Starting phenix.real_space_refine on Wed Mar 4 11:39:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k79_22697/03_2026/7k79_22697.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k79_22697/03_2026/7k79_22697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k79_22697/03_2026/7k79_22697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k79_22697/03_2026/7k79_22697.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k79_22697/03_2026/7k79_22697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k79_22697/03_2026/7k79_22697.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 8616 2.51 5 N 2175 2.21 5 O 2423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13272 Number of models: 1 Model: "" Number of chains: 4 Chain: "K" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3413 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 397} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "L" Number of atoms: 4355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4355 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 507} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "O" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4284 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 499} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1220 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 3.30, per 1000 atoms: 0.25 Number of scatterers: 13272 At special positions: 0 Unit cell: (113.42, 125.08, 98.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 2423 8.00 N 2175 7.00 C 8616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS L 99 " - pdb=" SG CYS L 215 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 579.6 milliseconds 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3118 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 5 sheets defined 57.6% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'K' and resid 13 through 24 removed outlier: 3.857A pdb=" N TYR K 21 " --> pdb=" O ARG K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 66 Processing helix chain 'K' and resid 69 through 74 Processing helix chain 'K' and resid 85 through 91 removed outlier: 4.212A pdb=" N GLU K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA K 91 " --> pdb=" O TRP K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 107 Processing helix chain 'K' and resid 143 through 151 removed outlier: 3.632A pdb=" N LYS K 149 " --> pdb=" O LYS K 145 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TRP K 150 " --> pdb=" O GLU K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 185 removed outlier: 3.953A pdb=" N SER K 185 " --> pdb=" O ASP K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 196 Processing helix chain 'K' and resid 257 through 266 removed outlier: 4.281A pdb=" N ILE K 261 " --> pdb=" O SER K 257 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG K 262 " --> pdb=" O ILE K 258 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR K 263 " --> pdb=" O SER K 259 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE K 264 " --> pdb=" O VAL K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 288 removed outlier: 3.975A pdb=" N TYR K 284 " --> pdb=" O GLY K 280 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU K 286 " --> pdb=" O LYS K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 308 removed outlier: 4.031A pdb=" N ARG K 307 " --> pdb=" O ILE K 304 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG K 308 " --> pdb=" O VAL K 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 304 through 308' Processing helix chain 'K' and resid 346 through 350 Processing helix chain 'K' and resid 368 through 371 removed outlier: 3.695A pdb=" N ASN K 371 " --> pdb=" O LYS K 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 368 through 371' Processing helix chain 'K' and resid 372 through 380 Processing helix chain 'K' and resid 383 through 390 removed outlier: 3.971A pdb=" N LEU K 390 " --> pdb=" O THR K 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 398 through 402 removed outlier: 4.151A pdb=" N LYS K 401 " --> pdb=" O LYS K 398 " (cutoff:3.500A) Processing helix chain 'K' and resid 423 through 434 removed outlier: 3.671A pdb=" N SER K 433 " --> pdb=" O ILE K 429 " (cutoff:3.500A) Processing helix chain 'K' and resid 455 through 460 Processing helix chain 'L' and resid 58 through 72 removed outlier: 3.696A pdb=" N LEU L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU L 63 " --> pdb=" O PRO L 59 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N PHE L 64 " --> pdb=" O ASP L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 106 removed outlier: 4.307A pdb=" N PHE L 101 " --> pdb=" O GLU L 97 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU L 106 " --> pdb=" O TRP L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 122 removed outlier: 3.575A pdb=" N LEU L 122 " --> pdb=" O ALA L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 145 Processing helix chain 'L' and resid 153 through 173 removed outlier: 3.519A pdb=" N LYS L 157 " --> pdb=" O SER L 153 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR L 173 " --> pdb=" O MET L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 181 removed outlier: 4.103A pdb=" N GLU L 181 " --> pdb=" O GLU L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 190 removed outlier: 4.112A pdb=" N HIS L 189 " --> pdb=" O VAL L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 203 through 224 Processing helix chain 'L' and resid 230 through 241 removed outlier: 4.221A pdb=" N VAL L 234 " --> pdb=" O ASP L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 249 Processing helix chain 'L' and resid 249 through 266 removed outlier: 3.506A pdb=" N ALA L 253 " --> pdb=" O GLU L 249 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN L 266 " --> pdb=" O HIS L 262 " (cutoff:3.500A) Processing helix chain 'L' and resid 279 through 302 removed outlier: 3.598A pdb=" N LEU L 302 " --> pdb=" O GLY L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 343 through 357 removed outlier: 3.536A pdb=" N ASP L 354 " --> pdb=" O SER L 350 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 360 No H-bonds generated for 'chain 'L' and resid 358 through 360' Processing helix chain 'L' and resid 366 through 384 removed outlier: 3.963A pdb=" N LEU L 370 " --> pdb=" O PRO L 366 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR L 382 " --> pdb=" O ASP L 378 " (cutoff:3.500A) Processing helix chain 'L' and resid 393 through 422 removed outlier: 3.884A pdb=" N ARG L 397 " --> pdb=" O SER L 393 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER L 411 " --> pdb=" O ILE L 407 " (cutoff:3.500A) Processing helix chain 'L' and resid 428 through 445 Processing helix chain 'L' and resid 451 through 456 removed outlier: 3.667A pdb=" N ASN L 454 " --> pdb=" O GLU L 451 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS L 456 " --> pdb=" O PHE L 453 " (cutoff:3.500A) Processing helix chain 'L' and resid 458 through 477 removed outlier: 3.649A pdb=" N ILE L 463 " --> pdb=" O VAL L 459 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR L 464 " --> pdb=" O MET L 460 