILE C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE C 37 " --> pdb=" O ILE C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 74 through 91 removed outlier: 3.596A pdb=" N ASP C 88 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 114 removed outlier: 3.512A pdb=" N VAL C 98 " --> pdb=" O GLY C 94 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 140 removed outlier: 3.868A pdb=" N VAL C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 160 removed outlier: 3.800A pdb=" N MET C 152 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.836A pdb=" N SER C 166 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG C 167 " --> pdb=" O ALA C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 167' Processing helix chain 'C' and resid 168 through 182 removed outlier: 4.873A pdb=" N ASN C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 284 removed outlier: 4.518A pdb=" N ILE C 282 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 283 " --> pdb=" O CYS C 279 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLN C 284 " --> pdb=" O GLU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 334 through 338 removed outlier: 3.979A pdb=" N GLU C 337 " --> pdb=" O ARG C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 343 removed outlier: 3.505A pdb=" N VAL C 343 " --> pdb=" O GLU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 404 Processing helix chain 'C' and resid 413 through 426 Processing helix chain 'C' and resid 427 through 429 No H-bonds generated for 'chain 'C' and resid 427 through 429' Processing helix chain 'C' and resid 433 through 444 removed outlier: 3.762A pdb=" N ALA C 441 " --> pdb=" O TYR C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 456 Processing helix chain 'C' and resid 459 through 470 removed outlier: 3.536A pdb=" N THR C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 494 removed outlier: 4.334A pdb=" N LEU C 493 " --> pdb=" O ASP C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 517 Processing helix chain 'B' and resid 28 through 49 Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 73 through 80 Processing helix chain 'B' and resid 85 through 102 Processing helix chain 'B' and resid 107 through 125 removed outlier: 3.929A pdb=" N ILE B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 123 " --> pdb=" O SER B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 152 removed outlier: 3.711A pdb=" N ILE B 133 " --> pdb=" O HIS B 129 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 172 removed outlier: 3.732A pdb=" N LEU B 163 " --> pdb=" O ASP B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 removed outlier: 3.665A pdb=" N SER B 177 " --> pdb=" O LYS B 174 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLN B 178 " --> pdb=" O VAL B 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 174 through 178' Processing helix chain 'B' and resid 179 through 195 Proline residue: B 185 - end of helix removed outlier: 3.567A pdb=" N LYS B 193 " --> pdb=" O ASN B 189 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE B 195 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 294 removed outlier: 3.762A pdb=" N MET B 272 " --> pdb=" O ASP B 268 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU B 276 " --> pdb=" O MET B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 320 removed outlier: 3.614A pdb=" N MET B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.818A pdb=" N ILE B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.631A pdb=" N PHE B 351 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 418 Processing helix chain 'B' and resid 426 through 443 Processing helix chain 'B' and resid 446 through 458 removed outlier: 3.853A pdb=" N CYS B 450 " --> pdb=" O MET B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 469 removed outlier: 3.760A pdb=" N SER B 463 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 487 Processing helix chain 'B' and resid 512 through 530 Processing helix chain 'G' and resid 28 through 47 Processing helix chain 'G' and resid 48 through 50 No H-bonds generated for 'chain 'G' and resid 48 through 50' Processing helix chain 'G' and resid 71 through 77 Processing helix chain 'G' and resid 83 through 100 Processing helix chain 'G' and resid 105 through 124 removed outlier: 3.561A pdb=" N VAL G 109 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN G 120 " --> pdb=" O GLU G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 150 removed outlier: 3.643A pdb=" N SER G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 172 Processing helix chain 'G' and resid 181 through 195 removed outlier: 3.795A pdb=" N THR G 193 " --> pdb=" O ASN G 189 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL G 194 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 220 removed outlier: 3.881A pdb=" N THR G 220 " --> pdb=" O LEU G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 292 removed outlier: 3.607A pdb=" N TYR G 272 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE G 287 " --> pdb=" O PHE G 283 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE G 290 " --> pdb=" O MET G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 315 Processing helix chain 'G' and resid 324 through 335 Processing helix chain 'G' and resid 342 through 346 removed outlier: 3.587A pdb=" N GLU G 345 " --> pdb=" O ARG G 342 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU G 346 " --> pdb=" O PHE G 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 342 through 346' Processing helix chain 'G' and resid 389 through 413 Processing helix chain 'G' and resid 422 through 437 removed outlier: 3.810A pdb=" N LYS G 437 " --> pdb=" O GLN G 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 442 through 454 removed outlier: 3.592A pdb=" N MET G 446 " --> pdb=" O GLU G 442 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU G 454 " --> pdb=" O ALA G 450 " (cutoff:3.500A) Processing helix chain 'G' and resid 454 through 465 Processing helix chain 'G' and resid 467 through 482 removed outlier: 3.576A pdb=" N THR G 471 " --> pdb=" O ASN G 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 503 removed outlier: 3.718A pdb=" N GLN G 502 " --> pdb=" O ASP G 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 527 Processing helix chain 'H' and resid 3 through 8 Processing helix chain 'H' and resid 15 through 35 Processing helix chain 'H' and resid 59 through 66 removed outlier: 3.652A pdb=" N LEU H 63 " --> pdb=" O ASP H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 88 Processing helix chain 'H' and resid 92 through 111 removed outlier: 4.216A pdb=" N TYR H 109 " --> pdb=" O GLN H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 137 removed outlier: 4.299A pdb=" N ILE H 119 " --> pdb=" O HIS H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 158 removed outlier: 3.584A pdb=" N LEU H 148 " --> pdb=" O ASP H 144 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR H 158 " --> pdb=" O THR H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 179 removed outlier: 3.971A pdb=" N GLU H 170 " --> pdb=" O ASP H 166 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA H 171 " --> pdb=" O VAL H 167 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE H 179 " --> pdb=" O SER H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 263 Processing helix chain 'H' and resid 264 through 282 removed outlier: 3.885A pdb=" N ILE H 274 " --> pdb=" O ARG H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 307 Processing helix chain 'H' and resid 319 through 329 removed outlier: 3.904A pdb=" N THR H 325 " --> pdb=" O MET H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 344 Processing helix chain 'H' and resid 380 through 403 removed outlier: 4.047A pdb=" N ASP H 393 " --> pdb=" O ASP H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 413 through 426 Processing helix chain 'H' and resid 427 through 429 No H-bonds generated for 'chain 'H' and resid 427 through 429' Processing helix chain 'H' and resid 433 through 442 Processing helix chain 'H' and resid 445 through 456 removed outlier: 3.933A pdb=" N LYS H 449 " --> pdb=" O LEU H 445 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 474 Processing helix chain 'H' and resid 497 through 516 removed outlier: 3.878A pdb=" N THR H 509 " --> pdb=" O LEU H 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 35 removed outlier: 4.019A pdb=" N ALA D 35 " --> pdb=" O VAL D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 3.605A pdb=" N THR D 39 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU D 40 " --> pdb=" O ARG D 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 36 through 40' Processing helix chain 'D' and resid 61 through 67 Processing helix chain 'D' and resid 73 through 90 removed outlier: 3.574A pdb=" N THR D 78 " --> pdb=" O PRO D 74 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 107 Processing helix chain 'D' and resid 108 through 113 Processing helix chain 'D' and resid 117 through 140 removed outlier: 4.126A pdb=" N ILE D 121 " --> pdb=" O HIS D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 163 Processing helix chain 'D' and resid 171 through 184 Processing helix chain 'D' and resid 259 through 282 Processing helix chain 'D' and resid 296 through 306 Processing helix chain 'D' and resid 315 through 327 Processing helix chain 'D' and resid 378 through 401 removed outlier: 4.267A pdb=" N LYS D 401 " --> pdb=" O ARG D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 425 removed outlier: 3.537A pdb=" N MET D 414 " --> pdb=" O GLY D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 442 removed outlier: 4.103A pdb=" N LEU D 433 " --> pdb=" O GLY D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 452 removed outlier: 3.672A pdb=" N ARG D 447 " --> pdb=" O GLU D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 471 removed outlier: 3.539A pdb=" N ALA D 469 " --> pdb=" O ARG D 465 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN D 470 " --> pdb=" O ALA D 466 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY D 471 " --> pdb=" O ARG D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 514 Processing helix chain 'E' and resid 28 through 45 removed outlier: 4.253A pdb=" N LEU E 39 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N THR E 45 " --> pdb=" O GLN E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 76 removed outlier: 3.937A pdb=" N ILE E 72 " --> pdb=" O ASP