Starting phenix.real_space_refine on Thu Sep 26 14:14:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k79_22697/09_2024/7k79_22697.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k79_22697/09_2024/7k79_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k79_22697/09_2024/7k79_22697.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k79_22697/09_2024/7k79_22697.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k79_22697/09_2024/7k79_22697.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k79_22697/09_2024/7k79_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.36, per 1000 atoms: 0.63 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: 3.18 Conformation dependent library (CDL) restraints added in 1.7 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: 1.39 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: 3.56 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3313 1.33 - 1.45: 3032 1.45 - 1.58: 7137 1.58 - 1.70: 5 1.70 - 1.82: 93 Bond restraints: 13580 Sorted by residual: bond pdb=" CA LYS O 55 " pdb=" C LYS O 55 " ideal model delta sigma weight residual 1.523 1.591 -0.068 1.56e-02 4.11e+03 1.88e+01 bond pdb=" CA ARG K 58 " pdb=" CB ARG K 58 " ideal model delta sigma weight residual 1.527 1.592 -0.066 1.75e-02 3.27e+03 1.40e+01 bond pdb=" C TYR L 173 " pdb=" N MET L 174 " ideal model delta sigma weight residual 1.331 1.272 0.059 1.63e-02 3.76e+03 1.31e+01 bond pdb=" CA ARG N 15 " pdb=" CB ARG N 15 " ideal model delta sigma weight residual 1.531 1.578 -0.047 1.52e-02 4.33e+03 9.72e+00 bond pdb=" CA TYR K 67 " pdb=" CB TYR K 67 " ideal model delta sigma weight residual 1.526 1.556 -0.030 1.09e-02 8.42e+03 7.47e+00 ... (remaining 13575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 17405 3.68 - 7.36: 805 7.36 - 11.05: 136 11.05 - 14.73: 30 14.73 - 18.41: 4 Bond angle restraints: 18380 Sorted by residual: angle pdb=" N ILE L 606 " pdb=" CA ILE L 606 " pdb=" C ILE L 606 " ideal model delta sigma weight residual 112.83 104.34 8.49 9.90e-01 1.02e+00 7.36e+01 angle pdb=" CB ARG L 465 " pdb=" CG ARG L 465 " pdb=" CD ARG L 465 " ideal model delta sigma weight residual 111.30 128.70 -17.40 2.30e+00 1.89e-01 5.72e+01 angle pdb=" C GLU L 98 " pdb=" N CYS L 99 " pdb=" CA CYS L 99 " ideal model delta sigma weight residual 122.65 110.82 11.83 1.60e+00 3.91e-01 5.47e+01 angle pdb=" C VAL N 18 " pdb=" N ASP N 19 " pdb=" CA ASP N 19 " ideal model delta sigma weight residual 121.54 133.51 -11.97 1.91e+00 2.74e-01 3.93e+01 angle pdb=" C ARG L 214 " pdb=" N CYS L 215 " pdb=" CA CYS L 215 " ideal model delta sigma weight residual 122.49 112.88 9.61 1.55e+00 4.16e-01 3.84e+01 ... (remaining 18375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.39: 6899 18.39 - 36.77: 1038 36.77 - 55.16: 172 55.16 - 73.55: 21 73.55 - 91.93: 16 Dihedral angle restraints: 8146 sinusoidal: 3359 harmonic: 4787 Sorted by residual: dihedral pdb=" CA ARG N 186 " pdb=" C ARG N 186 " pdb=" N GLU N 187 " pdb=" CA GLU N 187 " ideal model delta harmonic sigma weight residual 180.00 144.31 35.69 0 5.00e+00 4.00e-02 5.09e+01 dihedral pdb=" CA PHE K 9 " pdb=" C PHE K 9 " pdb=" N LEU K 10 " pdb=" CA LEU K 10 " ideal model delta harmonic sigma weight residual 180.00 144.54 35.46 0 5.00e+00 4.00e-02 5.03e+01 dihedral pdb=" CB CYS L 99 " pdb=" SG CYS L 99 " pdb=" SG CYS L 215 " pdb=" CB CYS L 215 " ideal model delta sinusoidal sigma weight residual 93.00 145.08 -52.08 1 1.00e+01 1.00e-02 3.70e+01 ... (remaining 8143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1602 0.093 - 0.185: 380 0.185 - 0.278: 47 0.278 - 0.370: 14 0.370 - 0.462: 1 Chirality restraints: 2044 Sorted by residual: chirality pdb=" CB VAL O 443 " pdb=" CA VAL O 443 " pdb=" CG1 VAL O 443 " pdb=" CG2 VAL O 443 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" CG LEU L 289 " pdb=" CB LEU L 289 " pdb=" CD1 LEU L 289 " pdb=" CD2 LEU L 289 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CB ILE K 466 " pdb=" CA ILE K 466 " pdb=" CG1 ILE K 466 " pdb=" CG2 ILE K 466 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 2041 not shown) Planarity restraints: 2305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 65 " -0.046 2.00e-02 2.50e+03 3.77e-02 3.56e+01 pdb=" CG TRP L 65 " 0.103 2.00e-02 2.50e+03 pdb=" CD1 TRP L 65 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP L 65 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP L 65 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP L 65 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP L 65 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 65 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 65 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP L 65 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU O 141 " 0.026 2.00e-02 2.50e+03 5.38e-02 2.90e+01 pdb=" CD GLU O 141 " -0.093 2.00e-02 2.50e+03 pdb=" OE1 GLU O 141 " 0.033 2.00e-02 2.50e+03 pdb=" OE2 GLU O 141 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP O 346 " -0.042 2.00e-02 2.50e+03 3.36e-02 2.82e+01 pdb=" CG TRP O 346 " 0.088 2.00e-02 2.50e+03 pdb=" CD1 TRP O 346 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP O 346 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP O 346 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP O 346 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP O 346 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 346 