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE L 475 " --> pdb=" O SER L 471 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE L 476 " --> pdb=" O PHE L 472 " (cutoff:3.500A) Processing helix chain 'L' and resid 481 through 494 Processing helix chain 'L' and resid 501 through 522 removed outlier: 3.856A pdb=" N LEU L 519 " --> pdb=" O SER L 515 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU L 520 " --> pdb=" O LYS L 516 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP L 522 " --> pdb=" O LYS L 518 " (cutoff:3.500A) Processing helix chain 'L' and resid 536 through 552 removed outlier: 4.612A pdb=" N GLN L 542 " --> pdb=" O PHE L 538 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE L 545 " --> pdb=" O LEU L 541 " (cutoff:3.500A) Processing helix chain 'L' and resid 554 through 562 Processing helix chain 'L' and resid 590 through 601 Processing helix chain 'O' and resid 56 through 73 removed outlier: 4.370A pdb=" N ASP O 60 " --> pdb=" O GLU O 56 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE O 64 " --> pdb=" O ASP O 60 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN O 66 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASN O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 103 Processing helix chain 'O' and resid 107 through 118 Processing helix chain 'O' and resid 125 through 129 removed outlier: 3.724A pdb=" N GLY O 128 " --> pdb=" O LEU O 125 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 147 Processing helix chain 'O' and resid 154 through 171 removed outlier: 3.650A pdb=" N MET O 169 " --> pdb=" O SER O 165 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 174 No H-bonds generated for 'chain 'O' and resid 172 through 174' Processing helix chain 'O' and resid 175 through 182 removed outlier: 3.729A pdb=" N LEU O 179 " --> pdb=" O PRO O 175 " (cutoff:3.500A) Processing helix chain 'O' and resid 203 through 224 removed outlier: 4.186A pdb=" N CYS O 209 " --> pdb=" O GLN O 205 " (cutoff:3.500A) Processing helix chain 'O' and resid 230 through 232 No H-bonds generated for 'chain 'O' and resid 230 through 232' Processing helix chain 'O' and resid 233 through 241 removed outlier: 3.790A pdb=" N ILE O 239 " --> pdb=" O GLN O 235 " (cutoff:3.500A) Processing helix chain 'O' and resid 244 through 249 Processing helix chain 'O' and resid 249 through 266 removed outlier: 3.505A pdb=" N ALA O 253 " --> pdb=" O GLU O 249 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER O 255 " --> pdb=" O LEU O 251 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN O 266 " --> pdb=" O HIS O 262 " (cutoff:3.500A) Processing helix chain 'O' and resid 279 through 304 removed outlier: 3.747A pdb=" N SER O 283 " --> pdb=" O ASP O 279 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG O 291 " --> pdb=" O VAL O 287 " (cutoff:3.500A) Processing helix chain 'O' and resid 340 through 344 removed outlier: 3.649A pdb=" N VAL O 343 " --> pdb=" O SER O 340 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU O 344 " --> pdb=" O THR O 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 340 through 344' Processing helix chain 'O' and resid 346 through 357 removed outlier: 4.783A pdb=" N ASP O 354 " --> pdb=" O SER O 350 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU O 355 " --> pdb=" O LEU O 351 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP O 356 " --> pdb=" O ASP O 352 " (cutoff:3.500A) Processing helix chain 'O' and resid 366 through 386 removed outlier: 4.500A pdb=" N LEU O 370 " --> pdb=" O PRO O 366 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA O 372 " --> pdb=" O LYS O 368 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP O 378 " --> pdb=" O ARG O 374 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE O 379 " --> pdb=" O ARG O 375 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL O 384 " --> pdb=" O PHE O 380 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP O 385 " --> pdb=" O GLN O 381 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER O 386 " --> pdb=" O TYR O 382 " (cutoff:3.500A) Processing helix chain 'O' and resid 393 through 422 removed outlier: 3.915A pdb=" N ARG O 397 " --> pdb=" O SER O 393 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET O 417 " --> pdb=" O LYS O 413 " (cutoff:3.500A) Processing helix chain 'O' and resid 426 through 435 Processing helix chain 'O' and resid 435 through 445 removed outlier: 4.173A pdb=" N ILE O 439 " --> pdb=" O SER O 435 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN O 445 " --> pdb=" O LEU O 441 " (cutoff:3.500A) Processing helix chain 'O' and resid 451 through 456 Processing helix chain 'O' and resid 458 through 475 removed outlier: 4.063A pdb=" N THR O 464 " --> pdb=" O MET O 460 " (cutoff:3.500A) Processing helix chain 'O' and resid 481 through 494 removed outlier: 3.701A pdb=" N ALA O 494 " --> pdb=" O THR O 490 " (cutoff:3.500A) Processing helix chain 'O' and resid 497 through 500 removed outlier: 3.882A pdb=" N PHE O 500 " --> pdb=" O PRO O 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 497 through 500' Processing helix chain 'O' and resid 501 through 524 Processing helix chain 'O' and resid 535 through 552 removed outlier: 3.889A pdb=" N LYS O 539 " --> pdb=" O HIS O 535 " (cutoff:3.500A) Processing helix chain 'O' and resid 554 through 563 Processing helix chain 'O' and resid 602 through 606 removed outlier: 3.754A pdb=" N ASP O 605 " --> pdb=" O ASN O 602 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 25 removed outlier: 3.746A pdb=" N ARG N 25 " --> pdb=" O ILE N 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 22 through 25' Processing helix chain 'N' and resid 26 through 31 Processing helix chain 'N' and resid 83 through 97 removed outlier: 3.603A pdb=" N LEU N 87 " --> pdb=" O ARG N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 125 removed outlier: 3.639A pdb=" N LEU N 124 " --> pdb=" O ARG N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 142 removed outlier: 3.893A pdb=" N TYR N 132 " --> pdb=" O GLN N 128 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 157 removed outlier: 3.506A pdb=" N VAL N 153 " --> pdb=" O ALA N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 187 removed outlier: 3.627A pdb=" N GLU N 181 " --> pdb=" O THR N 177 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG N 185 " --> pdb=" O GLU N 181 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 131 through 132 removed outlier: 6.635A pdb=" N TYR K 131 " --> pdb=" O GLU K 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 199 through 201 removed outlier: 3.907A pdb=" N VAL K 199 " --> pdb=" O LYS K 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR K 277 " --> pdb=" O VAL K 199 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE K 312 " --> pdb=" O VAL K 338 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU K 337 " --> pdb=" O THR K 360 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 410 through 412 removed outlier: 6.121A pdb=" N LYS K 411 " --> pdb=" O VAL K 477 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 527 through 528 Processing sheet with id=AA5, first strand: chain 'O' and resid 527 through 528 550 hydrogen bonds defined for protein. 