Starting phenix.real_space_refine on Fri Jul 19 03:40:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4u_36892/07_2024/8k4u_36892_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4u_36892/07_2024/8k4u_36892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4u_36892/07_2024/8k4u_36892.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4u_36892/07_2024/8k4u_36892.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4u_36892/07_2024/8k4u_36892_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4u_36892/07_2024/8k4u_36892_neut.cif" } resolution = 3.2 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= 0.049 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 36 5.16 5 C 4052 2.51 5 N 1045 2.21 5 O 1189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6323 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1451 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 9, 'TRANS': 174} Chain: "B" Number of atoms: 4871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4871 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 563} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.52, per 1000 atoms: 0.71 Number of scatterers: 6323 At special positions: 0 Unit cell: (75.597, 82.287, 115.737, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 36 16.00 O 1189 8.00 N 1045 7.00 C 4052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 469 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 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 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 378 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 374 " 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1464 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 6 sheets defined 51.7% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 354 through 360 removed outlier: 3.892A pdb=" N LEU A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 401 removed outlier: 3.943A pdb=" N VAL A 398 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 401 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 51 removed outlier: 3.569A pdb=" N ALA B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 35 " --> pdb=" O ASP B 31 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU B 37 " --> pdb=" O ASN B 33 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ASN B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 81 removed outlier: 3.851A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.683A pdb=" N GLN B 96 " --> pdb=" O THR B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 130 removed outlier: 3.653A pdb=" N THR B 125 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 155 Processing helix chain 'B' and resid 157 through 167 removed outlier: 4.094A pdb=" N TRP B 163 " --> pdb=" O ASN B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 175 removed outlier: 3.675A pdb=" N GLY B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 193 removed outlier: 3.588A pdb=" N GLU B 182 " --> pdb=" O PRO B 178 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASN B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 Processing helix chain 'B' and resid 220 through 252 removed outlier: 3.637A pdb=" N GLU B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 3.681A pdb=" N GLN B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.596A pdb=" N TYR B 279 " --> pdb=" O THR B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 303 through 318 removed outlier: 3.758A pdb=" N PHE B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 311 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 removed outlier: 4.223A pdb=" N TRP B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ASN B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 379 removed outlier: 3.602A pdb=" N PHE B 369 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 370 " --> pdb=" O MET B 366 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS B 373 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.259A pdb=" N SER B 387 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 412 removed outlier: 3.670A pdb=" N HIS B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 404 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY B 405 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 422 Processing helix chain 'B' and resid 433 through 446 removed outlier: 3.660A pdb=" N PHE B 438 