Starting phenix.real_space_refine on Thu Jul 31 09:23:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k79_22697/07_2025/7k79_22697.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k79_22697/07_2025/7k79_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7k79_22697/07_2025/7k79_22697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k79_22697/07_2025/7k79_22697.map" model { file = "/net/cci-nas-00/data/ceres_data/7k79_22697/07_2025/7k79_22697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k79_22697/07_2025/7k79_22697.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 8.19, per 1000 atoms: 0.62 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: 3.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.20 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: 4.67 Time building geometry restraints manager: 3.75 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: 0.010 Normalize map: mean=0, sd=1: 16.880 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 31.870 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.180 ------------------------------------------------------------------------------- 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 : 11.21 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.103 0.008 TRP L 65 HIS 0.023 0.003 HIS L 262 PHE 0.070 0.005 PHE K 356 TYR 0.054 0.005 TYR L 172 ARG 0.028 0.004 ARG K 128 Details of bonding type rmsd hydrogen bonds : bond 0.15410 ( 550) hydrogen bonds : angle 7.62345 ( 1608) SS BOND : bond 0.00429 ( 1) SS BOND : angle 5.28956 ( 2) covalent geometry : bond 0.00931 (13580) covalent geometry : angle 1.80582 (18380) *********************** 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 : 1.743 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: 0.7211 (tpt) REVERT: O 303 GLN cc_start: 0.9040 (tt0) cc_final: 0.8778 (tt0) outliers start: 2 outliers final: 0 residues processed: 98 average time/residue: 0.2245 time to fit residues: 34.9394 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 : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 289 ASN ** K 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 142 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.057531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.049244 restraints weight = 95429.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.050477 restraints weight = 53082.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.051327 restraints weight = 34991.983| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13581 Z= 0.155 Angle : 0.815 10.790 18382 Z= 0.423 Chirality : 0.047 0.227 2044 Planarity : 0.006 0.065 2305 Dihedral : 6.650 28.253 1747 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 1.42 % Allowed : 12.35 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.19), residues: 1579 helix: -1.24 (0.16), residues: 886 sheet: -1.00 (0.90), residues: 34 loop : -2.67 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP L 65 HIS 0.006 0.001 HIS L 262 PHE 0.023 0.002 PHE L 167 TYR 0.023 0.002 TYR L 301 ARG 0.009 0.001 ARG L 146 Details of bonding type rmsd hydrogen bonds : bond 0.04734 ( 550) hydrogen bonds : angle 5.49191 ( 1608) SS BOND : bond 0.00102 ( 1) SS BOND : angle 3.06518 ( 2) covalent geometry : bond 0.00344 (13580) covalent geometry : angle 0.81440 (18380) *********************** 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 106 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 369 TRP cc_start: 0.8009 (t-100) cc_final: 0.6736 (t-100) REVERT: L 100 MET cc_start: 0.8970 (mpp) cc_final: 0.8427 (mpp) REVERT: L 103 MET cc_start: 0.8246 (mtt) cc_final: 0.7853 (mtt) REVERT: L 376 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8724 (mp0) REVERT: L 458 MET cc_start: 0.7188 (ptp) cc_final: 0.6796 (ptp) REVERT: O 119 MET cc_start: 0.8259 (ttt) cc_final: 0.7939 (tmm) REVERT: O 418 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7482 (t80) outliers start: 21 outliers final: 13 residues processed: 99 average time/residue: 0.2169 time to fit residues: 34.1324 Evaluate side-chains 86 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain O residue 565 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 135 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 129 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 141 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3663 r_free = 0.3663 target = 0.058391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.050037 restraints weight = 95274.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.051345 restraints weight = 52051.