1608 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: 1.90 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3313 1.33 - 1.45: 3032 1.45 - 1.58: 7137 1.58 - 1.70: 5 1.70 - 1.82: 93 Bond restraints: 13580 Sorted by residual: bond pdb=" CA LYS O 55 " pdb=" C LYS O 55 " ideal model delta sigma weight residual 1.523 1.591 -0.068 1.56e-02 4.11e+03 1.88e+01 bond pdb=" CA ARG K 58 " pdb=" CB ARG K 58 " ideal model delta sigma weight residual 1.527 1.592 -0.066 1.75e-02 3.27e+03 1.40e+01 bond pdb=" C TYR L 173 " pdb=" N MET L 174 " ideal model delta sigma weight residual 1.331 1.272 0.059 1.63e-02 3.76e+03 1.31e+01 bond pdb=" CA ARG N 15 " pdb=" CB ARG N 15 " ideal model delta sigma weight residual 1.531 1.578 -0.047 1.52e-02 4.33e+03 9.72e+00 bond pdb=" CA TYR K 67 " pdb=" CB TYR K 67 " ideal model delta sigma weight residual 1.526 1.556 -0.030 1.09e-02 8.42e+03 7.47e+00 ... (remaining 13575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 17405 3.68 - 7.36: 805 7.36 - 11.05: 136 11.05 - 14.73: 30 14.73 - 18.41: 4 Bond angle restraints: 18380 Sorted by residual: angle pdb=" N ILE L 606 " pdb=" CA ILE L 606 " pdb=" C ILE L 606 " ideal model delta sigma weight residual 112.83 104.34 8.49 9.90e-01 1.02e+00 7.36e+01 angle pdb=" CB ARG L 465 " pdb=" CG ARG L 465 " pdb=" CD ARG L 465 " ideal model delta sigma weight residual 111.30 128.70 -17.40 2.30e+00 1.89e-01 5.72e+01 angle pdb=" C GLU L 98 " pdb=" N CYS L 99 " pdb=" CA CYS L 99 " ideal model delta sigma weight residual 122.65 110.82 11.83 1.60e+00 3.91e-01 5.47e+01 angle pdb=" C VAL N 18 " pdb=" N ASP N 19 " pdb=" CA ASP N 19 " ideal model delta sigma weight residual 121.54 133.51 -11.97 1.91e+00 2.74e-01 3.93e+01 angle pdb=" C ARG L 214 " pdb=" N CYS L 215 " pdb=" CA CYS L 215 " ideal model delta sigma weight residual 122.49 112.88 9.61 1.55e+00 4.16e-01 3.84e+01 ... (remaining 18375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.39: 6899 18.39 - 36.77: 1038 36.77 - 55.16: 172 55.16 - 73.55: 21 73.55 - 91.93: 16 Dihedral angle restraints: 8146 sinusoidal: 3359 harmonic: 4787 Sorted by residual: dihedral pdb=" CA ARG N 186 " pdb=" C ARG N 186 " pdb=" N GLU N 187 " pdb=" CA GLU N 187 " ideal model delta harmonic sigma weight residual 180.00 144.31 35.69 0 5.00e+00 4.00e-02 5.09e+01 dihedral pdb=" CA PHE K 9 " pdb=" C PHE K 9 " pdb=" N LEU K 10 " pdb=" CA LEU K 10 " ideal model delta harmonic sigma weight residual 180.00 144.54 35.46 0 5.00e+00 4.00e-02 5.03e+01 dihedral pdb=" CB CYS L 99 " pdb=" SG CYS L 99 " pdb=" SG CYS L 215 " pdb=" CB CYS L 215 " ideal model delta sinusoidal sigma weight residual 93.00 145.08 -52.08 1 1.00e+01 1.00e-02 3.70e+01 ... (remaining 8143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1602 0.093 - 0.185: 380 0.185 - 0.278: 47 0.278 - 0.370: 14 0.370 - 0.462: 1 Chirality restraints: 2044 Sorted by residual: chirality pdb=" CB VAL O 443 " pdb=" CA VAL O 443 " pdb=" CG1 VAL O 443 " pdb=" CG2 VAL O 443 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" CG LEU L 289 " pdb=" CB LEU L 289 " pdb=" CD1 LEU L 289 " pdb=" CD2 LEU L 289 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CB ILE K 466 " pdb=" CA ILE K 466 " pdb=" CG1 ILE K 466 " pdb=" CG2 ILE K 466 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 2041 not shown) Planarity restraints: 2305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 65 " -0.046 2.00e-02 2.50e+03 3.77e-02 3.56e+01 pdb=" CG TRP L 65 " 0.103 2.00e-02 2.50e+03 pdb=" CD1 TRP L 65 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP L 65 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP L 65 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP L 65 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP L 65 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 65 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 65 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP L 65 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU O 141 " 0.026 2.00e-02 2.50e+03 5.38e-02 2.90e+01 pdb=" CD GLU O 141 " -0.093 2.00e-02 2.50e+03 pdb=" OE1 GLU O 141 " 0.033 2.00e-02 2.50e+03 pdb=" OE2 GLU O 141 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP O 346 " -0.042 2.00e-02 2.50e+03 3.36e-02 2.82e+01 pdb=" CG TRP O 346 " 0.088 2.00e-02 2.50e+03 pdb=" CD1 TRP O 346 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP O 346 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP O 346 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP O 346 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP O 346 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 346 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 346 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP O 346 " -0.018 2.00e-02 2.50e+03 ... (remaining 2302 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1539 2.74 - 3.28: 13707 3.28 - 3.82: 22487 3.82 - 4.36: 25688 4.36 - 4.90: 41162 Nonbonded interactions: 104583 Sorted by model distance: nonbonded pdb=" OG SER L 393 " pdb=" OD1 ASN L 395 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR K 360 " pdb=" O LYS K 441 " model vdw 2.197 3.040 nonbonded pdb=" OE1 GLU L 69 " pdb=" OG1 THR L 73 " model vdw 2.225 3.040 nonbonded pdb=" O ASP O 300 " pdb=" OG SER O 304 " model vdw 2.230 3.040 nonbonded pdb=" O LYS K 60 " pdb=" NH1 ARG K 64 " model vdw 2.247 3.120 ... (remaining 104578 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'L' and (resid 54 through 317 or (resid 318 through 319 and (name N or na \ me CA or name C or name O or name CB )) or resid 339 or (resid 340 and (name N o \ r name CA or name C or name O or name CB )) or resid 341 through 567 or resid 58 \ 9 through 608)) selection = (chain 'O' and (resid 54 through 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 567 or resid 589 through 608)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.080 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 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 : 0.009 0.082 13581 Z= 0.413 Angle : 1.807 18.409 18382 Z= 0.950 Chirality : 0.082 0.462 2044 Planarity : 0.010 0.096 2305 Dihedral : 17.449 91.931 5025 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 0.13 % Allowed : 3.17 % Favored : 96.69 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.78 (0.18), residues: 1579 helix: -2.31 (0.15), residues: 839 sheet: -1.85 (0.81), residues: 44 loop : -2.71 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.004 ARG K 128 TYR 0.054 0.005 TYR L 172 PHE 0.070 0.005 PHE K 356 TRP 0.103 0.008 TRP L 65 HIS 0.023 0.003 HIS L 262 Details of bonding type rmsd covalent geometry : bond 0.00931 (13580) covalent geometry : angle 1.80582 (18380) SS BOND : bond 0.00429 ( 1) SS BOND : angle 5.28956 ( 2) hydrogen bonds : bond 0.15410 ( 550) hydrogen bonds : angle 7.62345 ( 1608) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.517 Fit side-chains REVERT: K 369 TRP cc_start: 0.7807 (t-100) cc_final: 0.6971 (t-100) REVERT: L 226 MET cc_start: 0.7435 (mmm) cc_final: 0.7212 (tpt) REVERT: O 303 GLN cc_start: 0.9041 (tt0) cc_final: 0.8778 (tt0) outliers start: 2 outliers final: 0 residues processed: 98 average time/residue: 0.0825 time to fit residues: 13.1036 Evaluate side-chains 79 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 444 ASN ** O 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 96 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.057880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.049536 restraints weight = 95995.