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 464 removed outlier: 4.695A pdb=" N TRP B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.519A pdb=" N TRP B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS B 483 " --> pdb=" O GLU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 513 through 533 removed outlier: 4.026A pdb=" N THR B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.562A pdb=" N LYS B 552 " --> pdb=" O THR B 548 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS B 553 " --> pdb=" O ASP B 549 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU B 554 " --> pdb=" O ALA B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 570 Processing helix chain 'B' and resid 570 through 575 Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 588 through 599 removed outlier: 3.632A pdb=" N TRP B 594 " --> pdb=" O PRO B 590 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 598 " --> pdb=" O TRP B 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 344 through 348 removed outlier: 3.851A pdb=" N GLU A 344 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 390 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 389 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS A 423 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 369 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN A 428 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N PHE A 365 " --> pdb=" O ASN A 428 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 464 Processing sheet with id=AA4, first strand: chain 'B' and resid 132 through 133 removed outlier: 3.718A pdb=" N LEU B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 262 through 263 removed outlier: 6.440A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 352 removed outlier: 6.203A pdb=" N ASP B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) 242 hydrogen bonds defined for protein. 690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2010 1.34 - 1.46: 1635 1.46 - 1.58: 2805 1.58 - 1.69: 0 1.69 - 1.81: 57 Bond restraints: 6507 Sorted by residual: bond pdb=" CA GLY B 582 " pdb=" C GLY B 582 " ideal model delta sigma weight residual 1.511 1.523 -0.013 6.90e-03 2.10e+04 3.38e+00 bond pdb=" C ASP B 499 " pdb=" N PRO B 500 " ideal model delta sigma weight residual 1.335 1.355 -0.021 1.28e-02 6.10e+03 2.64e+00 bond pdb=" C VAL B 581 " pdb=" N GLY B 582 " ideal model delta sigma weight residual 1.340 1.330 0.010 6.60e-03 2.30e+04 2.33e+00 bond pdb=" C LEU B 320 " pdb=" N PRO B 321 " ideal model delta sigma weight residual 1.330 1.347 -0.017 1.25e-02 6.40e+03 1.94e+00 bond pdb=" C ARG B 177 " pdb=" N PRO B 178 " ideal model delta sigma weight residual 1.336 1.352 -0.016 1.23e-02 6.61e+03 1.72e+00 ... (remaining 6502 not shown) Histogram of bond angle deviations from ideal: 99.87 - 106.72: 221 106.72 - 113.57: 3404 113.57 - 120.42: 2558 120.42 - 127.27: 2554 127.27 - 134.12: 100 Bond angle restraints: 8837 Sorted by residual: angle pdb=" C ILE B 379 " pdb=" N GLN B 380 " pdb=" CA GLN B 380 " ideal model delta sigma weight residual 121.54 131.31 -9.77 1.91e+00 2.74e-01 2.62e+01 angle pdb=" N ILE B 291 " pdb=" CA ILE B 291 " pdb=" C ILE B 291 " ideal model delta sigma weight residual 111.91 108.44 3.47 8.90e-01 1.26e+00 1.52e+01 angle pdb=" N GLY A 448 " pdb=" CA GLY A 448 " pdb=" C GLY A 448 " ideal model delta sigma weight residual 110.56 115.53 -4.97 1.36e+00 5.41e-01 1.34e+01 angle pdb=" C LEU B 143 " pdb=" N LEU B 144 " pdb=" CA LEU B 144 " ideal model delta sigma weight residual 121.54 128.29 -6.75 1.91e+00 2.74e-01 1.25e+01 angle pdb=" N LYS B 234 " pdb=" CA LYS B 234 " pdb=" C LYS B 234 " ideal model delta sigma weight residual 109.81 116.56 -6.75 2.21e+00 2.05e-01 9.34e+00 ... (remaining 8832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 3545 16.39 - 32.78: 216 32.78 - 49.18: 68 49.18 - 65.57: 11 65.57 - 81.96: 1 Dihedral angle restraints: 3841 sinusoidal: 1558 harmonic: 2283 Sorted by residual: dihedral pdb=" CA ALA B 396 " pdb=" C ALA B 396 " pdb=" N ASN B 397 " pdb=" CA ASN B 397 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA GLN B 380 " pdb=" C GLN B 380 " pdb=" N TYR B 381 " pdb=" CA TYR B 381 " ideal model delta harmonic sigma weight residual 180.00 160.47 19.53 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ASP B 149 " pdb=" C ASP B 149 " pdb=" N ASN B 150 " pdb=" CA ASN B 