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.052218 restraints weight = 33763.102| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2391 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 : 0.705 9.485 18382 Z= 0.361 Chirality : 0.044 0.222 2044 Planarity : 0.005 0.057 2305 Dihedral : 5.716 26.203 1747 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.43 % Allowed : 15.59 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.21), residues: 1579 helix: -0.52 (0.17), residues: 878 sheet: -0.96 (0.90), residues: 34 loop : -2.37 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 65 HIS 0.006 0.001 HIS L 262 PHE 0.018 0.001 PHE L 167 TYR 0.021 0.001 TYR L 335 ARG 0.007 0.001 ARG L 146 Details of bonding type rmsd hydrogen bonds : bond 0.04058 ( 550) hydrogen bonds : angle 4.96663 ( 1608) SS BOND : bond 0.01590 ( 1) SS BOND : angle 3.31195 ( 2) covalent geometry : bond 0.00263 (13580) covalent geometry : angle 0.70420 (18380) *********************** 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: 36 poor density : 85 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 369 TRP cc_start: 0.8248 (t-100) cc_final: 0.7374 (t-100) REVERT: L 100 MET cc_start: 0.8936 (mpp) cc_final: 0.8304 (mpp) REVERT: L 103 MET cc_start: 0.8320 (mtt) cc_final: 0.7935 (mtt) REVERT: L 226 MET cc_start: 0.7410 (mmm) cc_final: 0.7140 (tpt) REVERT: L 232 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7037 (mtm110) REVERT: L 376 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8690 (mp0) REVERT: L 394 ASN cc_start: 0.7166 (OUTLIER) cc_final: 0.6876 (p0) REVERT: L 458 MET cc_start: 0.7189 (ptp) cc_final: 0.6805 (ptp) REVERT: O 119 MET cc_start: 0.8315 (ttt) cc_final: 0.8030 (tmm) REVERT: O 158 TYR cc_start: 0.7138 (OUTLIER) cc_final: 0.4965 (t80) REVERT: O 418 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.7565 (t80) REVERT: O 460 MET cc_start: 0.8194 (tpt) cc_final: 0.7968 (tpt) REVERT: N 157 MET cc_start: 0.5699 (mtt) cc_final: 0.5257 (mmp) outliers start: 36 outliers final: 17 residues processed: 114 average time/residue: 0.2262 time to fit residues: 40.3318 Evaluate side-chains 98 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 232 ARG 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 100 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 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 O residue 544 ASP 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 55 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 chunk 140 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 25 optimal weight: 0.1980 chunk 36 optimal weight: 9.9990 chunk 134 optimal weight: 0.0070 overall best weight: 0.5802 ------------------------------------------------------------------------------- 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** ** O 121 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 = 0.3703 r_free = 0.3703 target = 0.059443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.050991 restraints weight = 92597.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.052346 restraints weight = 50133.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.053251 restraints weight = 32382.776| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13581 Z= 0.109 Angle : 0.649 7.675 18382 Z= 0.334 Chirality : 0.043 0.213 2044 Planarity : 0.004 0.050 2305 Dihedral : 5.258 25.634 1747 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.51 % Allowed : 16.94 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.21), residues: 1579 helix: -0.10 (0.18), residues: 876 sheet: -1.31 (0.81), residues: 43 loop : -2.31 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP N 190 HIS 0.005 0.001 HIS L 262 PHE 0.014 0.001 PHE L 167 TYR 0.022 0.001 TYR L 301 ARG 0.004 0.000 ARG O 232 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 550) hydrogen bonds : angle 4.70070 ( 1608) SS BOND : bond 0.00604 ( 1) SS BOND : angle 2.97573 ( 2) covalent geometry : bond 0.00231 (13580) covalent geometry : angle 0.64788 (18380) *********************** 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 136 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 84 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 24 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7269 (tp) REVERT: K 369 TRP cc_start: 0.8326 (t-100) cc_final: 0.7848 (t-100) REVERT: L 115 MET cc_start: 0.8747 (mmm) cc_final: 0.8184 (mmm) REVERT: L 376 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8672 (mp0) REVERT: L 394 ASN cc_start: 0.7126 (OUTLIER) cc_final: 0.6830 (p0) REVERT: L 458 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6823 (ptp) REVERT: O 119 MET cc_start: 0.8165 (ttt) cc_final: 0.7906 (tmm) REVERT: O 158 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.4879 (t80) REVERT: O 183 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.6453 (m-80) REVERT: O 354 ASP cc_start: 0.8513 (m-30) cc_final: 0.7851 (p0) REVERT: O 418 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7571 (t80) REVERT: O 458 MET cc_start: 0.7297 (ptt) cc_final: 0.7002 (ptt) REVERT: N 157 MET cc_start: 0.5575 (mtt) cc_final: 0.5128 (mmp) outliers start: 52 outliers final: 22 residues processed: 130 average time/residue: 0.2338 time to fit residues: 46.9178 Evaluate side-chains 106 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 444 ASN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 164 TRP 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 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 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 O residue 544 ASP 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 148 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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** ** 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 = 0.3678 r_free = 0.3678 target = 0.058584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.050171 restraints weight = 93715.