Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 18:24:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpc_32682/04_2023/7wpc_32682_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpc_32682/04_2023/7wpc_32682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpc_32682/04_2023/7wpc_32682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpc_32682/04_2023/7wpc_32682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpc_32682/04_2023/7wpc_32682_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpc_32682/04_2023/7wpc_32682_neut.pdb" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.012 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 44 5.16 5 Cl 1 4.86 5 C 5162 2.51 5 N 1335 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "A ARG 495": "NH1" <-> "NH2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "B PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B ARG 490": "NH1" <-> "NH2" Residue "B ARG 495": "NH1" <-> "NH2" Residue "B GLU 513": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D GLU 310": "OE1" <-> "OE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D GLU 433": "OE1" <-> "OE2" Residue "D GLU 457": "OE1" <-> "OE2" Residue "D GLU 495": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D ARG 559": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8057 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1582 Classifications: {'peptide': 197} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 183} Chain: "B" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1518 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 10, 'TRANS': 177} Chain breaks: 3 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.71, per 1000 atoms: 0.58 Number of scatterers: 8057 At special positions: 0 Unit cell: (99.704, 98.056, 127.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Cl 1 17.00 S 44 16.00 O 1514 8.00 N 1335 7.00 C 5162 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.04 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG C 1 " - " ASN A 340 " " NAG D 903 " - " ASN D 90 " " NAG D 904 " - " ASN D 322 " " NAG D 905 " - " ASN D 546 " " NAG E 1 " - " ASN B 340 " Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 902 " pdb="ZN ZN D 902 " - pdb=" NE2 HIS D 374 " 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1848 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 8 sheets defined 44.5% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.958A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.992A pdb=" N ASN A 367 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU A 368 " --> pdb=" O LEU A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 368' Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 363 through 368 removed outlier: 3.972A pdb=" N TYR B 366 " --> pdb=" O SER B 363 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU B 368 " --> pdb=" O LEU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.557A pdb=" N ASP B 386 " --> pdb=" O LYS B 383 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU B 387 " --> pdb=" O LEU B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 387' Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.509A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 80 removed outlier: 3.809A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.047A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 removed outlier: 3.590A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.611A pdb=" N ALA D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.718A pdb=" N ARG D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 176 through 194 removed outlier: 3.558A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.503A pdb=" N TYR D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 208 Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'D' and resid 222 through 227 Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.646A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.929A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 298 Processing helix chain 'D' and resid 303 through 316 Processing helix chain 'D' and resid 324 through 330 removed outlier: 3.640A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.604A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.795A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.728A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.536A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.501A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.648A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.594A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 538 through 542' Processing helix chain 'D' and resid 550 through 559 removed outlier: 3.809A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.884A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.506A pdb=" N TYR D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.693A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 375 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA3, first strand: chain 'A' and resid 470 through 471 removed outlier: 3.579A pdb=" N TYR A 486 " --> pdb=" O TYR A 470 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 353 through 355 removed outlier: 4.169A pdb=" N LYS B 375 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AA6, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AA7, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.772A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.661A pdb=" N ARG D 357 " --> pdb=" O TRP D 349 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 280 hydrogen bonds defined for protein. 