E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 97 removed outlier: 3.643A pdb=" N MET E 85 " --> pdb=" O PRO E 81 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE E 86 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 120 removed outlier: 3.729A pdb=" N ARG E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 143 removed outlier: 3.689A pdb=" N VAL E 128 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU E 130 " --> pdb=" O SER E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 147 removed outlier: 3.721A pdb=" N VAL E 147 " --> pdb=" O PRO E 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 144 through 147' Processing helix chain 'E' and resid 157 through 172 removed outlier: 4.625A pdb=" N THR E 166 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER E 167 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS E 171 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 189 Processing helix chain 'E' and resid 211 through 215 removed outlier: 3.572A pdb=" N SER E 214 " --> pdb=" O GLY E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 267 removed outlier: 3.589A pdb=" N LEU E 265 " --> pdb=" O THR E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 285 removed outlier: 3.546A pdb=" N ILE E 283 " --> pdb=" O GLN E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 308 Processing helix chain 'E' and resid 317 through 329 Processing helix chain 'E' and resid 381 through 405 removed outlier: 3.576A pdb=" N MET E 385 " --> pdb=" O THR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 428 removed outlier: 3.509A pdb=" N ILE E 417 " --> pdb=" O GLY E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 456 removed outlier: 4.062A pdb=" N ILE E 448 " --> pdb=" O ALA E 444 " (cutoff:3.500A) Proline residue: E 449 - end of helix Processing helix chain 'E' and resid 459 through 472 removed outlier: 3.629A pdb=" N VAL E 463 " --> pdb=" O LYS E 459 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL E 470 " --> pdb=" O LYS E 466 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN E 472 " --> pdb=" O TYR E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 519 Processing sheet with id=AA1, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.546A pdb=" N ASP F 10 " --> pdb=" O LYS F 532 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS F 532 " --> pdb=" O ASP F 10 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER F 12 " --> pdb=" O LEU F 530 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU F 530 " --> pdb=" O SER F 12 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ILE F 527 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N MET B 60 " --> pdb=" O ILE F 527 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASP F 529 " --> pdb=" O MET B 60 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLN B 62 " --> pdb=" O ASP F 529 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE F 531 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 52 through 55 removed outlier: 3.859A pdb=" N THR F 55 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASP F 42 " --> pdb=" O ASP C 521 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N VAL C 523 " --> pdb=" O ASP F 42 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N MET F 44 " --> pdb=" O VAL C 523 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLY C 525 " --> pdb=" O MET F 44 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N VAL F 46 " --> pdb=" O GLY C 525 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 17 " --> pdb=" O ILE C 522 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER C 524 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS C 15 " --> pdb=" O SER C 524 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 181 through 182 removed outlier: 3.660A pdb=" N TYR F 181 " --> pdb=" O ARG F 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 197 through 201 removed outlier: 6.678A pdb=" N LEU F 198 " --> pdb=" O LEU F 377 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLY F 379 " --> pdb=" O LEU F 198 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA F 200 " --> pdb=" O GLY F 379 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU F 350 " --> pdb=" O LYS F 365 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU F 350 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL F 230 " --> pdb=" O GLU F 350 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL F 352 " --> pdb=" O ARG F 228 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG F 228 " --> pdb=" O VAL F 352 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL F 285 " --> pdb=" O ASN F 231 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LYS F 233 " --> pdb=" O VAL F 285 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU F 287 " --> pdb=" O LYS F 233 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA F 235 " --> pdb=" O LEU F 287 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE F 286 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 252 through 254 removed outlier: 6.468A pdb=" N VAL F 252 " --> pdb=" O ASP C 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 408 through 410 Processing sheet with id=AA7, first strand: chain 'F' and resid 486 through 488 Processing sheet with id=AA8, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.203A pdb=" N VAL A 517 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N MET G 58 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASN A 519 " --> pdb=" O MET G 58 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET G 59 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR G 67 " --> pdb=" O MET G 59 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 62 through 64 removed outlier: 3.549A pdb=" N THR A 64 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ASP A 49 " --> pdb=" O ASP B 534 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N VAL B 536 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 51 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR B 538 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A 53 " --> pdb=" O THR B 538 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 199 through 205 removed outlier: 3.647A pdb=" N GLY A 377 " --> pdb=" O LYS A 204 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 219 through 220 removed outlier: 4.403A pdb=" N ILE A 354 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU A 359 " --> pdb=" O VAL A 352 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 310 through 313 removed outlier: 6.349A pdb=" N PHE A 290 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 235 " --> pdb=" O CYS A 346 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS A 346 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 237 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY A 344 " --> pdb=" O ILE A 237 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 261 through 264 removed outlier: 4.048A pdb=" N ASP B 261 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 258 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 406 through 408 Processing sheet with id=AB6, first strand: chain 'A' and resid 476 through 479 removed outlier: 3.773A pdb=" N GLY A 486 " --> pdb=" O GLY A 477 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.531A pdb=" N LYS C 48 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 142 through 143 removed outlier: 3.731A pdb=" N ILE C 142 " --> pdb=" O LEU C 407 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 184 through 187 removed outlier: 3.687A pdb=" N PHE C 185 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 192 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 187 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG C 190 " --> pdb=" O GLU C 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 202 through 205 removed outlier: 3.693A pdb=" N GLU C 202 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR C 373 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 215 " --> pdb=" O THR C 373 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 218 through 220 removed outlier: 3.740A pdb=" N ILE C 363 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 220 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C 361 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU C 358 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE C 355 " --> pdb=" O GLU C 358 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 360 " --> pdb=" O LYS C 353 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 238 through 240 Processing sheet with id=AC4, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.915A pdb=" N LYS B 209 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 388 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 211 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL B 390 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 389 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU B 222 " --> pdb=" O VAL B 389 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 228 through 229 removed outlier: 3.760A pdb=" N LEU B 229 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 374 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N LYS B 372 " --> pdb=" O ASN B 366 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ASN B 366 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 374 " --> pdb=" O GLU B 364 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLU B 364 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 376 " --> pdb=" O ALA B 362 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA B 362 " --> pdb=" O ILE B 376 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLY B 378 " --> pdb=" O GLU B 360 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER B 358 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLU B 360 " --> pdb=" O LYS B 243 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B 241 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 246 through 249 removed outlier: 3.515A pdb=" N ASP B 327 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 421 through 423 Processing sheet with id=AC8, first strand: chain 'B' and resid 491 through 493 Processing sheet with id=AC9, first strand: chain 'G' and resid 23 through 27 removed outlier: 3.830A pdb=" N LYS G 533 " --> pdb=" O SER G 24 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ASP G 530 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL D 50 " --> pdb=" O ASP G 530 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ARG