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.051489 restraints weight = 51159.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.052332 restraints weight = 33244.032| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13581 Z= 0.119 Angle : 0.652 9.584 18382 Z= 0.335 Chirality : 0.043 0.224 2044 Planarity : 0.004 0.049 2305 Dihedral : 5.118 24.790 1747 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.98 % Allowed : 18.49 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.21), residues: 1579 helix: 0.05 (0.18), residues: 880 sheet: -1.32 (0.89), residues: 38 loop : -2.26 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 190 HIS 0.004 0.001 HIS L 262 PHE 0.012 0.001 PHE L 167 TYR 0.022 0.001 TYR L 335 ARG 0.004 0.000 ARG L 465 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 550) hydrogen bonds : angle 4.65607 ( 1608) SS BOND : bond 0.00150 ( 1) SS BOND : angle 3.04844 ( 2) covalent geometry : bond 0.00265 (13580) covalent geometry : angle 0.65100 (18380) *********************** 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 137 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 78 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 369 TRP cc_start: 0.8339 (t-100) cc_final: 0.7749 (t-100) REVERT: L 115 MET cc_start: 0.8710 (mmm) cc_final: 0.8041 (mmm) REVERT: L 376 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8733 (mp0) REVERT: L 394 ASN cc_start: 0.7199 (OUTLIER) cc_final: 0.6452 (p0) REVERT: L 458 MET cc_start: 0.7256 (OUTLIER) cc_final: 0.6859 (ptp) REVERT: O 119 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7928 (tmm) REVERT: O 142 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7917 (pm20) REVERT: O 158 TYR cc_start: 0.6915 (OUTLIER) cc_final: 0.4750 (t80) REVERT: O 183 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.6335 (m-80) REVERT: O 418 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.7602 (t80) REVERT: O 598 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8225 (pp30) REVERT: N 157 MET cc_start: 0.5538 (mtt) cc_final: 0.5102 (mmp) outliers start: 59 outliers final: 35 residues processed: 126 average time/residue: 0.2073 time to fit residues: 41.7405 Evaluate side-chains 119 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 75 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 24 LEU 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 400 THR 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 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 61 LEU Chi-restraints excluded: chain O residue 65 TRP 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 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 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 17 THR Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 187 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 116 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 9 optimal weight: 0.0470 chunk 120 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 overall best weight: 1.0082 ------------------------------------------------------------------------------- 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** ** 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 = 0.3705 r_free = 0.3705 target = 0.059459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.050803 restraints weight = 93169.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.052178 restraints weight = 49524.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.053102 restraints weight = 31631.778| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13581 Z= 0.111 Angle : 0.644 10.253 18382 Z= 0.327 Chirality : 0.043 0.222 2044 Planarity : 0.004 0.052 2305 Dihedral : 4.994 24.742 1747 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.78 % Allowed : 20.24 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.21), residues: 1579 helix: 0.14 (0.18), residues: 879 sheet: -1.31 (0.88), residues: 38 loop : -2.19 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 190 HIS 0.004 0.001 HIS L 262 PHE 0.011 0.001 PHE N 176 TYR 0.019 0.001 TYR L 301 ARG 0.003 0.000 ARG K 128 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 550) hydrogen bonds : angle 4.55922 ( 1608) SS BOND : bond 0.00217 ( 1) SS BOND : angle 2.97074 ( 2) covalent geometry : bond 0.00243 (13580) covalent geometry : angle 0.64341 (18380) *********************** 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 138 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 82 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 369 TRP cc_start: 0.8323 (t-100) cc_final: 0.7220 (t-100) REVERT: L 115 MET cc_start: 0.8681 (mmm) cc_final: 0.8427 (mmm) REVERT: L 231 ILE cc_start: 0.8891 (tt) cc_final: 0.8672 (tp) REVERT: L 376 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8726 (mp0) REVERT: L 458 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6809 (ptp) REVERT: O 78 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.6950 (m-10) REVERT: O 