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.050807 restraints weight = 53008.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.051634 restraints weight = 34739.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.052286 restraints weight = 25599.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.052533 restraints weight = 20330.122| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13581 Z= 0.147 Angle : 0.812 10.689 18382 Z= 0.420 Chirality : 0.047 0.227 2044 Planarity : 0.006 0.064 2305 Dihedral : 6.549 28.363 1747 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 1.42 % Allowed : 11.88 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.19), residues: 1579 helix: -1.24 (0.16), residues: 886 sheet: -0.94 (0.91), residues: 34 loop : -2.66 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 363 TYR 0.024 0.002 TYR L 301 PHE 0.024 0.001 PHE L 167 TRP 0.031 0.003 TRP L 65 HIS 0.005 0.001 HIS L 262 Details of bonding type rmsd covalent geometry : bond 0.00324 (13580) covalent geometry : angle 0.81190 (18380) SS BOND : bond 0.00141 ( 1) SS BOND : angle 3.08125 ( 2) hydrogen bonds : bond 0.04652 ( 550) hydrogen bonds : angle 5.45283 ( 1608) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: K 369 TRP cc_start: 0.8051 (t-100) cc_final: 0.6849 (t-100) REVERT: L 226 MET cc_start: 0.7169 (mmm) cc_final: 0.6949 (tpt) REVERT: L 376 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8645 (mp0) REVERT: L 458 MET cc_start: 0.7185 (ptp) cc_final: 0.6764 (ptp) REVERT: O 119 MET cc_start: 0.8224 (ttt) cc_final: 0.7912 (tmm) REVERT: O 142 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7951 (pm20) REVERT: O 418 TYR cc_start: 0.8028 (OUTLIER) cc_final: 0.7505 (t80) outliers start: 21 outliers final: 11 residues processed: 102 average time/residue: 0.0901 time to fit residues: 14.8100 Evaluate side-chains 86 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 444 ASN Chi-restraints excluded: chain L residue 261 ILE Chi-restraints excluded: chain L residue 376 GLU Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain O residue 141 GLU Chi-restraints excluded: chain O residue 142 GLN Chi-restraints excluded: chain O residue 158 TYR Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 432 ILE Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 119 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 70 optimal weight: 0.2980 chunk 137 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 450 ASN ** K 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 222 GLN ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 461 GLN O 598 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.058531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.050171 restraints weight = 95633.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.051480 restraints weight = 52020.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.052359 restraints weight = 33729.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.052976 restraints weight = 24633.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.053373 restraints weight = 19569.176| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13581 Z= 0.121 Angle : 0.702 8.628 18382 Z= 0.359 Chirality : 0.044 0.220 2044 Planarity : 0.005 0.057 2305 Dihedral : 5.680 26.715 1747 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.50 % Allowed : 14.91 % Favored : 82.59 % 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: -1.95 (0.21), residues: 1579 helix: -0.51 (0.17), residues: 884 sheet: -0.99 (0.90), residues: 34 loop : -2.39 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 146 TYR 0.016 0.001 TYR O 301 PHE 0.020 0.001 PHE L 167 TRP 0.017 0.002 TRP L 65 HIS 0.006 0.001 HIS L 262 Details of bonding type rmsd covalent geometry : bond 0.00262 (13580) covalent geometry : angle 0.70094 (18380) SS BOND : bond 0.00399 ( 1) SS BOND : angle 2.83157 ( 2) hydrogen bonds : bond 0.04046 ( 550) hydrogen bonds : angle 4.94954 ( 1608) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 84 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 369 TRP cc_start: 0.8322 (t-100) cc_final: 0.7466 (t-100) REVERT: L 100 MET cc_start: 0.8912 (mpp) cc_final: 0.8215 (mpp) REVERT: L 103 MET cc_start: 0.8267 (mtt) cc_final: 0.7873 (mtt) REVERT: L 376 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8688 (mp0) REVERT: L 394 ASN cc_start: 0.7084 (OUTLIER) cc_final: 0.6781 (p0) REVERT: L 458 MET cc_start: 0.7150 (ptp) cc_final: 0.6767 (ptp) REVERT: O 119 MET cc_start: 0.8317 (ttt) cc_final: 0.8064 (tmm) REVERT: O 158 TYR cc_start: 0.7118 (OUTLIER) cc_final: 0.4995 (t80) REVERT: O 418 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7577 (t80) REVERT: O 460 MET cc_start: 0.8237 (tpt) cc_final: 0.7993 (tpt) REVERT: N 157 MET cc_start: 0.5577 (mtt) cc_final: 0.5185 (mmp) outliers start: 37 outliers final: 14 residues processed: 113 average time/residue: 0.0925 time to fit residues: 16.5806 Evaluate side-chains 90 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 261 ILE Chi-restraints excluded: chain L residue 376 GLU Chi-restraints excluded: chain L residue 394 ASN Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain O residue 142 GLN Chi-restraints excluded: chain O residue 143 TYR Chi-restraints excluded: chain O residue 158 TYR Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 381 GLN Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 187 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 41 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 32 optimal weight: 0.3980 chunk 95 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 268 HIS ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.057390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.049015 restraints weight = 94026.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.050298 restraints weight = 50732.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.051148 restraints weight = 32786.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.051752 restraints weight = 24051.