G 532 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER D 59 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR D 57 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 151 through 152 removed outlier: 3.556A pdb=" N GLU G 506 " --> pdb=" O VAL G 417 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 208 through 213 removed outlier: 3.828A pdb=" N ILE G 383 " --> pdb=" O LYS G 208 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU G 210 " --> pdb=" O ILE G 383 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY G 387 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE G 384 " --> pdb=" O LYS G 221 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS G 221 " --> pdb=" O PHE G 384 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 226 through 228 removed outlier: 3.673A pdb=" N ILE G 372 " --> pdb=" O VAL G 226 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL G 228 " --> pdb=" O LEU G 370 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 319 through 320 removed outlier: 3.708A pdb=" N VAL G 320 " --> pdb=" O ALA G 298 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS G 300 " --> pdb=" O VAL G 320 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LYS G 245 " --> pdb=" O LEU G 297 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE G 299 " --> pdb=" O LYS G 245 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ALA G 247 " --> pdb=" O ILE G 299 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N VAL G 340 " --> pdb=" O ILE G 246 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE G 248 " --> pdb=" O VAL G 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'G' and resid 319 through 320 removed outlier: 3.708A pdb=" N VAL G 320 " --> pdb=" O ALA G 298 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS G 300 " --> pdb=" O VAL G 320 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LYS G 245 " --> pdb=" O LEU G 297 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE G 299 " --> pdb=" O LYS G 245 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ALA G 247 " --> pdb=" O ILE G 299 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 56 through 57 removed outlier: 3.855A pdb=" N THR H 57 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS H 45 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N MET H 44 " --> pdb=" O VAL E 521 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE E 525 " --> pdb=" O MET H 46 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL H 48 " --> pdb=" O ILE E 525 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS E 20 " --> pdb=" O MET E 526 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 139 through 140 Processing sheet with id=AD8, first strand: chain 'H' and resid 192 through 195 removed outlier: 6.922A pdb=" N GLU H 192 " --> pdb=" O LEU H 374 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ILE H 376 " --> pdb=" O GLU H 192 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N MET H 194 " --> pdb=" O ILE H 376 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE H 207 " --> pdb=" O THR H 373 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 211 through 212 removed outlier: 4.148A pdb=" N THR H 361 " --> pdb=" O LEU H 212 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N PHE H 362 " --> pdb=" O VAL H 350 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL H 350 " --> pdb=" O PHE H 362 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLU H 364 " --> pdb=" O GLY H 348 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY H 348 " --> pdb=" O ASP H 227 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 230 through 232 removed outlier: 6.276A pdb=" N LEU H 231 " --> pdb=" O ILE H 292 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL H 291 " --> pdb=" O LEU H 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'H' and resid 249 through 250 removed outlier: 5.578A pdb=" N TYR H 250 " --> pdb=" O LEU E 258 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 477 through 479 Processing sheet with id=AE4, first strand: chain 'D' and resid 16 through 17 removed outlier: 3.508A pdb=" N SER D 16 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASN E 53 " --> pdb=" O VAL D 516 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU D 518 " --> pdb=" O ASN E 53 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR E 66 " --> pdb=" O LYS E 54 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AE6, first strand: chain 'D' and resid 196 through 201 removed outlier: 3.605A pdb=" N LYS D 198 " --> pdb=" O PHE D 372 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU D 374 " --> pdb=" O LYS D 198 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY D 376 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 371 " --> pdb=" O VAL D 211 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 214 through 217 removed outlier: 3.851A pdb=" N GLU D 356 " --> pdb=" O ILE D 353 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 353 " --> pdb=" O GLU D 356 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU D 349 " --> pdb=" O PHE D 360 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 309 through 311 Processing sheet with id=AE9, first strand: chain 'D' and resid 475 through 478 removed outlier: 3.942A pdb=" N ALA D 485 " --> pdb=" O GLY D 476 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP D 478 " --> pdb=" O ASP D 483 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP D 483 " --> pdb=" O ASP D 478 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 202 through 208 removed outlier: 6.545A pdb=" N ARG E 203 " --> pdb=" O ILE E 375 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU E 377 " --> pdb=" O ARG E 203 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N CYS E 205 " --> pdb=" O LEU E 377 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLY E 379 " --> pdb=" O CYS E 205 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE E 207 " --> pdb=" O GLY E 379 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 220 through 223 removed outlier: 3.686A pdb=" N MET E 221 " --> pdb=" O PHE E 363 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 239 through 242 Processing sheet with id=AF4, first strand: chain 'E' and resid 408 through 410 Processing sheet with id=AF5, first strand: chain 'E' and resid 478 through 480 1688 hydrogen bonds defined for protein. 4956 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.35 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6491 1.33 - 1.45: 6729 1.45 - 1.58: 19143 1.58 - 1.70: 89 1.70 - 1.83: 324 Bond restraints: 32776 Sorted by residual: bond pdb=" CA PHE C 185 " pdb=" CB PHE C 185 " ideal model delta sigma weight residual 1.533 1.592 -0.059 1.72e-02 3.38e+03 1.17e+01 bond pdb=" CB ASP D 307 " pdb=" CG ASP D 307 " ideal model delta sigma weight residual 1.516 1.588 -0.072 2.50e-02 1.60e+03 8.38e+00 bond pdb=" CB TRP E 319 " pdb=" CG TRP E 319 " ideal model delta sigma weight residual 1.498 1.586 -0.088 3.10e-02 1.04e+03 8.03e+00 bond pdb=" C ILE D 19 " pdb=" N PRO D 20 " ideal model delta sigma weight residual 1.336 1.370 -0.035 1.23e-02 6.61e+03 7.92e+00 bond pdb=" CA ASP A 247 " pdb=" CB ASP A 247 " ideal model delta sigma weight residual 1.532 1.574 -0.041 1.53e-02 4.27e+03 7.29e+00 ... (remaining 32771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.61: 43539 4.61 - 9.22: 609 9.22 - 13.83: 93 13.83 - 18.44: 22 18.44 - 23.05: 2 Bond angle restraints: 44265 Sorted by residual: angle pdb=" CB LYS B 384 " pdb=" CG LYS B 384 " pdb=" CD LYS B 384 " ideal model delta sigma weight residual 111.30 127.28 -15.98 2.30e+00 1.89e-01 4.82e+01 angle pdb=" CB LYS H 265 " pdb=" CG LYS H 265 " pdb=" CD LYS H 265 " ideal model delta sigma weight residual 111.30 127.22 -15.92 2.30e+00 1.89e-01 4.79e+01 angle pdb=" CA LYS B 321 " pdb=" CB LYS B 321 " pdb=" CG LYS B 321 " ideal model delta sigma weight residual 114.10 127.94 -13.84 2.00e+00 2.50e-01 4.79e+01 angle pdb=" C HIS D 282 " pdb=" N HIS D 283 " pdb=" CA HIS D 283 " ideal model delta sigma weight residual 122.46 132.20 -9.74 1.41e+00 5.03e-01 4.77e+01 angle pdb=" CA GLU F 77 " pdb=" CB GLU F 77 " pdb=" CG GLU F 77 " ideal model delta sigma weight residual 114.10 127.65 -13.55 2.00e+00 2.50e-01 4.59e+01 ... (remaining 44260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.09: 19191 32.09 - 64.17: 1036 64.17 - 96.26: 55 96.26 - 128.35: 0 128.35 - 160.43: 3 Dihedral angle restraints: 20285 sinusoidal: 8169 harmonic: 12116 Sorted by residual: dihedral pdb=" CA LYS D 247 " pdb=" C LYS D 247 " pdb=" N ALA D 248 " pdb=" CA ALA D 248 " ideal model delta harmonic sigma weight residual 180.00 128.49 51.51 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" O2A ADP E 601 " pdb=" O3A ADP E 601 " pdb=" PA ADP E 601 " pdb=" PB ADP E 601 " ideal model delta sinusoidal sigma weight residual 300.00 139.57 160.43 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" O2A ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PA ADP B 601 " pdb=" PB ADP B 601 " ideal model delta sinusoidal sigma weight residual 300.00 158.66 141.34 1 2.00e+01 2.50e-03 4.27e+01 ... (remaining 20282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.173: 5231 0.173 - 0.346: 52 0.346 - 0.518: 3 0.518 - 0.691: 0 0.691 - 0.864: 1 Chirality restraints: 5287 Sorted by residual: chirality pdb=" CG LEU B 409 " pdb=" CB LEU B 409 " pdb=" CD1 LEU B 409 " pdb=" CD2 LEU B 409 " both_signs ideal model delta sigma weight residual False -2.59 -1.73 -0.86 2.00e-01 2.50e+01 1.87e+01 chirality pdb=" CB ILE H 69 " pdb=" CA ILE H 69 " pdb=" CG1 ILE H 69 " pdb=" CG2 ILE H 69 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.48e+00 chirality pdb=" CB VAL D 72 " pdb=" CA VAL D 72 " pdb=" CG1 VAL D 72 " pdb=" CG2 VAL D 72 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 5284 not shown) Planarity restraints: 5647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 247 " -0.022 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C ASP A 247 " 0.075 2.00e-02 2.50e+03 pdb=" O ASP A 247 " -0.029 2.00e-02 2.50e+03 pdb=" N LYS A 248 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 254 " -0.019 2.00e-02 2.50e+03 3.87e-02 1.49e+01 pdb=" CD GLU H 254 " 0.067 2.00e-02 2.50e+03 pdb=" OE1 GLU H 254 " -0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU H 254 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 70 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ASP D 70 " 0.064 