119 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7900 (tmm) REVERT: O 142 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7778 (pm20) REVERT: O 158 TYR cc_start: 0.6900 (OUTLIER) cc_final: 0.4758 (t80) REVERT: O 169 MET cc_start: 0.7533 (tmm) cc_final: 0.7283 (tmm) REVERT: O 183 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.6339 (m-80) REVERT: O 354 ASP cc_start: 0.8392 (m-30) cc_final: 0.7733 (p0) REVERT: O 418 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.7585 (t80) REVERT: O 458 MET cc_start: 0.7291 (ptt) cc_final: 0.6954 (ptt) REVERT: O 598 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8060 (pp30) outliers start: 56 outliers final: 35 residues processed: 129 average time/residue: 0.2103 time to fit residues: 43.0287 Evaluate side-chains 121 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 77 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 400 THR 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 164 TRP 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 261 ILE Chi-restraints excluded: chain L residue 376 GLU 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 86 THR 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 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 526 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain O residue 598 GLN Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 187 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 125 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 420 GLN ** 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** L 189 HIS ** L 268 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.056037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.047846 restraints weight = 97068.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.049068 restraints weight = 52775.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.049895 restraints weight = 34284.033| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13581 Z= 0.239 Angle : 0.777 11.663 18382 Z= 0.404 Chirality : 0.047 0.226 2044 Planarity : 0.005 0.059 2305 Dihedral : 5.808 25.246 1747 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 4.59 % Allowed : 20.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.20), residues: 1579 helix: -0.36 (0.17), residues: 877 sheet: -0.48 (1.17), residues: 19 loop : -2.29 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 71 HIS 0.007 0.002 HIS K 108 PHE 0.022 0.002 PHE K 387 TYR 0.030 0.002 TYR L 418 ARG 0.007 0.001 ARG K 8 Details of bonding type rmsd hydrogen bonds : bond 0.04880 ( 550) hydrogen bonds : angle 5.12701 ( 1608) SS BOND : bond 0.01076 ( 1) SS BOND : angle 3.75771 ( 2) covalent geometry : bond 0.00535 (13580) covalent geometry : angle 0.77567 (18380) *********************** 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 136 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 68 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 369 TRP cc_start: 0.8342 (t-100) cc_final: 0.7522 (t-100) REVERT: L 204 MET cc_start: 0.8573 (mmm) cc_final: 0.8334 (mmm) REVERT: L 394 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.6825 (p0) REVERT: L 458 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.7089 (ptp) REVERT: O 119 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7948 (tmm) REVERT: O 142 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8010 (pm20) REVERT: O 183 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.6288 (m-80) REVERT: O 418 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.7610 (t80) outliers start: 68 outliers final: 41 residues processed: 126 average time/residue: 0.2343 time to fit residues: 46.7527 Evaluate side-chains 110 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 63 time to evaluate : 1.402 ------------------------------------------------------------------------------- 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 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 400 THR 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 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 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 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 171 ILE 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 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 526 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain O residue 596 GLU Chi-restraints excluded: chain N residue 79 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 88 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 420 GLN ** 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** L 268 HIS ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.056179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.047943 restraints weight = 96805.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.049175 restraints weight = 52893.