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.052045 restraints weight = 19180.231| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13581 Z= 0.159 Angle : 0.685 7.792 18382 Z= 0.358 Chirality : 0.044 0.219 2044 Planarity : 0.005 0.049 2305 Dihedral : 5.637 25.032 1747 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.91 % Allowed : 17.54 % Favored : 78.54 % 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: -1.77 (0.21), residues: 1579 helix: -0.33 (0.18), residues: 888 sheet: -1.31 (0.86), residues: 34 loop : -2.34 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 465 TYR 0.022 0.002 TYR L 335 PHE 0.014 0.001 PHE L 167 TRP 0.026 0.002 TRP L 71 HIS 0.004 0.001 HIS K 108 Details of bonding type rmsd covalent geometry : bond 0.00358 (13580) covalent geometry : angle 0.68396 (18380) SS BOND : bond 0.00452 ( 1) SS BOND : angle 3.25744 ( 2) hydrogen bonds : bond 0.04239 ( 550) hydrogen bonds : angle 4.93693 ( 1608) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 76 time to evaluate : 0.620 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: K 24 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7295 (tp) REVERT: K 363 ARG cc_start: 0.8180 (tpm170) cc_final: 0.7980 (tpm170) REVERT: K 369 TRP cc_start: 0.8356 (t-100) cc_final: 0.7444 (t-100) REVERT: K 396 ASP cc_start: 0.4672 (OUTLIER) cc_final: 0.3741 (t70) REVERT: L 231 ILE cc_start: 0.8890 (tt) cc_final: 0.8623 (tp) REVERT: L 376 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8834 (mp0) REVERT: L 377 LEU cc_start: 0.9517 (mm) cc_final: 0.9221 (tt) REVERT: L 394 ASN cc_start: 0.7172 (OUTLIER) cc_final: 0.6470 (p0) REVERT: L 458 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.6913 (ptp) REVERT: O 119 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8013 (tmm) REVERT: O 183 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.6372 (m-80) REVERT: O 418 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.7636 (t80) REVERT: O 458 MET cc_start: 0.7240 (ptt) cc_final: 0.6905 (ptt) REVERT: N 157 MET cc_start: 0.5978 (mtt) cc_final: 0.5473 (mmp) outliers start: 58 outliers final: 34 residues processed: 125 average time/residue: 0.0979 time to fit residues: 19.2191 Evaluate side-chains 112 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 70 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 128 ARG Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 396 ASP Chi-restraints excluded: chain K residue 407 HIS Chi-restraints excluded: chain K residue 444 ASN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 261 ILE Chi-restraints excluded: chain L residue 376 GLU Chi-restraints excluded: chain L residue 394 ASN Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 418 TYR Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 458 MET Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 595 GLU Chi-restraints excluded: chain O residue 119 MET Chi-restraints excluded: chain O residue 142 GLN Chi-restraints excluded: chain O residue 143 TYR Chi-restraints excluded: chain O residue 158 TYR Chi-restraints excluded: chain O residue 183 PHE Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 357 GLN Chi-restraints excluded: chain O residue 381 GLN Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain O residue 565 LEU Chi-restraints excluded: chain O residue 596 GLU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 187 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 84 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.058283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.049818 restraints weight = 93652.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.051146 restraints weight = 49991.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.052025 restraints weight = 32063.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.052646 restraints weight = 23376.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.052940 restraints weight = 18586.910| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13581 Z= 0.122 Angle : 0.658 12.851 18382 Z= 0.338 Chirality : 0.044 0.228 2044 Planarity : 0.004 0.048 2305 Dihedral : 5.331 24.761 1747 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.25 % Allowed : 19.30 % Favored : 76.45 % 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: -1.52 (0.21), residues: 1579 helix: -0.06 (0.18), residues: 876 sheet: -1.20 (0.96), residues: 29 loop : -2.30 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 465 TYR 0.015 0.001 TYR O 137 PHE 0.012 0.001 PHE L 167 TRP 0.021 0.002 TRP N 190 HIS 0.004 0.001 HIS L 262 Details of bonding type rmsd covalent geometry : bond 0.00274 (13580) covalent geometry : angle 0.65727 (18380) SS BOND : bond 0.00691 ( 1) SS BOND : angle 3.09019 ( 2) hydrogen bonds : bond 0.03819 ( 550) hydrogen bonds : angle 4.74884 ( 1608) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 80 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 369 TRP cc_start: 0.8385 (t-100) cc_final: 0.7220 (t-100) REVERT: L 115 MET cc_start: 0.8772 (mmm) cc_final: 0.8198 (mmm) REVERT: L 231 ILE cc_start: 0.8829 (tt) cc_final: 0.8588 (tp) REVERT: L 377 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9229 (tt) REVERT: L 394 ASN cc_start: 0.7182 (OUTLIER) cc_final: 0.6442 (p0) REVERT: L 458 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6907 (ptp) REVERT: O 78 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7726 (m-10) REVERT: O 119 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7939 (tmm) REVERT: O 142 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7838 (pm20) REVERT: O 183 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.6119 (m-80) REVERT: O 418 TYR cc_start: 0.7970 (OUTLIER) cc_final: 0.7601 (t80) outliers start: 63 outliers final: 33 residues processed: 134 average time/residue: 0.0944 time to fit residues: 19.6978 Evaluate side-chains 114 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 73 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 128 ARG Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 407 HIS Chi-restraints excluded: chain K residue 444 ASN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 261 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 394 ASN Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 418 TYR Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 458 MET Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 547 ILE Chi-restraints excluded: chain L residue 595 GLU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 78 TYR Chi-restraints excluded: chain O residue 119 MET Chi-restraints excluded: chain O residue 142 GLN Chi-restraints excluded: chain O residue 143 TYR Chi-restraints excluded: chain O residue 158 TYR Chi-restraints excluded: chain O residue 183 PHE Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 357 GLN Chi-restraints excluded: chain O residue 381 GLN Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 446 PHE Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 180 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 128 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 552 ASN ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.057693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.049194 restraints weight = 94260.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.050494 restraints weight = 51039.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.051376 restraints weight = 33106.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.051929 restraints weight = 24237.