795 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: 2.15 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2559 1.35 - 1.47: 2162 1.47 - 1.59: 3493 1.59 - 1.71: 0 1.71 - 1.83: 65 Bond restraints: 8279 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" N VAL B 480 " pdb=" CA VAL B 480 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.31e+00 bond pdb=" N TYR B 486 " pdb=" CA TYR B 486 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.19e-02 7.06e+03 7.59e+00 bond pdb=" N LEU B 514 " pdb=" CA LEU B 514 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.23e-02 6.61e+03 5.54e+00 bond pdb=" N CYS B 485 " pdb=" CA CYS B 485 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.38e+00 ... (remaining 8274 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.23: 310 107.23 - 113.93: 4383 113.93 - 120.63: 3426 120.63 - 127.32: 3021 127.32 - 134.02: 107 Bond angle restraints: 11247 Sorted by residual: angle pdb=" N VAL D 339 " pdb=" CA VAL D 339 " pdb=" C VAL D 339 " ideal model delta sigma weight residual 113.71 108.44 5.27 9.50e-01 1.11e+00 3.07e+01 angle pdb=" CA GLY B 482 " pdb=" C GLY B 482 " pdb=" O GLY B 482 " ideal model delta sigma weight residual 122.01 118.07 3.94 9.70e-01 1.06e+00 1.65e+01 angle pdb=" N GLY A 499 " pdb=" CA GLY A 499 " pdb=" C GLY A 499 " ideal model delta sigma weight residual 111.34 118.64 -7.30 1.82e+00 3.02e-01 1.61e+01 angle pdb=" N GLU D 145 " pdb=" CA GLU D 145 " pdb=" C GLU D 145 " ideal model delta sigma weight residual 109.81 118.47 -8.66 2.21e+00 2.05e-01 1.54e+01 angle pdb=" CA PHE B 512 " pdb=" CB PHE B 512 " pdb=" CG PHE B 512 " ideal model delta sigma weight residual 113.80 117.43 -3.63 1.00e+00 1.00e+00 1.32e+01 ... (remaining 11242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 4286 17.40 - 34.79: 440 34.79 - 52.19: 90 52.19 - 69.59: 14 69.59 - 86.98: 4 Dihedral angle restraints: 4834 sinusoidal: 1954 harmonic: 2880 Sorted by residual: dihedral pdb=" CA PHE A 372 " pdb=" C PHE A 372 " pdb=" N THR A 373 " pdb=" CA THR A 373 " ideal model delta harmonic sigma weight residual 180.00 159.39 20.61 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA PHE A 371 " pdb=" C PHE A 371 " pdb=" N PHE A 372 " pdb=" CA PHE A 372 " ideal model delta harmonic sigma weight residual 180.00 -161.17 -18.83 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" C ASN B 484 " pdb=" N ASN B 484 " pdb=" CA ASN B 484 " pdb=" CB ASN B 484 " ideal model delta harmonic sigma weight residual -122.60 -131.62 9.02 0 2.50e+00 1.60e-01 1.30e+01 ... (remaining 4831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1033 0.064 - 0.129: 152 0.129 - 0.193: 6 0.193 - 0.258: 4 0.258 - 0.322: 2 Chirality restraints: 1197 Sorted by residual: chirality pdb=" CA LEU B 515 " pdb=" N LEU B 515 " pdb=" C LEU B 515 " pdb=" CB LEU B 515 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 2.35e+00 chirality pdb=" CA ASN B 484 " pdb=" N ASN B 484 " pdb=" C ASN B 484 " pdb=" CB ASN B 484 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1194 not shown) Planarity restraints: 1453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 564 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO D 565 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 565 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 565 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 499 " -0.040 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO D 500 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 500 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 500 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 582 " -0.037 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO D 583 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 583 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 583 " -0.031 5.00e-02 4.00e+02 ... (remaining 1450 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1689 2.78 - 3.31: 6569 3.31 - 3.84: 13351 3.84 - 4.37: 15369 4.37 - 4.90: 26616 Nonbonded interactions: 63594 Sorted by model distance: nonbonded pdb=" OE2 GLU D 402 " pdb="ZN ZN D 902 " model vdw 2.253 2.230 nonbonded pdb=" O THR D 118 " pdb=" OG1 THR D 122 " model vdw 2.303 2.440 nonbonded pdb=" OG1 THR B 412 " pdb=" OD2 ASP B 417 " model vdw 2.337 2.440 nonbonded pdb=" OG SER D 109 " pdb=" OD1 ASP D 111 " model vdw 2.349 2.440 nonbonded pdb=" OG SER B 466 " pdb=" OE1 GLU B 468 " model vdw 2.354 2.440 ... (remaining 63589 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 329 through 369 or resid 372 through 499 or resid 501 thro \ ugh 515 or resid 523 through 525)) selection = (chain 'B' and resid 329 through 525) } ncs_group { reference = chain 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 5.240 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: 0.000 Extract box with map and model: 22.250 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 25.460 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 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 : 0.004 0.064 8279 Z= 0.237 Angle : 0.720 9.460 11247 Z= 0.420 Chirality : 0.048 0.322 1197 Planarity : 0.006 0.063 1448 Dihedral : 14.233 86.984 2956 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % 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: -4.19 (0.20), residues: 968 helix: -2.98 (0.17), residues: 385 sheet: -0.65 (0.53), residues: 69 loop : -2.98 (0.22), residues: 514 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 0.913 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 205 average