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.049998 restraints weight = 34526.567| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13581 Z= 0.208 Angle : 0.747 12.131 18382 Z= 0.387 Chirality : 0.047 0.299 2044 Planarity : 0.005 0.047 2305 Dihedral : 5.779 24.744 1747 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 3.91 % Allowed : 22.13 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.20), residues: 1579 helix: -0.43 (0.17), residues: 882 sheet: -0.89 (1.12), residues: 20 loop : -2.25 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 71 HIS 0.007 0.001 HIS L 189 PHE 0.015 0.002 PHE N 102 TYR 0.035 0.002 TYR L 301 ARG 0.007 0.001 ARG K 8 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 550) hydrogen bonds : angle 5.08870 ( 1608) SS BOND : bond 0.00174 ( 1) SS BOND : angle 3.93270 ( 2) covalent geometry : bond 0.00471 (13580) covalent geometry : angle 0.74550 (18380) *********************** 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 127 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 69 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 369 TRP cc_start: 0.8380 (t-100) cc_final: 0.7567 (t-100) REVERT: K 393 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6390 (pttm) REVERT: L 376 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8824 (mp0) REVERT: L 394 ASN cc_start: 0.7346 (OUTLIER) cc_final: 0.6832 (p0) REVERT: L 458 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7093 (ptp) REVERT: L 460 MET cc_start: 0.8398 (tpp) cc_final: 0.8166 (tpp) REVERT: O 119 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7793 (tmm) REVERT: O 142 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8018 (pm20) REVERT: O 183 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.5899 (m-80) REVERT: O 418 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.7619 (t80) outliers start: 58 outliers final: 41 residues processed: 118 average time/residue: 0.2209 time to fit residues: 40.7935 Evaluate side-chains 116 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 67 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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 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 400 THR 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 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 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 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 183 PHE Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 244 THR Chi-restraints excluded: chain O residue 263 THR 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 526 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain O residue 596 GLU Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 148 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 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** ** L 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 552 ASN ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.057074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.048747 restraints weight = 95380.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.050016 restraints weight = 51631.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.050874 restraints weight = 33599.938| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13581 Z= 0.156 Angle : 0.707 13.234 18382 Z= 0.363 Chirality : 0.046 0.284 2044 Planarity : 0.004 0.047 2305 Dihedral : 5.554 25.824 1747 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 3.71 % Allowed : 22.67 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.21), residues: 1579 helix: -0.18 (0.17), residues: 878 sheet: -1.41 (0.90), residues: 29 loop : -2.19 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 71 HIS 0.006 0.001 HIS K 108 PHE 0.012 0.001 PHE N 102 TYR 0.025 0.002 TYR L 335 ARG 0.005 0.000 ARG K 8 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 550) hydrogen bonds : angle 4.87676 ( 1608) SS BOND : bond 0.00037 ( 1) SS BOND : angle 3.55407 ( 2) covalent geometry : bond 0.00356 (13580) covalent geometry : angle 0.70570 (18380) *********************** 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 128 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 73 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 393 LYS cc_start: 0.6841 (OUTLIER) cc_final: 0.6285 (pttm) REVERT: L 376 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8793 (mp0) REVERT: L 394 ASN cc_start: 0.7226 (OUTLIER) cc_final: 0.6577 (p0) REVERT: L 458 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.7089 (ptp) REVERT: O 119 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7767 (tmm) REVERT: O 142 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8029 (pm20) REVERT: O 183 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.5802 (m-80) REVERT: O 418 TYR cc_start: 0.8055 (OUTLIER) cc_final: 0.7686 (t80) REVERT: O 458 MET cc_start: 0.7189 (ptt) cc_final: 0.6870 (pmm) REVERT: N 157 MET cc_start: 0.5969 (mtt) cc_final: 0.5478 (mmp) outliers start: 55 outliers final: 38 residues processed: 120 average time/residue: 0.2991 time to fit residues: 56.9570 Evaluate side-chains 117 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 71 time to evaluate : 3.651 ------------------------------------------------------------------------------- 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 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 393 LYS Chi-restraints excluded: chain K residue 400 THR