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.052377 restraints weight = 19563.394| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13581 Z= 0.139 Angle : 0.679 10.813 18382 Z= 0.348 Chirality : 0.044 0.224 2044 Planarity : 0.004 0.049 2305 Dihedral : 5.320 24.053 1747 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 4.32 % Allowed : 20.78 % Favored : 74.90 % 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: -1.45 (0.21), residues: 1579 helix: -0.05 (0.18), residues: 877 sheet: -1.14 (0.97), residues: 29 loop : -2.19 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 185 TYR 0.024 0.001 TYR L 335 PHE 0.011 0.001 PHE L 167 TRP 0.020 0.002 TRP N 190 HIS 0.004 0.001 HIS K 108 Details of bonding type rmsd covalent geometry : bond 0.00316 (13580) covalent geometry : angle 0.67814 (18380) SS BOND : bond 0.00030 ( 1) SS BOND : angle 3.34015 ( 2) hydrogen bonds : bond 0.04002 ( 550) hydrogen bonds : angle 4.81800 ( 1608) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 76 time to evaluate : 0.354 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: K 369 TRP cc_start: 0.8377 (t-100) cc_final: 0.7640 (t-100) REVERT: L 115 MET cc_start: 0.8772 (mmm) cc_final: 0.8060 (mmm) REVERT: L 231 ILE cc_start: 0.8886 (tt) cc_final: 0.8666 (tp) REVERT: L 394 ASN cc_start: 0.7261 (OUTLIER) cc_final: 0.6518 (p0) REVERT: L 458 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6884 (ptp) REVERT: O 78 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7752 (m-10) REVERT: O 119 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7823 (tmm) REVERT: O 142 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7814 (pm20) REVERT: O 183 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.6213 (m-80) REVERT: O 418 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.7587 (t80) REVERT: O 458 MET cc_start: 0.7179 (ptt) cc_final: 0.6865 (ptt) REVERT: O 598 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8300 (pp30) outliers start: 64 outliers final: 38 residues processed: 131 average time/residue: 0.0961 time to fit residues: 19.7533 Evaluate side-chains 118 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 72 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 93 TRP Chi-restraints excluded: chain K residue 128 ARG Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 407 HIS Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 261 ILE Chi-restraints excluded: chain L residue 341 THR Chi-restraints excluded: chain L residue 394 ASN Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 418 TYR Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 458 MET Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 595 GLU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 78 TYR Chi-restraints excluded: chain O residue 119 MET Chi-restraints excluded: chain O residue 141 GLU Chi-restraints excluded: chain O residue 142 GLN Chi-restraints excluded: chain O residue 143 TYR Chi-restraints excluded: chain O residue 158 TYR Chi-restraints excluded: chain O residue 183 PHE Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 357 GLN Chi-restraints excluded: chain O residue 381 GLN Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 446 PHE Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain O residue 596 GLU Chi-restraints excluded: chain O residue 598 GLN Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 180 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.057419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.048973 restraints weight = 95207.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.050233 restraints weight = 51973.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.051085 restraints weight = 33926.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.051546 restraints weight = 24975.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.052040 restraints weight = 20558.749| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13581 Z= 0.161 Angle : 0.694 12.596 18382 Z= 0.357 Chirality : 0.045 0.224 2044 Planarity : 0.004 0.047 2305 Dihedral : 5.430 24.284 1747 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 4.52 % Allowed : 21.32 % Favored : 74.16 % 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: -1.50 (0.21), residues: 1579 helix: -0.12 (0.18), residues: 879 sheet: -0.21 (1.17), residues: 19 loop : -2.21 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 8 TYR 0.020 0.002 TYR L 418 PHE 0.011 0.001 PHE N 102 TRP 0.017 0.002 TRP L 346 HIS 0.005 0.001 HIS K 108 Details of bonding type rmsd covalent geometry : bond 0.00366 (13580) covalent geometry : angle 0.69360 (18380) SS BOND : bond 0.01084 ( 1) SS BOND : angle 3.29441 ( 2) hydrogen bonds : bond 0.04121 ( 550) hydrogen bonds : angle 4.86007 ( 1608) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 71 time to evaluate : 0.485 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: K 369 TRP cc_start: 0.8400 (t-100) cc_final: 0.7631 (t-100) REVERT: K 393 LYS cc_start: 0.6698 (OUTLIER) cc_final: 0.6275 (pttm) REVERT: L 231 ILE cc_start: 0.8899 (tt) cc_final: 0.8667 (tp) REVERT: L 376 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8842 (mp0) REVERT: L 394 ASN cc_start: 0.7259 (OUTLIER) cc_final: 0.6711 (p0) REVERT: L 458 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6974 (ptp) REVERT: O 78 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.7823 (m-10) REVERT: O 119 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7840 (tmm) REVERT: O 142 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7845 (pm20) REVERT: O 183 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.6160 (m-80) REVERT: O 315 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: O 418 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.7653 (t80) REVERT: O 598 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8109 (pp30) outliers start: 67 outliers final: 46 residues processed: 128 average time/residue: 0.0950 time to fit residues: 18.9148 Evaluate side-chains 126 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 69 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 128 ARG Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 393 LYS Chi-restraints excluded: chain K residue 396 ASP Chi-restraints excluded: chain K residue 407 HIS Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 261 ILE Chi-restraints excluded: chain L residue 341 THR Chi-restraints excluded: chain L residue 376 GLU Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 394 ASN Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 418 TYR Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 458 MET Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 547 ILE Chi-restraints excluded: chain L residue 595 GLU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 78 TYR Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 119 MET Chi-restraints excluded: chain O residue 141 GLU Chi-restraints excluded: chain O residue 142 GLN Chi-restraints excluded: chain O residue 143 TYR Chi-restraints excluded: chain O residue 158 TYR Chi-restraints excluded: chain O residue 183 PHE Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 315 GLU Chi-restraints excluded: chain O residue 357 GLN Chi-restraints excluded: chain O residue 381 GLN Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 432 ILE Chi-restraints excluded: chain O residue 446 PHE Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain O residue 596 GLU Chi-restraints excluded: chain O residue 598 GLN Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 180 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 24 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 113 optimal weight: 0.3980 chunk 10 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 348 ASN K 371 ASN ** K 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.057431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.049116 restraints weight = 93691.