time/residue: 1.0987 time to fit residues: 240.5417 Evaluate side-chains 169 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 0.908 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.3062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 49 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 0.0770 chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 0.2980 chunk 87 optimal weight: 0.1980 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 471 GLN A 474 ASN A 478 ASN B 357 ASN ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN B 484 ASN B 503 GLN D 33 ASN D 51 ASN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN D 121 ASN D 154 ASN D 194 ASN D 221 GLN D 277 ASN D 300 GLN D 378 HIS D 522 GLN D 531 GLN D 599 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 8279 Z= 0.247 Angle : 0.543 7.893 11247 Z= 0.280 Chirality : 0.044 0.214 1197 Planarity : 0.005 0.051 1448 Dihedral : 4.174 19.049 1072 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % 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: -2.61 (0.24), residues: 968 helix: -1.37 (0.24), residues: 400 sheet: -0.37 (0.58), residues: 72 loop : -2.27 (0.25), residues: 496 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 0.984 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 187 average time/residue: 1.2146 time to fit residues: 241.4776 Evaluate side-chains 177 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 170 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 3 average time/residue: 0.8295 time to fit residues: 4.1036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.0060 chunk 27 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 87 optimal weight: 0.2980 chunk 94 optimal weight: 0.3980 chunk 77 optimal weight: 0.6980 chunk 86 optimal weight: 0.1980 chunk 29 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN A 445 ASN A 457 ASN A 474 ASN B 391 ASN ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN D 194 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 8279 Z= 0.196 Angle : 0.499 6.100 11247 Z= 0.256 Chirality : 0.043 0.212 1197 Planarity : 0.004 0.052 1448 Dihedral : 4.048 19.486 1072 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % 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: -1.87 (0.25), residues: 968 helix: -0.50 (0.26), residues: 398 sheet: 0.03 (0.61), residues: 72 loop : -2.11 (0.25), residues: 498 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 0.844 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 7 residues processed: 174 average time/residue: 1.1624 time to fit residues: 215.5909 Evaluate side-chains 175 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 168 time to evaluate : 0.821 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 1 average time/residue: 0.1497 time to fit residues: 1.4075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.0970 chunk 65 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 0.0770 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 414 ASN ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 8279 Z= 0.268 Angle : 0.531 6.242 11247 Z= 0.269 Chirality : 0.044 0.209 1197 Planarity : 0.004 0.039 1448 Dihedral : 4.215 19.923 1072 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 3.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.26), residues: 968 helix: -0.20 (0.26), residues: 409 sheet: -0.00 (0.61), residues: 70 loop : -1.97 (0.25), residues: 489 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 176 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 193 average time/residue: 1.1467 time to fit residues: 236.0364 Evaluate side-chains 181 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 168 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 4 average time/residue: 0.9232 time to fit residues: 5.1901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 79 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN A 502 HIS ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN D 194 ASN D 239 HIS D 388 GLN ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.107 8279 Z= 0.463 Angle : 0.628 9.174 11247 Z= 0.316 Chirality : 0.049 0.209 1197 Planarity : 0.005 0.045 1448 Dihedral : 4.686 24.955 1072 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 4.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.26), residues: 968 helix: -0.24 (0.26), residues: 404 sheet: -0.05 (0.61), residues: 70 loop : -1.90 (0.25), residues: 494 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 172 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 16 residues processed: 194 average time/residue: 1.1080 time to fit residues: 229.6227 Evaluate side-chains 195 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 0.904 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 0.6189 time to fit residues: 4.6991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 77 optimal weight: 0.0060 chunk 43 optimal weight: 0.2980 chunk 7 optimal weight: 0.0980 chunk 30 optimal weight: 0.0000 chunk 48 optimal weight: 4.9990 chunk 89 optimal weight: 0.4980 overall best weight: 0.