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 346 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP O 346 " -0.018 2.00e-02 2.50e+03 ... (remaining 2302 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1539 2.74 - 3.28: 13707 3.28 - 3.82: 22487 3.82 - 4.36: 25688 4.36 - 4.90: 41162 Nonbonded interactions: 104583 Sorted by model distance: nonbonded pdb=" OG SER L 393 " pdb=" OD1 ASN L 395 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR K 360 " pdb=" O LYS K 441 " model vdw 2.197 3.040 nonbonded pdb=" OE1 GLU L 69 " pdb=" OG1 THR L 73 " model vdw 2.225 3.040 nonbonded pdb=" O ASP O 300 " pdb=" OG SER O 304 " model vdw 2.230 3.040 nonbonded pdb=" O LYS K 60 " pdb=" NH1 ARG K 64 " model vdw 2.247 3.120 ... (remaining 104578 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'L' and (resid 54 through 317 or (resid 318 through 319 and (name N or na \ me CA or name C or name O or name CB )) or resid 339 or (resid 340 and (name N o \ r name CA or name C or name O or name CB )) or resid 341 through 567 or resid 58 \ 9 through 608)) selection = (chain 'O' and (resid 54 through 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 567 or resid 589 through 608)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.340 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: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.330 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.940 ------------------------------------------------------------------------------- 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 13580 Z= 0.584 Angle : 1.806 18.409 18380 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 *********************** 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 fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 2.012 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: 0.2716 time to fit residues: 42.3642 Evaluate side-chains 79 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 13580 Z= 0.217 Angle : 0.814 10.790 18380 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 *********************** 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 fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 369 TRP cc_start: 0.7950 (t-100) cc_final: 0.6709 (t-100) REVERT: L 100 MET cc_start: 0.8786 (mpp) cc_final: 0.8262 (mpp) REVERT: L 103 MET cc_start: 0.8006 (mtt) cc_final: 0.7657 (mtt) REVERT: L 376 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8690 (mp0) REVERT: L 458 MET cc_start: 0.7114 (ptp) cc_final: 0.6769 (ptp) REVERT: O 119 MET cc_start: 0.8239 (ttt) cc_final: 0.7910 (tmm) REVERT: O 418 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.7247 (t80) outliers start: 21 outliers final: 13 residues processed: 99 average time/residue: 0.2094 time to fit residues: 33.1282 Evaluate side-chains 86 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 1.505 ------------------------------------------------------------------------------- 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 79 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 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 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 ** L 268 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13580 Z= 0.232 Angle : 0.737 7.787 18380 Z= 0.382 Chirality : 0.045 0.227 2044 Planarity : 0.005 0.057 2305 Dihedral : 6.021 25.779 1747 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 3.24 % Allowed : 16.60 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.08 (0.20), residues: 1579 helix: -0.64 (0.17), residues: 880 sheet: -1.23 (0.87), residues: 34 loop : -2.37 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 346 HIS 0.005 0.001 HIS L 262 PHE 0.017 0.002 PHE L 167 TYR 0.023 0.002 TYR L 335 ARG 0.009 0.001 ARG K 363 *********************** 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 126 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 78 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 65 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8268 (t80) REVERT: L 115 MET cc_start: 0.8909 (mmm) cc_final: 0.8484 (mmm) REVERT: L 231 ILE cc_start: 0.8898 (tt) cc_final: 0.8632 (tp) REVERT: L 376 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8744 (mp0) REVERT: L 394 ASN cc_start: 0.7255 (OUTLIER) cc_final: 0.6827 (p0) REVERT: L 458 MET cc_start: 0.7152 (ptp) cc_final: 0.6815 (ptp) REVERT: O 119 MET cc_start: 0.8274 (ttt) cc_final: 0.7971 (tmm) REVERT: O 183 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.6043 (m-80) REVERT: O 418 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.7390 (t80) REVERT: O 460 MET cc_start: 0.8390 (tpt) cc_final: 0.8125 (tpt) outliers start: 48 outliers final: 21 residues processed: 118 average time/residue: 0.2169 time to fit residues: 40.0443 Evaluate side-chains 98 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 72 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 65 TYR Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 407 HIS Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 261 ILE Chi-restraints excluded: chain L residue 376 GLU Chi-restraints excluded: chain L residue 394 ASN Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 418 TYR 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 183 PHE 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 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain O residue 565 LEU