2.00e-02 2.50e+03 pdb=" O ASP D 70 " -0.025 2.00e-02 2.50e+03 pdb=" N VAL D 71 " -0.021 2.00e-02 2.50e+03 ... (remaining 5644 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.89: 4 1.89 - 2.64: 446 2.64 - 3.40: 40574 3.40 - 4.15: 77570 4.15 - 4.90: 139390 Nonbonded interactions: 257984 Sorted by model distance: nonbonded pdb=" O2B ADP G 601 " pdb=" F3 AF3 G 603 " model vdw 1.141 2.990 nonbonded pdb=" O2B ADP A 601 " pdb=" F3 AF3 A 603 " model vdw 1.301 2.990 nonbonded pdb=" O2B ADP A 601 " pdb="AL AF3 A 603 " model vdw 1.693 2.760 nonbonded pdb=" O2B ADP G 601 " pdb="AL AF3 G 603 " model vdw 1.694 2.760 nonbonded pdb="MG MG A 602 " pdb=" F1 AF3 A 603 " model vdw 2.092 2.120 ... (remaining 257979 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.520 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 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 : 0.010 0.607 32781 Z= 0.813 Angle : 1.319 23.049 44265 Z= 0.688 Chirality : 0.058 0.864 5287 Planarity : 0.008 0.121 5647 Dihedral : 18.120 160.434 12435 Min Nonbonded Distance : 1.141 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.98 % Favored : 95.92 % Rotamer: Outliers : 2.45 % Allowed : 30.74 % Favored : 66.81 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.74 (0.10), residues: 4192 helix: -3.14 (0.07), residues: 2087 sheet: -0.51 (0.27), residues: 385 loop : -1.83 (0.13), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG A 481 TYR 0.056 0.002 TYR H 250 PHE 0.044 0.002 PHE H 457 TRP 0.036 0.003 TRP C 435 HIS 0.019 0.001 HIS H 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.31 (32776) covalent geometry : angle 1.31947 / 0.69 (44265) hydrogen bonds : bond 0.15561 / 10.38 ( 1688) hydrogen bonds : angle 7.46578 / 5.14 ( 4956) Misc. bond : bond 0.60716 / 35.21 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 513 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 203 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7634 (mtp85) REVERT: F 214 TYR cc_start: 0.7709 (t80) cc_final: 0.7337 (t80) REVERT: F 256 ASP cc_start: 0.8039 (t0) cc_final: 0.7309 (p0) REVERT: F 299 TYR cc_start: 0.6339 (t80) cc_final: 0.6073 (t80) REVERT: F 490 LEU cc_start: 0.8791 (mm) cc_final: 0.8531 (mt) REVERT: A 348 LEU cc_start: 0.8568 (mp) cc_final: 0.8273 (mm) REVERT: A 488 MET cc_start: 0.8066 (mmm) cc_final: 0.7762 (mmm) REVERT: C 331 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8716 (mt) REVERT: C 350 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7698 (tp) REVERT: B 58 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6270 (m-30) REVERT: G 144 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7523 (mm-30) REVERT: G 302 TRP cc_start: 0.8845 (m100) cc_final: 0.8556 (m100) REVERT: G 470 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6410 (tp-100) REVERT: H 46 MET cc_start: 0.7518 (mmm) cc_final: 0.7271 (mmt) REVERT: H 67 MET cc_start: 0.6140 (tmm) cc_final: 0.5813 (tmm) REVERT: H 128 GLU cc_start: 0.7557 (mp0) cc_final: 0.7275 (mp0) REVERT: D 163 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7487 (mt) REVERT: D 194 MET cc_start: 0.6479 (tpp) cc_final: 0.6261 (tpp) REVERT: D 247 LYS cc_start: 0.7350 (mmtm) cc_final: 0.6843 (mmtt) REVERT: D 426 THR cc_start: 0.8579 (p) cc_final: 0.8285 (t) REVERT: E 27 GLU cc_start: 0.7551 (tp30) cc_final: 0.7298 (tp30) REVERT: E 62 LYS cc_start: 0.7255 (tptp) cc_final: 0.6921 (tmtt) REVERT: E 121 ILE cc_start: 0.5991 (OUTLIER) cc_final: 0.5299 (tp) REVERT: E 307 LYS cc_start: 0.7120 (pptt) cc_final: 0.6882 (tmmt) outliers start: 86 outliers final: 69 residues processed: 575 average time/residue: 0.2326 time to fit residues: 209.6259 Evaluate side-chains 577 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 500 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 383 PHE Chi-restraints excluded: chain F residue 426 TYR Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 122 HIS Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 359 TYR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 158 LYS Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 455 VAL Chi-restraints excluded: chain G residue 470 GLN Chi-restraints excluded: chain G residue 474 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 115 HIS Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 245 ASN Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 374 LEU Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 402 ILE Chi-restraints excluded: chain H residue 504 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 59 HIS Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 196 HIS Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 409 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 82 GLN F 498 ASN A 91 GLN A 178 HIS ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN B 315 HIS B 406 HIS B 484 HIS ** G 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 HIS ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 294 GLN H 346 HIS D 119 GLN D 241 ASN D 431 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.060430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.051457 restraints weight = 104818.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.053123 restraints weight = 53036.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.054228 restraints weight = 32548.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.054988 restraints weight = 22865.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.055525 restraints weight = 17668.195| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 32781 Z= 0.232 Angle : 0.770 12.547 44265 Z= 0.389 Chirality : 0.047 0.237 5287 Planarity : 0.005 0.057 5647 Dihedral : 8.474 178.072 4698 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.91 % Favored : 96.99 % Rotamer: Outliers : 4.27 % Allowed : 24.96 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.12), residues: 4192 helix: 0.22 (0.10), residues: 2150 sheet: -0.30 (0.23), residues: 519 loop : -1.46 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 314 TYR 0.024 0.002 TYR E 505 PHE 0.020 0.002 PHE D 348 TRP 0.013 0.002 TRP E 319 HIS 0.008 0.001 HIS H 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.23 (32776) covalent geometry : angle 0.76987 / 0.39 (44265) hydrogen bonds : bond 0.05291 / 3.48 ( 1688) hydrogen bonds : angle 4.25671 / 2.97 ( 4956) Misc. bond : bond 0.00559 / 0.34 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 494 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 140 THR cc_start: 0.7828 (p) cc_final: 0.7557 (t) REVERT: F 193 ASN cc_start: 0.8505 (p0) cc_final: 0.8156 (p0) REVERT: F 205 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7907 (mm-40) REVERT: F 298 LYS cc_start: 0.8012 (mppt) cc_final: 0.7391 (mppt) REVERT: F 388 MET cc_start: 0.8060 (mmt) cc_final: 0.7843 (mmm) REVERT: F 481 LYS cc_start: 0.8633 (mmmm) cc_final: 0.8364 (mmmm) REVERT: A 62 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8221 (mtm) REVERT: A 247 ASP cc_start: 0.7790 (t70) cc_final: 0.7309 (t0) REVERT: A 275 MET cc_start: 0.8667 (mmm) cc_final: 0.8402 (tpt) REVERT: A 408 TYR cc_start: 0.8938 (m-80) cc_final: 0.8665 (m-10) REVERT: A 441 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8546 (ttmm) REVERT: A 445 MET cc_start: 0.7898 (tpp) cc_final: 0.7693 (ttm) REVERT: C 18 SER cc_start: 0.8292 (OUTLIER) cc_final: 0.7288 (p) REVERT: C 294 LYS cc_start: 0.8504 (mmmm) cc_final: 0.8183 (mmmm) REVERT: C 317 LYS cc_start: 0.8573 (tptp) cc_final: 0.8347 (tptp) REVERT: C 330 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.8041 (ttp80) REVERT: C 461 ARG cc_start: 0.7858 (mtm-85) cc_final: 0.7593 (ptp90) REVERT: B 57 MET cc_start: 0.8953 (mmm) cc_final: 0.8656 (mmm) REVERT: B 60 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8275 (ttm) REVERT: B 327 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.6756 (t70) REVERT: B 372 LYS cc_start: 0.6882 (tppt) cc_final: 0.6549 (mmmt) REVERT: B 384 LYS cc_start: 0.8607 (mmmm) cc_final: 0.7890 (mmmm) REVERT: B 494 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8652 (m-40) REVERT: G 237 MET cc_start: 0.8863 (mtt) cc_final: 0.8549 (mtt) REVERT: G 277 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7918 (ttpp) REVERT: G 400 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8160 (mm) REVERT: G 458 MET cc_start: 0.8165 (mtp) cc_final: 0.7835 (mtp) REVERT: G 470 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7443 (tp-100) REVERT: G 472 MET cc_start: 0.8247 (tpp) cc_final: 0.7993 (tpp) REVERT: H 46 MET cc_start: 0.8242 (mmm) cc_final: 0.8023 (mmt) REVERT: H 225 VAL cc_start: 0.8148 (t) cc_final: 0.7859 (t) REVERT: H 404 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6631 (p0) REVERT: D 47 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8515 (mmtt) REVERT: D 194 MET cc_start: 0.6959 (tpp) cc_final: 0.6727 (tpp) REVERT: D 302 TYR cc_start: 0.8624 (t80) cc_final: 0.8374 (t80) REVERT: D 346 GLN cc_start: 0.7334 (mp10) cc_final: 0.7055 (mp10) REVERT: E 55 MET cc_start: 0.8192 (tpp) cc_final: 0.7904 (tpp) REVERT: E 57 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8297 (mp) REVERT: E 324 LEU cc_start: 0.9233 (tp) cc_final: 0.9031 (tt) outliers start: 150 outliers final: 60 residues processed: 605 average time/residue: 0.2410 time to fit residues: 224.2421 Evaluate side-chains 511 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 437 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 381 ASN Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 168 TRP Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 359 TYR Chi-restraints excluded: chain C residue 475 CYS Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 494 ASN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 277 LYS Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 346 LEU Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain G residue 400 LEU Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 466 MET Chi-restraints excluded: chain G residue 470 GLN Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain H residue 364 GLU Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 404 ASP Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 471 SER Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 233 HIS Chi-restraints excluded: chain D residue 258 HIS Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 196 HIS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 246 PHE Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 525 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 316 optimal weight: 0.6980 chunk 300 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 297 optimal weight: 0.9990 chunk 397 optimal weight: 3.9990 chunk 266 optimal weight: 0.7980 chunk 161 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 413 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 ASN B 262 ASN ** G 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN E 79 GLN E 359 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.060569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.051477 restraints weight = 102925.