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN D 194 ASN D 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8279 Z= 0.174 Angle : 0.526 9.406 11247 Z= 0.264 Chirality : 0.043 0.210 1197 Planarity : 0.004 0.048 1448 Dihedral : 4.244 20.667 1072 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % 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: -1.21 (0.26), residues: 968 helix: 0.20 (0.27), residues: 395 sheet: 0.03 (0.62), residues: 72 loop : -1.81 (0.25), residues: 501 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 173 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 187 average time/residue: 1.1993 time to fit residues: 238.3776 Evaluate side-chains 182 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 171 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.0871 time to fit residues: 1.4302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 0.0980 chunk 51 optimal weight: 0.3980 chunk 92 optimal weight: 0.3980 chunk 57 optimal weight: 0.5980 chunk 56 optimal weight: 0.3980 chunk 42 optimal weight: 0.5980 chunk 36 optimal weight: 10.0000 chunk 55 optimal weight: 0.2980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN D 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 8279 Z= 0.234 Angle : 0.531 9.056 11247 Z= 0.269 Chirality : 0.044 0.209 1197 Planarity : 0.004 0.052 1448 Dihedral : 4.248 22.662 1072 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % 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: -1.14 (0.26), residues: 968 helix: 0.23 (0.27), residues: 399 sheet: 0.10 (0.60), residues: 72 loop : -1.77 (0.26), residues: 497 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 192 average time/residue: 1.1940 time to fit residues: 243.5561 Evaluate side-chains 189 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 177 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 1.6457 time to fit residues: 4.7199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 0.0670 chunk 8 optimal weight: 0.4980 chunk 72 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 0.0980 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN D 388 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 8279 Z= 0.241 Angle : 0.544 9.137 11247 Z= 0.275 Chirality : 0.044 0.209 1197 Planarity : 0.004 0.058 1448 Dihedral : 4.281 20.859 1072 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % 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: -1.11 (0.27), residues: 968 helix: 0.23 (0.27), residues: 399 sheet: 0.17 (0.60), residues: 70 loop : -1.71 (0.26), residues: 499 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 176 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 187 average time/residue: 1.1861 time to fit residues: 236.1225 Evaluate side-chains 187 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 175 time to evaluate : 0.859 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 2 average time/residue: 0.8930 time to fit residues: 3.1268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.0570 chunk 88 optimal weight: 0.0970 chunk 51 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 85 optimal weight: 0.0770 chunk 56 optimal weight: 0.9980 chunk 91 optimal weight: 0.2980 overall best weight: 0.2054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8279 Z= 0.181 Angle : 0.524 9.156 11247 Z= 0.262 Chirality : 0.043 0.210 1197 Planarity : 0.004 0.059 1448 Dihedral : 4.132 20.842 1072 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.27), residues: 968 helix: 0.46 (0.28), residues: 390 sheet: 0.27 (0.60), residues: 72 loop : -1.63 (0.26), residues: 506 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 176 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 186 average time/residue: 1.2945 time to fit residues: 255.3791 Evaluate side-chains 183 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 171 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 1.6758 time to fit residues: 5.0239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.1980 chunk 43 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 88 optimal weight: 0.0570 chunk 76 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 0.1980 overall best weight: 0.2898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 GLN D 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8279 Z= 0.219 Angle : 0.542 8.844 11247 Z= 0.272 Chirality : 0.044 0.209 1197 Planarity : 0.004 0.055 1448 Dihedral : 4.177 21.733 1072 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.27), residues: 968 helix: 0.48 (0.27), residues: 397 sheet: 0.28 (0.59), residues: 70 loop : -1.60 (0.26), residues: 501 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 183 average time/residue: 1.1895 time to fit residues: 231.3443 Evaluate side-chains 183 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 0.839 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 3 average time/residue: 1.0961 time to fit residues: 4.7018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 11 optimal weight: 0.0870 chunk 21 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 0.0170 chunk 9 optimal weight: 0.4980 chunk 14 optimal weight: 0.0060 chunk 66 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 overall best weight: 0.2212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.168459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.136781 restraints weight = 11191.064| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.14 r_work: 0.3656 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 8279 Z= 0.189 Angle : 0.535 8.704 11247 Z= 0.270 Chirality : 0.043 0.209 1197 Planarity : 0.004 0.064 1448 Dihedral : 4.127 20.824 1072 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.27), residues: 968 helix: 0.56 (0.28), residues: 397 sheet: 0.39 (0.60), residues: 72 loop : -1.57 (0.27), residues: 499 =============================================================================== Job complete usr+sys time: 4392.96 seconds wall clock time: 78 minutes 6.77 seconds (4686.77 seconds total)