Chi-restraints excluded: chain N residue 79 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 9.9990 chunk 108 optimal weight: 0.2980 chunk 74 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 144 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 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 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 303 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13580 Z= 0.154 Angle : 0.667 8.611 18380 Z= 0.344 Chirality : 0.043 0.221 2044 Planarity : 0.004 0.052 2305 Dihedral : 5.408 26.030 1747 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.17 % Allowed : 18.56 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.66 (0.21), residues: 1579 helix: -0.22 (0.18), residues: 877 sheet: -1.05 (0.88), residues: 34 loop : -2.31 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 71 HIS 0.005 0.001 HIS L 262 PHE 0.013 0.001 PHE L 167 TYR 0.023 0.001 TYR O 105 ARG 0.004 0.001 ARG L 465 *********************** 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 132 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 85 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 115 MET cc_start: 0.8869 (mmm) cc_final: 0.8431 (mmm) REVERT: L 376 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8665 (mp0) REVERT: L 458 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6848 (ptp) REVERT: O 119 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7961 (tmm) REVERT: O 158 TYR cc_start: 0.6676 (OUTLIER) cc_final: 0.4557 (t80) REVERT: O 183 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.6157 (m-80) REVERT: O 418 TYR cc_start: 0.7714 (OUTLIER) cc_final: 0.7407 (t80) REVERT: O 458 MET cc_start: 0.7362 (ptt) cc_final: 0.7091 (ptt) REVERT: N 157 MET cc_start: 0.5401 (mtt) cc_final: 0.5120 (mmp) outliers start: 47 outliers final: 24 residues processed: 126 average time/residue: 0.2468 time to fit residues: 48.0062 Evaluate side-chains 106 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 76 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 128 ARG Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 400 THR 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 414 LEU 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 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 357 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 596 GLU Chi-restraints excluded: chain N residue 79 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 105 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13580 Z= 0.288 Angle : 0.734 12.923 18380 Z= 0.381 Chirality : 0.046 0.225 2044 Planarity : 0.005 0.050 2305 Dihedral : 5.732 23.939 1747 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 4.59 % Allowed : 20.04 % Favored : 75.37 % 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 (0.21), residues: 1579 helix: -0.36 (0.17), residues: 880 sheet: -1.30 (0.94), residues: 29 loop : -2.28 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP N 190 HIS 0.005 0.001 HIS K 108 PHE 0.016 0.002 PHE K 387 TYR 0.026 0.002 TYR L 418 ARG 0.006 0.001 ARG K 363 *********************** 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 138 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 70 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 303 TYR cc_start: 0.6225 (OUTLIER) cc_final: 0.4133 (t80) REVERT: L 115 MET cc_start: 0.8905 (mmm) cc_final: 0.8667 (mmm) REVERT: L 231 ILE cc_start: 0.8967 (tt) cc_final: 0.8754 (tp) REVERT: L 394 ASN cc_start: 0.7376 (OUTLIER) cc_final: 0.6604 (p0) REVERT: L 458 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6962 (ptp) REVERT: O 119 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7991 (tmm) REVERT: O 142 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7890 (pm20) REVERT: O 183 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.6304 (m-80) REVERT: O 418 TYR cc_start: 0.7844 (OUTLIER) cc_final: 0.7407 (t80) outliers start: 68 outliers final: 35 residues processed: 128 average time/residue: 0.2196 time to fit residues: 43.7040 Evaluate side-chains 111 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 69 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 128 ARG Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 303 TYR 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 136 LEU Chi-restraints excluded: chain L residue 164 TRP 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 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 263 THR Chi-restraints excluded: chain O residue 357 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 N residue 79 VAL Chi-restraints excluded: chain N residue 180 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 348 ASN K 371 ASN ** K 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13580 Z= 0.173 Angle : 0.676 10.997 18380 Z= 0.344 Chirality : 0.044 0.219 2044 Planarity : 0.004 0.048 2305 Dihedral : 5.361 24.671 1747 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.12 % Allowed : 21.73 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.51 (0.21), residues: 1579 helix: -0.14 (0.18), residues: 885 sheet: -0.06 (1.19), residues: 19 loop : -2.21 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 346 HIS 0.004 0.001 HIS K 108 PHE 0.011 0.001 PHE O 167 TYR 0.017 0.001 TYR O 137 ARG 0.004 0.000 ARG L 465 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 79 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 