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.050402 restraints weight = 50509.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.051263 restraints weight = 32650.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.051862 restraints weight = 23921.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.052178 restraints weight = 19084.997| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13581 Z= 0.130 Angle : 0.671 12.417 18382 Z= 0.343 Chirality : 0.044 0.226 2044 Planarity : 0.004 0.046 2305 Dihedral : 5.273 24.380 1747 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 4.59 % Allowed : 22.13 % Favored : 73.28 % 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: -1.38 (0.21), residues: 1579 helix: 0.01 (0.18), residues: 873 sheet: -0.05 (1.17), residues: 19 loop : -2.19 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 8 TYR 0.024 0.001 TYR L 335 PHE 0.011 0.001 PHE N 102 TRP 0.024 0.002 TRP L 71 HIS 0.005 0.001 HIS K 108 Details of bonding type rmsd covalent geometry : bond 0.00295 (13580) covalent geometry : angle 0.66982 (18380) SS BOND : bond 0.00481 ( 1) SS BOND : angle 3.38820 ( 2) hydrogen bonds : bond 0.03880 ( 550) hydrogen bonds : angle 4.73658 ( 1608) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 74 time to evaluate : 0.548 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: K 393 LYS cc_start: 0.6656 (OUTLIER) cc_final: 0.6256 (pttm) REVERT: L 231 ILE cc_start: 0.8836 (tt) cc_final: 0.8631 (tp) REVERT: L 376 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8697 (mp0) REVERT: L 394 ASN cc_start: 0.7230 (OUTLIER) cc_final: 0.6681 (p0) REVERT: L 458 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6991 (ptp) REVERT: O 78 TYR cc_start: 0.8401 (OUTLIER) cc_final: 0.7357 (m-10) REVERT: O 119 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7845 (tmm) REVERT: O 142 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7817 (pm20) REVERT: O 183 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.6024 (m-80) REVERT: O 418 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.7611 (t80) REVERT: O 458 MET cc_start: 0.7210 (ptt) cc_final: 0.6837 (pmm) REVERT: O 598 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8135 (pp30) outliers start: 68 outliers final: 47 residues processed: 132 average time/residue: 0.0946 time to fit residues: 19.7534 Evaluate side-chains 128 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 71 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 128 ARG Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 393 LYS Chi-restraints excluded: chain K residue 396 ASP Chi-restraints excluded: chain K residue 407 HIS Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 220 LEU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 261 ILE Chi-restraints excluded: chain L residue 341 THR Chi-restraints excluded: chain L residue 376 GLU Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 394 ASN Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 418 TYR Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 458 MET Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 547 ILE Chi-restraints excluded: chain L residue 595 GLU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 78 TYR Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 119 MET Chi-restraints excluded: chain O residue 142 GLN Chi-restraints excluded: chain O residue 143 TYR Chi-restraints excluded: chain O residue 158 TYR Chi-restraints excluded: chain O residue 183 PHE Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 357 GLN Chi-restraints excluded: chain O residue 381 GLN Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 432 ILE Chi-restraints excluded: chain O residue 446 PHE Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 526 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain O residue 596 GLU Chi-restraints excluded: chain O residue 598 GLN Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 180 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 49 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 141 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 43 optimal weight: 0.0980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.057219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.048837 restraints weight = 95174.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.050116 restraints weight = 51317.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.050956 restraints weight = 33173.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.051549 restraints weight = 24433.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.051899 restraints weight = 19545.959| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13581 Z= 0.149 Angle : 0.707 15.845 18382 Z= 0.357 Chirality : 0.045 0.269 2044 Planarity : 0.004 0.046 2305 Dihedral : 5.332 25.107 1747 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 4.45 % Allowed : 22.94 % Favored : 72.60 % 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: -1.41 (0.21), residues: 1579 helix: -0.02 (0.18), residues: 872 sheet: -0.06 (1.16), residues: 19 loop : -2.19 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 8 TYR 0.018 0.001 TYR L 418 PHE 0.011 0.001 PHE N 102 TRP 0.055 0.002 TRP K 369 HIS 0.005 0.001 HIS K 108 Details of bonding type rmsd covalent geometry : bond 0.00338 (13580) covalent geometry : angle 0.70584 (18380) SS BOND : bond 0.00093 ( 1) SS BOND : angle 3.56341 ( 2) hydrogen bonds : bond 0.03988 ( 550) hydrogen bonds : angle 4.79330 ( 1608) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 69 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 393 LYS cc_start: 0.6739 (OUTLIER) cc_final: 0.6356 (pttm) REVERT: L 376 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8849 (mp0) REVERT: L 394 ASN cc_start: 0.7288 (OUTLIER) cc_final: 0.6754 (p0) REVERT: L 458 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6873 (ptp) REVERT: O 119 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7776 (tmm) REVERT: O 133 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8026 (pp) REVERT: O 142 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7847 (pm20) REVERT: O 183 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.5920 (m-80) REVERT: O 315 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: O 418 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7669 (t80) REVERT: O 458 MET cc_start: 0.7241 (ptt) cc_final: 0.6852 (pmm) REVERT: O 598 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8298 (pp30) outliers start: 66 outliers final: 49 residues processed: 126 average time/residue: 0.0931 time to fit residues: 18.5965 Evaluate side-chains 129 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 69 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 