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.053247 restraints weight = 49548.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.054406 restraints weight = 29636.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.055187 restraints weight = 20463.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.055688 restraints weight = 15658.804| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32781 Z= 0.131 Angle : 0.632 13.664 44265 Z= 0.313 Chirality : 0.044 0.173 5287 Planarity : 0.004 0.046 5647 Dihedral : 7.403 178.520 4588 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.86 % Favored : 97.07 % Rotamer: Outliers : 3.13 % Allowed : 26.30 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.13), residues: 4192 helix: 1.35 (0.11), residues: 2142 sheet: -0.14 (0.23), residues: 493 loop : -1.26 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 16 TYR 0.022 0.001 TYR A 297 PHE 0.021 0.001 PHE C 185 TRP 0.012 0.001 TRP C 435 HIS 0.007 0.001 HIS C 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (32776) covalent geometry : angle 0.63226 / 0.31 (44265) hydrogen bonds : bond 0.03950 / 2.61 ( 1688) hydrogen bonds : angle 3.90452 / 2.72 ( 4956) Misc. bond : bond 0.00057 / 0.03 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 456 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 133 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8251 (t0) REVERT: F 140 THR cc_start: 0.7910 (p) cc_final: 0.7635 (t) REVERT: F 193 ASN cc_start: 0.8531 (p0) cc_final: 0.8230 (p0) REVERT: F 205 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7908 (mm-40) REVERT: A 247 ASP cc_start: 0.8020 (t70) cc_final: 0.7786 (t0) REVERT: A 408 TYR cc_start: 0.9001 (m-80) cc_final: 0.8757 (m-80) REVERT: C 117 MET cc_start: 0.8358 (ttm) cc_final: 0.8153 (ttt) REVERT: C 274 TYR cc_start: 0.8842 (t80) cc_final: 0.8535 (t80) REVERT: B 60 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8201 (ttm) REVERT: B 372 LYS cc_start: 0.7031 (tppt) cc_final: 0.6730 (mmmt) REVERT: B 384 LYS cc_start: 0.8638 (mmmm) cc_final: 0.8019 (mmmm) REVERT: G 183 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7768 (mtp) REVERT: G 237 MET cc_start: 0.8901 (mtt) cc_final: 0.8601 (mtt) REVERT: G 458 MET cc_start: 0.8244 (mtp) cc_final: 0.7760 (mtp) REVERT: G 470 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7550 (tp-100) REVERT: G 472 MET cc_start: 0.8287 (tpp) cc_final: 0.7927 (tpp) REVERT: H 101 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7211 (tm-30) REVERT: H 307 LYS cc_start: 0.8497 (ptpp) cc_final: 0.8135 (ptpp) REVERT: H 395 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8282 (mm) REVERT: H 487 MET cc_start: 0.8358 (ppp) cc_final: 0.7940 (ppp) REVERT: D 17 GLN cc_start: 0.8308 (tp40) cc_final: 0.7907 (tp40) REVERT: D 120 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8502 (tt) REVERT: D 346 GLN cc_start: 0.7307 (mp10) cc_final: 0.7032 (mp10) REVERT: E 55 MET cc_start: 0.8215 (tpp) cc_final: 0.7762 (tpp) REVERT: E 300 MET cc_start: 0.7292 (mmm) cc_final: 0.6767 (mmm) REVERT: E 311 MET cc_start: 0.8505 (ttm) cc_final: 0.8226 (ttm) REVERT: E 324 LEU cc_start: 0.9096 (tp) cc_final: 0.8808 (tt) REVERT: E 380 SER cc_start: 0.8394 (m) cc_final: 0.7919 (p) outliers start: 110 outliers final: 65 residues processed: 528 average time/residue: 0.2336 time to fit residues: 190.5912 Evaluate side-chains 505 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 433 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 383 PHE Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 168 TRP Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 359 TYR Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 475 CYS Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 183 MET Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 346 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 115 HIS Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain H residue 364 GLU Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 521 ILE Chi-restraints excluded: chain H residue 526 MET Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 233 HIS Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 258 HIS Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain E residue 59 HIS Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 196 HIS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 328 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 187 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 150 optimal weight: 0.0470 chunk 128 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 238 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 257 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN H 37 ASN H 71 HIS ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 GLN E 303 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.059949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.050837 restraints weight = 102619.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.052631 restraints weight = 49527.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.053799 restraints weight = 29603.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.054598 restraints weight = 20472.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.055120 restraints weight = 15580.227| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32781 Z= 0.121 Angle : 0.612 12.181 44265 Z= 0.300 Chirality : 0.043 0.196 5287 Planarity : 0.003 0.043 5647 Dihedral : 7.121 177.135 4581 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.98 % Favored : 96.95 % Rotamer: Outliers : 3.62 % Allowed : 25.87 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.13), residues: 4192 helix: 1.84 (0.11), residues: 2147 sheet: -0.17 (0.23), residues: 501 loop : -1.13 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 481 TYR 0.020 0.001 TYR D 302 PHE 0.012 0.001 PHE D 174 TRP 0.011 0.001 TRP C 435 HIS 0.007 0.001 HIS C 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (32776) covalent geometry : angle 0.61230 / 0.30 (44265) hydrogen bonds : bond 0.03653 / 2.42 ( 1688) hydrogen bonds : angle 3.71737 / 2.59 ( 4956) Misc. bond : bond 0.00033 / 0.02 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 462 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 133 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8352 (t0) REVERT: F 140 THR cc_start: 0.7847 (p) cc_final: 0.7579 (t) REVERT: F 193 ASN cc_start: 0.8490 (p0) cc_final: 0.8208 (p0) REVERT: F 489 ASP cc_start: 0.7976 (t0) cc_final: 0.7352 (p0) REVERT: F 494 LYS cc_start: 0.8706 (mmmm) cc_final: 0.8278 (mmmm) REVERT: A 247 ASP cc_start: 0.7900 (t70) cc_final: 0.7478 (t0) REVERT: C 229 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6812 (mtt) REVERT: C 274 TYR cc_start: 0.8987 (t80) cc_final: 0.8691 (t80) REVERT: C 352 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8948 (mm) REVERT: B 60 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8201 (ttm) REVERT: B 261 ASP cc_start: 0.8191 (m-30) cc_final: 0.7905 (p0) REVERT: B 384 LYS cc_start: 0.8569 (mmmm) cc_final: 0.7994 (mmmm) REVERT: G 19 ASP cc_start: 0.6964 (t0) cc_final: 0.4794 (t0) REVERT: G 183 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7720 (mtp) REVERT: G 237 MET cc_start: 0.8957 (mtt) cc_final: 0.8657 (mtt) REVERT: G 307 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7268 (mm-30) REVERT: G 458 MET cc_start: 0.8188 (mtp) cc_final: 0.7721 (mtp) REVERT: G 470 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7584 (tp-100) REVERT: H 221 MET cc_start: 0.8019 (ttp) cc_final: 0.7685 (ttp) REVERT: H 404 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7104 (p0) REVERT: H 487 MET cc_start: 0.8386 (ppp) cc_final: 0.7879 (ppp) REVERT: D 47 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8455 (mmtt) REVERT: D 120 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8490 (tt) REVERT: D 264 GLN cc_start: 0.7777 (tp40) cc_final: 0.7539 (tp40) REVERT: D 346 GLN cc_start: 0.7314 (mp10) cc_final: 0.6989 (mp10) REVERT: E 38 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.7036 (pp20) REVERT: E 300 MET cc_start: 0.7492 (mmm) cc_final: 0.6718 (mmm) REVERT: E 304 TYR cc_start: 0.8313 (m-80) cc_final: 0.7983 (m-80) REVERT: E 311 MET cc_start: 0.8530 (ttm) cc_final: 0.8297 (ttm) REVERT: E 324 LEU cc_start: 0.9077 (tp) cc_final: 0.8755 (tt) outliers start: 127 outliers final: 76 residues processed: 546 average time/residue: 0.2337 time to fit residues: 198.7228 Evaluate side-chains 522 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 436 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 383 PHE Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 168 TRP Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 475 CYS Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 183 MET Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain G residue 346 LEU Chi-restraints excluded: chain G residue 389 ASN Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 115 HIS Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain H residue 364 GLU Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain H residue 404 ASP Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 526 MET Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 233 HIS Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 258 HIS Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 59 HIS Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 525 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 124 optimal weight: 2.9990 chunk 267 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 chunk 329 optimal weight: 0.9990 chunk 414 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 chunk 346 optimal weight: 2.9990 chunk 383 optimal weight: 2.9990 chunk 412 optimal weight: 0.0570 chunk 198 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN B 301 GLN B 394 ASN ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 HIS E 145 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.057382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.048389 restraints weight = 103048.