115 MET cc_start: 0.8850 (mmm) cc_final: 0.8249 (mmm) REVERT: L 394 ASN cc_start: 0.7290 (OUTLIER) cc_final: 0.6455 (p0) REVERT: L 458 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6912 (ptp) REVERT: O 78 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.7739 (m-10) REVERT: O 119 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7844 (tmm) REVERT: O 142 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7799 (pm20) REVERT: O 183 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.6063 (m-80) REVERT: O 315 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: O 418 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.7452 (t80) outliers start: 61 outliers final: 41 residues processed: 132 average time/residue: 0.2272 time to fit residues: 46.2840 Evaluate side-chains 122 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 73 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 128 ARG Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 173 ASP 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 136 LEU Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 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 75 ILE Chi-restraints excluded: chain O residue 78 TYR Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 119 MET Chi-restraints excluded: chain O residue 141 GLU Chi-restraints excluded: chain O residue 142 GLN Chi-restraints excluded: chain O residue 143 TYR Chi-restraints excluded: chain O residue 158 TYR Chi-restraints excluded: chain O residue 183 PHE Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 315 GLU Chi-restraints excluded: chain O residue 357 GLN Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 432 ILE Chi-restraints excluded: chain O residue 446 PHE Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain O residue 596 GLU Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 180 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 268 HIS ** L 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13580 Z= 0.222 Angle : 0.700 13.914 18380 Z= 0.357 Chirality : 0.044 0.220 2044 Planarity : 0.004 0.062 2305 Dihedral : 5.410 24.319 1747 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 4.93 % Allowed : 22.13 % Favored : 72.94 % 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: -1.52 (0.21), residues: 1579 helix: -0.13 (0.18), residues: 879 sheet: -0.11 (1.15), residues: 19 loop : -2.22 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 346 HIS 0.005 0.001 HIS K 108 PHE 0.011 0.001 PHE N 102 TYR 0.024 0.002 TYR L 335 ARG 0.007 0.001 ARG K 363 *********************** 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 146 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 73 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 393 LYS cc_start: 0.7082 (OUTLIER) cc_final: 0.6563 (pttm) REVERT: L 115 MET cc_start: 0.8782 (mmm) cc_final: 0.8422 (mmm) REVERT: L 376 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8795 (mp0) REVERT: L 394 ASN cc_start: 0.7368 (OUTLIER) cc_final: 0.6753 (p0) REVERT: L 458 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.7006 (ptp) REVERT: O 78 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.7762 (m-10) REVERT: O 119 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7735 (tmm) REVERT: O 142 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7842 (pm20) REVERT: O 183 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.6001 (m-80) REVERT: O 315 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: O 418 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.7466 (t80) REVERT: O 458 MET cc_start: 0.7414 (ptt) cc_final: 0.6991 (pmm) REVERT: O 598 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8339 (pp30) outliers start: 73 outliers final: 51 residues processed: 138 average time/residue: 0.2172 time to fit residues: 46.5355 Evaluate side-chains 132 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 70 time to evaluate : 1.566 ------------------------------------------------------------------------------- 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 83 LEU Chi-restraints excluded: chain K residue 128 ARG Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 173 ASP Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 334 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 136 LEU Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 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 75 ILE Chi-restraints excluded: chain O residue 78 TYR Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 119 MET Chi-restraints excluded: chain O residue 142 GLN Chi-restraints excluded: chain O residue 143 TYR Chi-restraints excluded: chain O residue 158 TYR Chi-restraints excluded: chain O residue 183 PHE Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 312 LEU Chi-restraints excluded: chain O residue 315 GLU Chi-restraints excluded: chain O residue 357 GLN Chi-restraints excluded: chain O residue 381 GLN Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 432 ILE Chi-restraints excluded: chain O residue 446 PHE Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 526 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain O residue 596 GLU Chi-restraints excluded: chain O residue 598 GLN Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 180 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 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 