128 ARG Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 173 ASP Chi-restraints excluded: chain K residue 334 LEU Chi-restraints excluded: chain K residue 393 LYS Chi-restraints excluded: chain K residue 407 HIS Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 220 LEU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 261 ILE Chi-restraints excluded: chain L residue 341 THR Chi-restraints excluded: chain L residue 376 GLU Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 394 ASN Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 418 TYR Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 458 MET Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 547 ILE Chi-restraints excluded: chain L residue 595 GLU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 119 MET Chi-restraints excluded: chain O residue 133 ILE Chi-restraints excluded: chain O residue 142 GLN Chi-restraints excluded: chain O residue 143 TYR Chi-restraints excluded: chain O residue 158 TYR Chi-restraints excluded: chain O residue 183 PHE Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 315 GLU Chi-restraints excluded: chain O residue 357 GLN Chi-restraints excluded: chain O residue 381 GLN Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 432 ILE Chi-restraints excluded: chain O residue 446 PHE Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 526 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain O residue 596 GLU Chi-restraints excluded: chain O residue 598 GLN Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 96 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 104 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.058186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.049783 restraints weight = 93578.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.051088 restraints weight = 50529.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.051961 restraints weight = 32443.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.052585 restraints weight = 23702.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.052966 restraints weight = 18837.378| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13581 Z= 0.119 Angle : 0.687 15.002 18382 Z= 0.345 Chirality : 0.044 0.274 2044 Planarity : 0.004 0.051 2305 Dihedral : 5.128 25.861 1747 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.91 % Allowed : 23.28 % Favored : 72.81 % 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 (0.21), residues: 1579 helix: 0.12 (0.18), residues: 876 sheet: 0.09 (1.17), residues: 19 loop : -2.13 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 128 TYR 0.024 0.001 TYR L 335 PHE 0.015 0.001 PHE O 597 TRP 0.050 0.002 TRP K 369 HIS 0.005 0.001 HIS K 108 Details of bonding type rmsd covalent geometry : bond 0.00261 (13580) covalent geometry : angle 0.68659 (18380) SS BOND : bond 0.00210 ( 1) SS BOND : angle 3.32977 ( 2) hydrogen bonds : bond 0.03736 ( 550) hydrogen bonds : angle 4.64746 ( 1608) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 81 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 393 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.6006 (pttm) REVERT: L 115 MET cc_start: 0.8711 (mmm) cc_final: 0.8053 (mmm) REVERT: L 376 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8653 (mp0) REVERT: L 394 ASN cc_start: 0.7254 (OUTLIER) cc_final: 0.6844 (p0) REVERT: L 458 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6949 (ptp) REVERT: O 133 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7973 (pp) REVERT: O 142 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7813 (pm20) REVERT: O 183 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.5989 (m-80) REVERT: O 418 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.7620 (t80) REVERT: O 598 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8235 (pp30) REVERT: N 157 MET cc_start: 0.5883 (mtt) cc_final: 0.5370 (mmp) outliers start: 58 outliers final: 46 residues processed: 126 average time/residue: 0.0966 time to fit residues: 19.0439 Evaluate side-chains 132 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 77 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 128 ARG Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 173 ASP Chi-restraints excluded: chain K residue 393 LYS Chi-restraints excluded: chain K residue 396 ASP Chi-restraints excluded: chain K residue 407 HIS Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 238 LEU Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 261 ILE Chi-restraints excluded: chain L residue 341 THR Chi-restraints excluded: chain L residue 376 GLU Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 394 ASN Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 418 TYR Chi-restraints excluded: chain L residue 428 LEU Chi-restraints excluded: chain L residue 458 MET Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 547 ILE Chi-restraints excluded: chain L residue 595 GLU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 133 ILE Chi-restraints excluded: chain O residue 142 GLN Chi-restraints excluded: chain O residue 143 TYR Chi-restraints excluded: chain O residue 158 TYR Chi-restraints excluded: chain O residue 183 PHE Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 357 GLN Chi-restraints excluded: chain O residue 381 GLN Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 432 ILE Chi-restraints excluded: chain O residue 446 PHE Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 526 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain O residue 596 GLU Chi-restraints excluded: chain O residue 598 GLN Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.0770 chunk 85 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.058000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.049550 restraints weight = 94273.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.050851 restraints weight = 50705.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.051732 restraints weight = 32675.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.052290 restraints weight = 23839.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.052726 restraints weight = 19222.936| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13581 Z= 0.124 Angle : 0.700 14.259 18382 Z= 0.350 Chirality : 0.045 0.393 2044 Planarity : 0.004 0.051 2305 Dihedral : 5.108 25.490 1747 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.18 % Allowed : 23.08 % Favored : 72.74 % 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: -1.23 (0.21), residues: 1579 helix: 0.16 (0.18), residues: 870 sheet: -0.80 (1.02), residues: 28 loop : -2.14 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 128 TYR 0.015 0.001 TYR O 301 PHE 0.011 0.001 PHE N 176 TRP 0.044 0.002 TRP K 369 HIS 0.005 0.001 HIS K 108 Details of bonding type rmsd covalent geometry : bond 0.00279 (13580) covalent geometry : angle 0.69948 (18380) SS BOND : bond 0.00196 ( 1) SS BOND : angle 3.28546 ( 2) hydrogen bonds : bond 0.03738 ( 550) hydrogen bonds : angle 4.62627 ( 1608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1943.64 seconds wall clock time: 34 minutes 36.41 seconds (2076.41 seconds total)