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.050151 restraints weight = 49412.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.051320 restraints weight = 29440.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.052106 restraints weight = 20249.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.052586 restraints weight = 15377.876| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32781 Z= 0.152 Angle : 0.638 12.344 44265 Z= 0.315 Chirality : 0.044 0.169 5287 Planarity : 0.003 0.058 5647 Dihedral : 7.056 176.593 4577 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.44 % Favored : 96.49 % Rotamer: Outliers : 3.59 % Allowed : 25.67 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.13), residues: 4192 helix: 2.03 (0.11), residues: 2150 sheet: -0.08 (0.23), residues: 514 loop : -1.02 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 481 TYR 0.021 0.001 TYR A 297 PHE 0.024 0.001 PHE C 185 TRP 0.011 0.001 TRP C 435 HIS 0.007 0.001 HIS H 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (32776) covalent geometry : angle 0.63839 / 0.32 (44265) hydrogen bonds : bond 0.04030 / 2.66 ( 1688) hydrogen bonds : angle 3.72289 / 2.61 ( 4956) Misc. bond : bond 0.00060 / 0.03 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 469 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 133 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8511 (t0) REVERT: F 140 THR cc_start: 0.7870 (p) cc_final: 0.7649 (t) REVERT: F 193 ASN cc_start: 0.8437 (p0) cc_final: 0.8191 (p0) REVERT: F 203 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7996 (mtp85) REVERT: F 296 CYS cc_start: 0.7800 (m) cc_final: 0.7539 (m) REVERT: F 489 ASP cc_start: 0.7966 (t0) cc_final: 0.7315 (p0) REVERT: F 494 LYS cc_start: 0.8698 (mmmm) cc_final: 0.8244 (mtpp) REVERT: A 247 ASP cc_start: 0.7881 (t70) cc_final: 0.7363 (t0) REVERT: A 310 MET cc_start: 0.8709 (tpp) cc_final: 0.8311 (ttp) REVERT: A 488 MET cc_start: 0.8360 (mmm) cc_final: 0.8132 (mmm) REVERT: A 509 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: C 274 TYR cc_start: 0.9090 (t80) cc_final: 0.8788 (t80) REVERT: C 305 MET cc_start: 0.7617 (tpp) cc_final: 0.7131 (tmm) REVERT: B 60 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8270 (ttm) REVERT: B 384 LYS cc_start: 0.8587 (mmmm) cc_final: 0.7982 (mmmm) REVERT: B 402 GLU cc_start: 0.7766 (tp30) cc_final: 0.7552 (tp30) REVERT: B 506 GLU cc_start: 0.8042 (tp30) cc_final: 0.7760 (tp30) REVERT: G 87 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8103 (mttp) REVERT: G 91 GLU cc_start: 0.7648 (tt0) cc_final: 0.7386 (tt0) REVERT: G 183 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7795 (mtp) REVERT: G 237 MET cc_start: 0.8989 (mtt) cc_final: 0.8717 (mtt) REVERT: G 307 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7264 (mm-30) REVERT: G 458 MET cc_start: 0.8223 (mtp) cc_final: 0.7772 (mtp) REVERT: G 470 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7674 (tp-100) REVERT: G 472 MET cc_start: 0.8353 (tpp) cc_final: 0.8046 (tpp) REVERT: H 199 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7529 (pttp) REVERT: H 221 MET cc_start: 0.8108 (ttp) cc_final: 0.7776 (ttp) REVERT: H 392 ARG cc_start: 0.7939 (mmp80) cc_final: 0.7612 (mmp80) REVERT: H 404 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7311 (p0) REVERT: H 487 MET cc_start: 0.8431 (ppp) cc_final: 0.7872 (ppp) REVERT: D 67 LYS cc_start: 0.8930 (mttt) cc_final: 0.8628 (mttp) REVERT: D 120 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8516 (tt) REVERT: D 301 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7783 (mm-40) REVERT: D 302 TYR cc_start: 0.8496 (t80) cc_final: 0.8273 (t80) REVERT: D 346 GLN cc_start: 0.7384 (mp10) cc_final: 0.7021 (mp10) REVERT: D 382 MET cc_start: 0.7905 (mtm) cc_final: 0.7526 (mtm) REVERT: E 311 MET cc_start: 0.8594 (ttm) cc_final: 0.8369 (ttm) outliers start: 126 outliers final: 75 residues processed: 551 average time/residue: 0.2356 time to fit residues: 200.2746 Evaluate side-chains 548 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 462 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 490 LEU Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 168 TRP Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 475 CYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 494 ASN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 183 MET Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain G residue 401 HIS Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain H residue 362 PHE Chi-restraints excluded: chain H residue 403 ASP Chi-restraints excluded: chain H residue 404 ASP Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 521 ILE Chi-restraints excluded: chain H residue 526 MET Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 233 HIS Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 258 HIS Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 59 HIS Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 482 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 252 optimal weight: 5.9990 chunk 278 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 205 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 chunk 376 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 236 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.055890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.047102 restraints weight = 102884.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.048813 restraints weight = 49055.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.049932 restraints weight = 29116.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.050693 restraints weight = 19992.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.051232 restraints weight = 15211.283| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32781 Z= 0.161 Angle : 0.658 12.171 44265 Z= 0.326 Chirality : 0.045 0.211 5287 Planarity : 0.003 0.066 5647 Dihedral : 6.993 175.602 4570 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.72 % Favored : 96.21 % Rotamer: Outliers : 3.82 % Allowed : 25.58 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.13), residues: 4192 helix: 2.04 (0.11), residues: 2173 sheet: -0.03 (0.23), residues: 525 loop : -0.97 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 167 TYR 0.018 0.001 TYR C 247 PHE 0.019 0.001 PHE D 174 TRP 0.011 0.001 TRP C 435 HIS 0.009 0.001 HIS H 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (32776) covalent geometry : angle 0.65794 / 0.33 (44265) hydrogen bonds : bond 0.04137 / 2.73 ( 1688) hydrogen bonds : angle 3.73473 / 2.62 ( 4956) Misc. bond : bond 0.00059 / 0.03 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 470 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 140 THR cc_start: 0.7891 (p) cc_final: 0.7684 (t) REVERT: F 193 ASN cc_start: 0.8348 (p0) cc_final: 0.8136 (p0) REVERT: F 203 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8009 (mtp85) REVERT: F 205 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7667 (mm-40) REVERT: F 296 CYS cc_start: 0.7979 (m) cc_final: 0.7700 (m) REVERT: F 384 MET cc_start: 0.7996 (ttt) cc_final: 0.7414 (ttt) REVERT: A 208 SER cc_start: 0.9034 (p) cc_final: 0.8815 (t) REVERT: A 247 ASP cc_start: 0.7914 (t70) cc_final: 0.7342 (t0) REVERT: A 310 MET cc_start: 0.8695 (tpp) cc_final: 0.8410 (ttp) REVERT: A 509 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: C 274 TYR cc_start: 0.9092 (t80) cc_final: 0.8851 (t80) REVERT: C 305 MET cc_start: 0.7595 (tpp) cc_final: 0.7341 (tmm) REVERT: C 359 TYR cc_start: 0.8168 (m-80) cc_final: 0.7961 (m-10) REVERT: C 511 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7152 (mm-30) REVERT: B 60 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8331 (ttm) REVERT: B 303 SER cc_start: 0.8565 (t) cc_final: 0.8352 (t) REVERT: B 327 ASP cc_start: 0.7132 (t0) cc_final: 0.6660 (t0) REVERT: B 372 LYS cc_start: 0.6996 (tppt) cc_final: 0.6716 (mmmt) REVERT: B 402 GLU cc_start: 0.7767 (tp30) cc_final: 0.7560 (tp30) REVERT: G 87 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8087 (mttp) REVERT: G 91 GLU cc_start: 0.7655 (tt0) cc_final: 0.7393 (tt0) REVERT: G 183 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7827 (mtp) REVERT: G 237 MET cc_start: 0.9009 (mtt) cc_final: 0.8764 (mtt) REVERT: G 307 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7317 (mm-30) REVERT: G 418 TYR cc_start: 0.8455 (m-80) cc_final: 0.8247 (m-80) REVERT: G 458 MET cc_start: 0.8171 (mtp) cc_final: 0.7739 (mtp) REVERT: G 470 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7742 (tp-100) REVERT: G 481 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8508 (ttpp) REVERT: H 199 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7603 (pttp) REVERT: H 241 LYS cc_start: 0.8508 (tppt) cc_final: 0.8290 (tppt) REVERT: H 392 ARG cc_start: 0.7811 (mmp80) cc_final: 0.7445 (mmp80) REVERT: H 404 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7436 (p0) REVERT: H 487 MET cc_start: 0.8463 (ppp) cc_final: 0.7923 (ppp) REVERT: H 522 MET cc_start: 0.8496 (mtt) cc_final: 0.8295 (mtm) REVERT: D 67 LYS cc_start: 0.8959 (mttt) cc_final: 0.8678 (mttp) REVERT: D 120 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8554 (tt) REVERT: D 185 MET cc_start: 0.6683 (ptt) cc_final: 0.6332 (ptt) REVERT: D 220 PHE cc_start: 0.7911 (t80) cc_final: 0.7686 (t80) REVERT: D 308 MET cc_start: 0.7825 (mtm) cc_final: 0.7617 (ptp) REVERT: D 346 GLN cc_start: 0.7509 (mp10) cc_final: 0.7098 (mp10) REVERT: D 382 MET cc_start: 0.7920 (mtm) cc_final: 0.7589 (mtm) REVERT: E 225 LYS cc_start: 0.8122 (ptpp) cc_final: 0.7879 (ptmm) REVERT: E 311 MET cc_start: 0.8604 (ttm) cc_final: 0.8397 (ttm) REVERT: E 335 ARG cc_start: 0.8154 (mmm-85) cc_final: 0.7897 (mmm-85) REVERT: E 359 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.7209 (tm-30) outliers start: 134 outliers final: 82 residues processed: 559 average time/residue: 0.2343 time to fit residues: 201.8509 Evaluate side-chains 542 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 448 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 490 LEU Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 168 TRP Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 475 CYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 494 ASN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 183 MET Chi-restraints excluded: chain G residue 204 PHE Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain G residue 389 ASN Chi-restraints excluded: chain G residue 401 HIS Chi-restraints excluded: chain G residue 481 LYS Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 233 CYS Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 362 PHE Chi-restraints excluded: chain H residue 364 GLU Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain H residue 403 ASP Chi-restraints excluded: chain H residue 404 ASP Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 521 ILE Chi-restraints excluded: chain H residue 526 MET Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 233 HIS Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 258 HIS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 246 PHE Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 359 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 58 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 403 optimal weight: 2.9990 chunk 365 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 402 optimal weight: 7.9990 chunk 335 optimal weight: 2.9990 chunk 300 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 435 GLN G 493 HIS ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 218 HIS H 294 GLN ** H 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.052703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.044168 restraints weight = 105713.