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 461 GLN ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13580 Z= 0.274 Angle : 0.735 12.434 18380 Z= 0.377 Chirality : 0.046 0.289 2044 Planarity : 0.005 0.076 2305 Dihedral : 5.619 24.208 1747 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 4.79 % Allowed : 22.67 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.68 (0.21), residues: 1579 helix: -0.28 (0.17), residues: 879 sheet: -0.25 (1.11), residues: 19 loop : -2.26 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 71 HIS 0.006 0.001 HIS K 108 PHE 0.013 0.002 PHE N 102 TYR 0.025 0.002 TYR L 418 ARG 0.005 0.001 ARG K 8 *********************** 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 141 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 70 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 393 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6806 (pttm) REVERT: L 376 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8834 (mp0) REVERT: L 394 ASN cc_start: 0.7370 (OUTLIER) cc_final: 0.6754 (p0) REVERT: L 458 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.7027 (ptp) REVERT: O 78 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.7681 (m-10) REVERT: O 119 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7750 (tmm) REVERT: O 142 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7891 (pm20) REVERT: O 183 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.5945 (m-80) REVERT: O 315 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: O 418 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.7426 (t80) REVERT: O 598 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8185 (pp30) REVERT: N 157 MET cc_start: 0.5764 (mtt) cc_final: 0.5358 (mmp) outliers start: 71 outliers final: 49 residues processed: 133 average time/residue: 0.2207 time to fit residues: 45.2265 Evaluate side-chains 129 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 69 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 128 ARG Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 173 ASP Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 334 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 136 LEU Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 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 503 LYS Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 547 ILE Chi-restraints excluded: chain L residue 595 GLU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 78 TYR Chi-restraints excluded: chain O residue 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 312 LEU Chi-restraints excluded: chain O residue 315 GLU Chi-restraints excluded: chain O residue 357 GLN Chi-restraints excluded: chain O residue 381 GLN Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 432 ILE Chi-restraints excluded: chain O residue 446 PHE Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 526 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain O residue 596 GLU Chi-restraints excluded: chain O residue 598 GLN Chi-restraints excluded: chain N residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 141 optimal weight: 0.1980 chunk 85 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 150 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 371 ASN ** 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** L 552 ASN ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13580 Z= 0.162 Angle : 0.699 12.763 18380 Z= 0.352 Chirality : 0.044 0.275 2044 Planarity : 0.004 0.054 2305 Dihedral : 5.146 25.479 1747 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.85 % Allowed : 24.29 % Favored : 71.86 % 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: -1.27 (0.21), residues: 1579 helix: 0.07 (0.18), residues: 878 sheet: 0.25 (1.16), residues: 19 loop : -2.11 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 71 HIS 0.005 0.001 HIS K 108 PHE 0.021 0.001 PHE O 597 TYR 0.025 0.001 TYR L 335 ARG 0.005 0.000 ARG L 465 *********************** 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 139 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 82 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 369 TRP cc_start: 0.8144 (t-100) cc_final: 0.7264 (t-100) REVERT: K 393 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6523 (pttm) REVERT: L 376 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8713 (mp0) REVERT: L 394 ASN cc_start: 0.7284 (OUTLIER) cc_final: 0.6683 (p0) REVERT: L 458 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6950 (ptp) REVERT: O 78 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7001 (m-10) REVERT: O 119 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7660 (tmm) REVERT: O 142 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7787 (pm20) REVERT: O 158 TYR cc_start: 0.6729 (OUTLIER) cc_final: 0.4608 (t80) REVERT: O 183 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.5612 (m-80) REVERT: O 418 TYR cc_start: 0.7714 (OUTLIER) cc_final: 0.7434 (t80) REVERT: O 458 MET cc_start: 0.7364 (ptt) cc_final: 0.6978 (pmm) REVERT: O 598 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8477 (pp30) outliers start: 57 outliers final: 40 residues processed: 130 average time/residue: 0.2191 time to fit residues: 44.0552 Evaluate side-chains 131 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 80 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 128 