Chi-restraints excluded: chain K residue 407 HIS Chi-restraints excluded: chain L residue 75 ILE 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 261 ILE Chi-restraints excluded: chain L residue 341 THR 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 547 ILE Chi-restraints excluded: chain L residue 595 GLU Chi-restraints excluded: chain O residue 61 LEU 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 244 THR Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 391 PHE 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 N residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 155 optimal weight: 0.1980 chunk 51 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.059233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.050832 restraints weight = 93076.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.052161 restraints weight = 49506.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.053069 restraints weight = 31792.510| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13581 Z= 0.117 Angle : 0.693 13.274 18382 Z= 0.349 Chirality : 0.044 0.276 2044 Planarity : 0.004 0.053 2305 Dihedral : 5.111 26.388 1747 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.10 % Allowed : 23.55 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.21), residues: 1579 helix: 0.13 (0.18), residues: 877 sheet: -1.02 (1.00), residues: 28 loop : -2.18 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP K 369 HIS 0.004 0.001 HIS K 108 PHE 0.019 0.001 PHE K 352 TYR 0.015 0.001 TYR O 301 ARG 0.003 0.000 ARG O 232 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 550) hydrogen bonds : angle 4.64106 ( 1608) SS BOND : bond 0.00473 ( 1) SS BOND : angle 3.02189 ( 2) covalent geometry : bond 0.00252 (13580) covalent geometry : angle 0.69184 (18380) ********************** 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 126 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 80 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 393 LYS cc_start: 0.6873 (OUTLIER) cc_final: 0.6262 (pttm) REVERT: L 169 MET cc_start: 0.8034 (tmm) cc_final: 0.7714 (tmm) REVERT: L 376 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8719 (mp0) REVERT: L 394 ASN cc_start: 0.7271 (OUTLIER) cc_final: 0.6531 (p0) REVERT: L 458 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6950 (ptp) REVERT: O 65 TRP cc_start: 0.7395 (OUTLIER) cc_final: 0.7083 (t-100) REVERT: O 142 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7866 (pm20) REVERT: O 183 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.5853 (m-80) REVERT: O 418 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7635 (t80) REVERT: O 458 MET cc_start: 0.7231 (ptt) cc_final: 0.6863 (pmm) REVERT: N 157 MET cc_start: 0.5427 (mtt) cc_final: 0.5142 (mmp) outliers start: 46 outliers final: 33 residues processed: 118 average time/residue: 0.2266 time to fit residues: 41.8504 Evaluate side-chains 118 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 77 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 LEU 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 400 THR Chi-restraints excluded: chain K residue 407 HIS Chi-restraints excluded: chain L residue 75 ILE 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 240 LEU Chi-restraints excluded: chain L residue 341 THR 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 547 ILE Chi-restraints excluded: chain L residue 595 GLU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 65 TRP Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 100 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 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 N residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 31 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 113 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 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** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.057626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.049267 restraints weight = 93956.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.050576 restraints weight = 49995.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.051444 restraints weight = 32164.598| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13581 Z= 0.134 Angle : 0.700 13.171 18382 Z= 0.351 Chirality : 0.045 0.398 2044 Planarity : 0.004 0.050 2305 Dihedral : 5.162 25.451 1747 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 3.04 % Allowed : 23.95 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.21), residues: 1579 helix: 0.12 (0.18), residues: 878 sheet: -0.25 (1.19), residues: 20 loop : -2.12 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP K 369 HIS 0.005 0.001 HIS K 108 PHE 0.012 0.001 PHE N 176 TYR 0.028 0.001 TYR L 335 ARG 0.003 0.000 ARG K 8 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 550) hydrogen bonds : angle 4.65543 ( 1608) SS BOND : bond 0.00380 ( 1) SS BOND : angle 3.21277 ( 2) covalent geometry : bond 0.00302 (13580) covalent geometry : angle 0.69892 (18380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4495.57 seconds wall clock time: 81 minutes 55.30 seconds (4915.30 seconds total)