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.045784 restraints weight = 52398.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.046833 restraints weight = 31786.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.047562 restraints weight = 22192.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.048033 restraints weight = 17064.391| |-----------------------------------------------------------------------------| r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 32781 Z= 0.204 Angle : 0.723 12.469 44265 Z= 0.359 Chirality : 0.046 0.197 5287 Planarity : 0.004 0.046 5647 Dihedral : 7.171 176.484 4568 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.82 % Favored : 96.09 % Rotamer: Outliers : 3.59 % Allowed : 26.24 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.13), residues: 4192 helix: 1.96 (0.11), residues: 2169 sheet: -0.11 (0.23), residues: 518 loop : -0.96 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 167 TYR 0.022 0.002 TYR D 302 PHE 0.025 0.002 PHE C 185 TRP 0.014 0.001 TRP C 435 HIS 0.006 0.001 HIS G 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (32776) covalent geometry : angle 0.72257 / 0.36 (44265) hydrogen bonds : bond 0.04806 / 3.16 ( 1688) hydrogen bonds : angle 3.90031 / 2.74 ( 4956) Misc. bond : bond 0.00080 / 0.05 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 468 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 203 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8006 (mtp85) REVERT: F 205 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8367 (mm-40) REVERT: A 247 ASP cc_start: 0.7958 (t70) cc_final: 0.7459 (t0) REVERT: A 488 MET cc_start: 0.8303 (mmm) cc_final: 0.8058 (mmp) REVERT: A 509 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: C 15 LYS cc_start: 0.8822 (ptmm) cc_final: 0.8504 (ptmm) REVERT: C 16 ARG cc_start: 0.8383 (ttt-90) cc_final: 0.8115 (ttt-90) REVERT: C 17 GLU cc_start: 0.7294 (mp0) cc_final: 0.6967 (mp0) REVERT: C 117 MET cc_start: 0.8597 (tpp) cc_final: 0.8082 (ttt) REVERT: C 511 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7097 (mm-30) REVERT: B 25 GLN cc_start: 0.7476 (tp40) cc_final: 0.7073 (tm-30) REVERT: B 303 SER cc_start: 0.8480 (t) cc_final: 0.8271 (t) REVERT: B 384 LYS cc_start: 0.8863 (mmmt) cc_final: 0.8378 (mmmm) REVERT: B 497 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8369 (ttmm) REVERT: G 91 GLU cc_start: 0.7692 (tt0) cc_final: 0.7396 (tt0) REVERT: G 183 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7970 (mtp) REVERT: G 307 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7413 (mm-30) REVERT: G 458 MET cc_start: 0.8193 (mtp) cc_final: 0.7880 (mtp) REVERT: G 470 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7608 (tm-30) REVERT: G 481 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8523 (ttpp) REVERT: H 128 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7292 (tp30) REVERT: H 132 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7590 (mp10) REVERT: H 487 MET cc_start: 0.8446 (ppp) cc_final: 0.7940 (ppp) REVERT: D 67 LYS cc_start: 0.8957 (mttt) cc_final: 0.8739 (mttp) REVERT: D 120 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8640 (tt) REVERT: D 185 MET cc_start: 0.6839 (ptt) cc_final: 0.6515 (ptt) REVERT: D 302 TYR cc_start: 0.8393 (t80) cc_final: 0.8123 (t80) REVERT: D 346 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7214 (mp10) REVERT: E 61 GLU cc_start: 0.7560 (mp0) cc_final: 0.7239 (mp0) REVERT: E 225 LYS cc_start: 0.8270 (ptpp) cc_final: 0.7746 (ptpp) REVERT: E 359 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6953 (tm-30) outliers start: 126 outliers final: 79 residues processed: 554 average time/residue: 0.2435 time to fit residues: 205.7189 Evaluate side-chains 541 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 452 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain C residue 54 MET Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 494 ASN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 183 MET Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain G residue 481 LYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 233 CYS Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 362 PHE Chi-restraints excluded: chain H residue 403 ASP Chi-restraints excluded: chain H residue 521 ILE Chi-restraints excluded: chain H residue 526 MET Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 233 HIS Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 258 HIS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 359 GLN Chi-restraints excluded: chain E residue 482 ILE Chi-restraints excluded: chain E residue 525 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 60 optimal weight: 0.0970 chunk 218 optimal weight: 3.9990 chunk 208 optimal weight: 0.4980 chunk 409 optimal weight: 0.5980 chunk 280 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 172 optimal weight: 0.0670 chunk 206 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 173 optimal weight: 0.5980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 435 GLN ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.055702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.047003 restraints weight = 102975.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.048730 restraints weight = 48633.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.049848 restraints weight = 28660.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.050615 restraints weight = 19644.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.051113 restraints weight = 14908.931| |-----------------------------------------------------------------------------| r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32781 Z= 0.125 Angle : 0.673 12.339 44265 Z= 0.330 Chirality : 0.043 0.265 5287 Planarity : 0.003 0.082 5647 Dihedral : 6.940 171.581 4568 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.41 % Favored : 96.47 % Rotamer: Outliers : 2.51 % Allowed : 27.61 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.13), residues: 4192 helix: 2.15 (0.11), residues: 2161 sheet: -0.08 (0.23), residues: 501 loop : -0.92 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 316 TYR 0.026 0.001 TYR B 24 PHE 0.020 0.001 PHE D 348 TRP 0.013 0.001 TRP C 435 HIS 0.005 0.001 HIS H 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (32776) covalent geometry : angle 0.67268 / 0.33 (44265) hydrogen bonds : bond 0.03679 / 2.44 ( 1688) hydrogen bonds : angle 3.69521 / 2.59 ( 4956) Misc. bond : bond 0.00024 / 0.02 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 468 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 203 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7946 (mtp85) REVERT: A 247 ASP cc_start: 0.7941 (t70) cc_final: 0.7400 (t0) REVERT: A 475 THR cc_start: 0.8983 (p) cc_final: 0.8773 (p) REVERT: A 488 MET cc_start: 0.8183 (mmm) cc_final: 0.7912 (mmp) REVERT: A 509 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: C 15 LYS cc_start: 0.8804 (ptmm) cc_final: 0.8427 (ptmm) REVERT: C 16 ARG cc_start: 0.8344 (ttt-90) cc_final: 0.8053 (ttt-90) REVERT: C 17 GLU cc_start: 0.7298 (mp0) cc_final: 0.6955 (mp0) REVERT: C 117 MET cc_start: 0.8487 (tpp) cc_final: 0.8068 (ttt) REVERT: C 437 TYR cc_start: 0.8306 (t80) cc_final: 0.7957 (t80) REVERT: B 25 GLN cc_start: 0.7325 (tp40) cc_final: 0.6729 (tm-30) REVERT: B 384 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8167 (mmmm) REVERT: G 183 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7871 (mtp) REVERT: G 307 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7382 (mm-30) REVERT: G 458 MET cc_start: 0.8166 (mtp) cc_final: 0.7845 (mtm) REVERT: G 470 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7920 (tp40) REVERT: H 326 LEU cc_start: 0.8739 (mm) cc_final: 0.8430 (mm) REVERT: H 487 MET cc_start: 0.8340 (ppp) cc_final: 0.8043 (ppp) REVERT: H 523 ARG cc_start: 0.7260 (tpt170) cc_final: 0.7025 (tpt170) REVERT: D 67 LYS cc_start: 0.8957 (mttt) cc_final: 0.8740 (mttp) REVERT: D 120 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8546 (tt) REVERT: D 346 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7179 (mp10) REVERT: E 225 LYS cc_start: 0.8182 (ptpp) cc_final: 0.7836 (ptpp) outliers start: 88 outliers final: 62 residues processed: 527 average time/residue: 0.2546 time to fit residues: 204.4527 Evaluate side-chains 508 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 440 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 183 MET Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 115 HIS Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 233 CYS Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 362 PHE Chi-restraints excluded: chain H residue 403 ASP Chi-restraints excluded: chain H residue 526 MET Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 233 HIS Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 258 HIS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 482 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 362 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 334 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 294 optimal weight: 0.6980 chunk 312 optimal weight: 2.9990 chunk 409 optimal weight: 0.7980 chunk 177 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 GLN ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.054942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.046298 restraints weight = 102389.