ARG Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 371 ASN 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 136 LEU Chi-restraints excluded: chain L residue 164 TRP Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 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 595 GLU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 78 TYR Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 119 MET Chi-restraints excluded: chain O residue 142 GLN Chi-restraints excluded: chain O residue 143 TYR Chi-restraints excluded: chain O residue 158 TYR Chi-restraints excluded: chain O residue 183 PHE Chi-restraints excluded: chain O residue 215 CYS Chi-restraints excluded: chain O residue 240 LEU Chi-restraints excluded: chain O residue 343 VAL Chi-restraints excluded: chain O residue 357 GLN Chi-restraints excluded: chain O residue 381 GLN Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 432 ILE Chi-restraints excluded: chain O residue 446 PHE Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 526 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain O residue 596 GLU Chi-restraints excluded: chain O residue 598 GLN Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 144 optimal weight: 7.9990 chunk 125 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** L 189 HIS ** L 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13580 Z= 0.178 Angle : 0.717 13.093 18380 Z= 0.357 Chirality : 0.045 0.389 2044 Planarity : 0.004 0.060 2305 Dihedral : 5.178 26.128 1747 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.64 % Allowed : 24.63 % Favored : 71.73 % 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: 0.13 (0.18), residues: 879 sheet: -0.07 (1.17), residues: 20 loop : -2.14 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 71 HIS 0.005 0.001 HIS L 189 PHE 0.016 0.001 PHE O 597 TYR 0.018 0.001 TYR K 467 ARG 0.005 0.000 ARG L 465 ********************** 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 132 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 78 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 369 TRP cc_start: 0.8186 (t-100) cc_final: 0.7236 (t-100) REVERT: K 393 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6553 (pttm) REVERT: L 204 MET cc_start: 0.7946 (mmp) cc_final: 0.7627 (mmm) REVERT: L 376 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8755 (mp0) REVERT: L 394 ASN cc_start: 0.7296 (OUTLIER) cc_final: 0.6735 (p0) REVERT: L 458 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.7000 (ptp) REVERT: O 119 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7673 (tmm) REVERT: O 142 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7813 (pm20) REVERT: O 158 TYR cc_start: 0.6790 (OUTLIER) cc_final: 0.4645 (t80) REVERT: O 183 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.5736 (m-80) REVERT: O 418 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.7431 (t80) REVERT: O 458 MET cc_start: 0.7327 (ptt) cc_final: 0.6944 (pmm) REVERT: O 598 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8399 (pp30) outliers start: 54 outliers final: 40 residues processed: 125 average time/residue: 0.2039 time to fit residues: 39.9641 Evaluate side-chains 127 residues out of total 1497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 77 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 128 ARG Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 173 ASP Chi-restraints excluded: chain K residue 199 VAL 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 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 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 493 THR 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 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 343 VAL Chi-restraints excluded: chain O residue 357 GLN Chi-restraints excluded: chain O residue 381 GLN Chi-restraints excluded: chain O residue 418 TYR Chi-restraints excluded: chain O residue 432 ILE Chi-restraints excluded: chain O residue 446 PHE Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 526 LEU Chi-restraints excluded: chain O residue 544 ASP Chi-restraints excluded: chain O residue 596 GLU Chi-restraints excluded: chain O residue 598 GLN Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 125 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 371 ASN ** L 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 598 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.059668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.051249 restraints weight = 91779.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.052594 restraints weight = 48768.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.053493 restraints weight = 31236.857| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13580 Z= 0.157 Angle : 0.708 15.983 18380 Z= 0.348 Chirality : 0.045 0.386 2044 Planarity : 0.004 0.054 2305 Dihedral : 4.998 25.557 1747 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.91 % Allowed : 24.49 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.17 (0.21), residues: 1579 helix: 0.20 (0.18), residues: 884 sheet: -0.65 (1.03), residues: 28 loop : -2.16 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP O 65 HIS 0.004 0.001 HIS K 108 PHE 0.011 0.001 PHE O 167 TYR 0.028 0.001 TYR L 335 ARG 0.005 0.000 ARG L 465 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2135.74 seconds wall clock time: 39 minutes 52.52 seconds (2392.52 seconds total)