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.048007 restraints weight = 48630.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.049126 restraints weight = 28869.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.049890 restraints weight = 19839.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.050369 restraints weight = 15023.828| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32781 Z= 0.142 Angle : 0.691 12.297 44265 Z= 0.339 Chirality : 0.044 0.239 5287 Planarity : 0.004 0.064 5647 Dihedral : 6.896 168.453 4567 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.70 % Favored : 96.18 % Rotamer: Outliers : 2.42 % Allowed : 27.49 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.13), residues: 4192 helix: 2.18 (0.11), residues: 2172 sheet: -0.09 (0.23), residues: 503 loop : -0.89 (0.16), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 316 TYR 0.024 0.001 TYR B 24 PHE 0.028 0.001 PHE C 185 TRP 0.015 0.001 TRP C 435 HIS 0.008 0.001 HIS A 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (32776) covalent geometry : angle 0.69147 / 0.34 (44265) hydrogen bonds : bond 0.03898 / 2.58 ( 1688) hydrogen bonds : angle 3.68513 / 2.58 ( 4956) Misc. bond : bond 0.00043 / 0.02 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 447 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 203 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7915 (mtp85) REVERT: A 247 ASP cc_start: 0.8017 (t70) cc_final: 0.7458 (t0) REVERT: A 475 THR cc_start: 0.9032 (p) cc_final: 0.8804 (p) REVERT: A 488 MET cc_start: 0.8222 (mmm) cc_final: 0.7951 (mmp) REVERT: A 509 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: C 15 LYS cc_start: 0.8823 (ptmm) cc_final: 0.8438 (ptmm) REVERT: C 17 GLU cc_start: 0.7297 (mp0) cc_final: 0.6946 (mp0) REVERT: C 437 TYR cc_start: 0.8315 (t80) cc_final: 0.7971 (t80) REVERT: B 25 GLN cc_start: 0.7397 (tp40) cc_final: 0.6908 (tm-30) REVERT: B 372 LYS cc_start: 0.6785 (tppt) cc_final: 0.6482 (mmmt) REVERT: B 384 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8142 (mmmm) REVERT: G 183 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7941 (mtp) REVERT: G 307 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7383 (mm-30) REVERT: G 366 LYS cc_start: 0.8283 (mmmt) cc_final: 0.7914 (tppt) REVERT: G 458 MET cc_start: 0.8188 (mtp) cc_final: 0.7865 (mtm) REVERT: G 470 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7941 (tp40) REVERT: H 326 LEU cc_start: 0.8740 (mm) cc_final: 0.8439 (mm) REVERT: H 487 MET cc_start: 0.8359 (ppp) cc_final: 0.8030 (ppp) REVERT: H 523 ARG cc_start: 0.7334 (tpt170) cc_final: 0.7060 (tpt170) REVERT: D 67 LYS cc_start: 0.8972 (mttt) cc_final: 0.8720 (mttp) REVERT: D 120 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8555 (tt) REVERT: D 346 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7224 (mp10) REVERT: E 203 ARG cc_start: 0.8680 (mmm160) cc_final: 0.8315 (mmm-85) outliers start: 85 outliers final: 65 residues processed: 503 average time/residue: 0.2446 time to fit residues: 188.3069 Evaluate side-chains 513 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 442 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 183 MET Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 115 HIS Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 233 CYS Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 362 PHE Chi-restraints excluded: chain H residue 403 ASP Chi-restraints excluded: chain H residue 526 MET Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 193 LYS Chi-restraints excluded: chain D residue 233 HIS Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 258 HIS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 482 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 226 optimal weight: 2.9990 chunk 291 optimal weight: 5.9990 chunk 153 optimal weight: 0.5980 chunk 262 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 305 optimal weight: 0.3980 chunk 323 optimal weight: 1.9990 chunk 365 optimal weight: 0.0170 chunk 388 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.055665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.046970 restraints weight = 103334.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.048708 restraints weight = 48877.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.049846 restraints weight = 28854.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.050619 restraints weight = 19715.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.051129 restraints weight = 14960.027| |-----------------------------------------------------------------------------| r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32781 Z= 0.129 Angle : 0.695 12.267 44265 Z= 0.340 Chirality : 0.043 0.236 5287 Planarity : 0.004 0.061 5647 Dihedral : 6.814 164.227 4567 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.51 % Favored : 96.37 % Rotamer: Outliers : 2.28 % Allowed : 27.55 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.13), residues: 4192 helix: 2.22 (0.11), residues: 2169 sheet: -0.12 (0.24), residues: 499 loop : -0.87 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 199 TYR 0.023 0.001 TYR D 302 PHE 0.016 0.001 PHE D 348 TRP 0.018 0.001 TRP C 435 HIS 0.006 0.001 HIS A 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (32776) covalent geometry : angle 0.69458 / 0.34 (44265) hydrogen bonds : bond 0.03621 / 2.40 ( 1688) hydrogen bonds : angle 3.63557 / 2.55 ( 4956) Misc. bond : bond 0.00030 / 0.02 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 457 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 203 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7847 (mtp85) REVERT: A 247 ASP cc_start: 0.8023 (t70) cc_final: 0.7465 (t0) REVERT: A 475 THR cc_start: 0.9012 (p) cc_final: 0.8789 (p) REVERT: A 488 MET cc_start: 0.8172 (mmm) cc_final: 0.7900 (mmp) REVERT: A 509 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: C 15 LYS cc_start: 0.8819 (ptmm) cc_final: 0.8486 (ptmm) REVERT: C 17 GLU cc_start: 0.7277 (mp0) cc_final: 0.6888 (mp0) REVERT: C 437 TYR cc_start: 0.8267 (t80) cc_final: 0.7990 (t80) REVERT: B 25 GLN cc_start: 0.7365 (tp40) cc_final: 0.6907 (tm-30) REVERT: B 372 LYS cc_start: 0.6760 (tppt) cc_final: 0.6463 (mmmt) REVERT: B 384 LYS cc_start: 0.8725 (mmmt) cc_final: 0.8098 (mmmm) REVERT: G 183 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7921 (mtp) REVERT: G 307 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7372 (mm-30) REVERT: G 366 LYS cc_start: 0.8080 (mmmt) cc_final: 0.7783 (tppt) REVERT: G 458 MET cc_start: 0.8163 (mtp) cc_final: 0.7846 (mtm) REVERT: G 470 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7941 (tp40) REVERT: H 326 LEU cc_start: 0.8745 (mm) cc_final: 0.8412 (mm) REVERT: H 487 MET cc_start: 0.8312 (ppp) cc_final: 0.8063 (ppp) REVERT: H 523 ARG cc_start: 0.7349 (tpt170) cc_final: 0.7071 (tpt170) REVERT: D 67 LYS cc_start: 0.8960 (mttt) cc_final: 0.8732 (mttp) REVERT: D 120 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8549 (tt) REVERT: D 264 GLN cc_start: 0.7892 (tp40) cc_final: 0.7636 (tp40) REVERT: D 302 TYR cc_start: 0.8163 (t80) cc_final: 0.7681 (t80) REVERT: D 346 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7182 (mp10) REVERT: E 203 ARG cc_start: 0.8651 (mmm160) cc_final: 0.8320 (mmm-85) outliers start: 80 outliers final: 66 residues processed: 502 average time/residue: 0.2442 time to fit residues: 187.9633 Evaluate side-chains 508 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 436 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 453 GLN Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 183 MET Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 115 HIS Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 233 CYS Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 362 PHE Chi-restraints excluded: chain H residue 403 ASP Chi-restraints excluded: chain H residue 526 MET Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 193 LYS Chi-restraints excluded: chain D residue 233 HIS Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 258 HIS Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 482 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 127 optimal weight: 0.8980 chunk 222 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 344 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 125 optimal weight: 0.5980 chunk 209 optimal weight: 0.8980 chunk 306 optimal weight: 4.9990 chunk 330 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 GLN B 394 ASN B 502 ASN ** G 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.055442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.046773 restraints weight = 103554.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.048508 restraints weight = 49067.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.049656 restraints weight = 29084.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.050416 restraints weight = 19867.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.050923 restraints weight = 15068.807| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32781 Z= 0.136 Angle : 0.702 12.294 44265 Z= 0.344 Chirality : 0.043 0.207 5287 Planarity : 0.004 0.057 5647 Dihedral : 6.777 163.423 4567 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.70 % Favored : 96.21 % Rotamer: Outliers : 2.42 % Allowed : 27.49 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.13), residues: 4192 helix: 2.22 (0.11), residues: 2174 sheet: -0.12 (0.23), residues: 511 loop : -0.85 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 199 TYR 0.022 0.001 TYR D 302 PHE 0.029 0.001 PHE C 185 TRP 0.019 0.001 TRP C 435 HIS 0.006 0.001 HIS A 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (32776) covalent geometry : angle 0.70184 / 0.34 (44265) hydrogen bonds : bond 0.03692 / 2.44 ( 1688) hydrogen bonds : angle 3.61038 / 2.53 ( 4956) Misc. bond : bond 0.00036 / 0.02 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6289.45 seconds wall clock time: 109 minutes 50.98 seconds (6590.98 seconds total)