150 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 3838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 494 0.031 - 0.061: 292 0.061 - 0.092: 86 0.092 - 0.123: 38 0.123 - 0.153: 11 Chirality restraints: 921 Sorted by residual: chirality pdb=" CA ASP B 499 " pdb=" N ASP B 499 " pdb=" C ASP B 499 " pdb=" CB ASP B 499 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA ARG B 177 " pdb=" N ARG B 177 " pdb=" C ARG B 177 " pdb=" CB ARG B 177 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA LEU B 450 " pdb=" N LEU B 450 " pdb=" C LEU B 450 " pdb=" CB LEU B 450 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 918 not shown) Planarity restraints: 1137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 582 " 0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO B 583 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 583 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 583 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 279 " 0.041 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO B 280 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 280 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 280 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 234 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO B 235 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 235 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 235 " 0.031 5.00e-02 4.00e+02 ... (remaining 1134 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 88 2.66 - 3.22: 5451 3.22 - 3.78: 9947 3.78 - 4.34: 14019 4.34 - 4.90: 22909 Nonbonded interactions: 52414 Sorted by model distance: nonbonded pdb=" OE2 GLU B 402 " pdb="ZN ZN B 701 " model vdw 2.101 2.230 nonbonded pdb=" OG1 THR B 362 " pdb=" OD2 ASP B 368 " model vdw 2.309 2.440 nonbonded pdb=" OD1 ASP B 382 " pdb=" OH TYR B 385 " model vdw 2.320 2.440 nonbonded pdb=" O ASN B 150 " pdb=" OG1 THR B 154 " model vdw 2.321 2.440 nonbonded pdb=" O ASN B 121 " pdb=" OG1 THR B 125 " model vdw 2.324 2.440 ... (remaining 52409 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.960 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.940 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 : 0.003 0.061 6507 Z= 0.199 Angle : 0.637 9.768 8837 Z= 0.352 Chirality : 0.045 0.153 921 Planarity : 0.006 0.069 1137 Dihedral : 11.919 81.959 2359 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.92 % Allowed : 7.96 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -4.11 (0.24), residues: 774 helix: -3.74 (0.14), residues: 383 sheet: -1.03 (0.85), residues: 42 loop : -1.49 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 427 HIS 0.004 0.001 HIS B 322 PHE 0.008 0.001 PHE B 230 TYR 0.023 0.001 TYR B 385 ARG 0.002 0.000 ARG B 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 187 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 LYS cc_start: 0.8381 (mtpt) cc_final: 0.8123 (mtpp) REVERT: A 401 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8830 (mm) REVERT: A 471 SER cc_start: 0.8031 (t) cc_final: 0.7810 (p) REVERT: A 478 TYR cc_start: 0.6661 (OUTLIER) cc_final: 0.6104 (m-80) REVERT: B 94 LYS cc_start: 0.8433 (tttt) cc_final: 0.8039 (ttmt) REVERT: B 163 TRP cc_start: 0.7593 (t60) cc_final: 0.7253 (t60) REVERT: B 276 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8294 (p) REVERT: B 408 MET cc_start: 0.8354 (mpt) cc_final: 0.8146 (mpt) REVERT: B 518 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.6831 (ppt90) REVERT: B 601 ASN cc_start: 0.7834 (m-40) cc_final: 0.7531 (t0) outliers start: 34 outliers final: 6 residues processed: 209 average time/residue: 0.2014 time to fit residues: 54.2021 Evaluate side-chains 126 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 518 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 60 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 69 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN B 53 ASN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN B 493 HIS B 535 HIS B 556 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 6507 Z= 0.202 Angle : 0.599 9.823 8837 Z= 0.305 Chirality : 0.043 0.209 921 Planarity : 0.005 0.049 1137 Dihedral : 6.493 58.529 866 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.05 % Allowed : 14.33 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -2.40 (0.27), residues: 774 helix: -1.88 (0.22), residues: 389 sheet: -0.94 (0.83), residues: 41 loop : -1.12 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 477 HIS 0.006 0.001 HIS B 493 PHE 0.015 0.001 PHE B 525 TYR 0.018 0.001 TYR A 442 ARG 0.007 0.000 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 0.784 Fit side-chains REVERT: A 460 VAL cc_start: 0.7707 (t) cc_final: 0.7439 (p) REVERT: A 471 SER cc_start: 0.8133 (t) cc_final: 0.7771 (p) REVERT: A 478 TYR cc_start: 0.6694 (OUTLIER) cc_final: 0.6018 (m-80) REVERT: B 74 GLU cc_start: 0.7617 (mp0) cc_final: 0.7253 (mp0) REVERT: B 94 LYS cc_start: 0.8396 (tttt) cc_final: 0.7982 (ttmt) REVERT: B 518 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.6753 (ppt90) REVERT: B 601 ASN cc_start: 0.7873 (m-40) cc_final: 0.7586 (t0) outliers start: 28 outliers final: 18 residues processed: 148 average time/residue: 0.1704 time to fit residues: 33.6724 Evaluate side-chains 136 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 572 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN B 277 ASN B 322 HIS B 535 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 6507 Z= 0.257 Angle : 0.594 11.145 8837 Z= 0.303 Chirality : 0.044 0.234 921 Planarity : 0.004 0.047 1137 Dihedral : 5.828 54.122 860 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.34 % Allowed : 16.35 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.83 (0.29), residues: 774 helix: -1.27 (0.25), residues: 387 sheet: -0.85 (0.82), residues: 41 loop : -1.01 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 477 HIS 0.004 0.001 HIS B 417 PHE 0.011 0.001 PHE B 400 TYR 0.017 0.002 TYR A 442 ARG 0.008 0.001 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8048 (tppt) cc_final: 0.7836 (tppt) REVERT: A 446 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8012 (mtp85) REVERT: A 460 VAL cc_start: 0.7883 (t) cc_final: 0.7619 (p) REVERT: A 471 SER cc_start: 0.8177 (t) cc_final: 0.7769 (p) REVERT: A 478 TYR cc_start: 0.6740 (OUTLIER) cc_final: 0.6079 (m-80) REVERT: B 94 LYS cc_start: 0.8417 (tttt) cc_final: 0.7968 (ttmt) REVERT: B 518 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.6810 (ppt90) REVERT: B 601 ASN cc_start: 0.7895 (m-40) cc_final: 0.7650 (t0) outliers start: 30 outliers final: 19 residues processed: 147 average time/residue: 0.1793 time to fit residues: 34.9508 Evaluate side-chains 136 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 572 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 277 ASN B 322 HIS B 535 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6507 Z= 0.237 Angle : 0.582 11.557 8837 Z= 0.294 Chirality : 0.043 0.211 921 Planarity : 0.004 0.045 1137 Dihedral : 5.630 48.111 859 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.07 % Allowed : 15.92 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.33 (0.30), residues: 774 helix: -0.85 (0.26), residues: 389 sheet: -0.89 (0.81), residues: 41 loop : -0.73 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 477 HIS 0.005 0.001 HIS B 417 PHE 0.014 0.001 PHE A 420 TYR 0.016 0.002 TYR B 385 ARG 0.009 0.001 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 125 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8092 (tppt) cc_final: 0.7867 (tppt) REVERT: A 446 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8072 (mtp85) REVERT: A 460 VAL cc_start: 0.7921 (t) cc_final: 0.7700 (p) REVERT: A 471 SER cc_start: 0.8250 (t) cc_final: 0.7787 (p) REVERT: A 478 TYR cc_start: 0.6843 (OUTLIER) cc_final: 0.6159 (m-80) REVERT: B 94 LYS cc_start: 0.8417 (tttt) cc_final: 0.7945 (ttmt) REVERT: B 483 LYS cc_start: 0.7718 (mttp) cc_final: 0.7492 (mttp) REVERT: B 518 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.6849 (ppt90) REVERT: B 601 ASN cc_start: 0.7890 (m-40) cc_final: 0.7678 (t0) outliers start: 35 outliers final: 23 residues processed: 148 average time/residue: 0.1904 time to fit residues: 37.0645 Evaluate side-chains 144 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 118 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 579 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 1.9990 chunk 1 optimal weight: 0.0570 chunk 55 optimal weight: 0.9990 chunk 30 optimal weight: 0.0370 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 18 optimal weight: 0.0370 chunk 25 optimal weight: 0.8980 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 277 ASN B 322 HIS ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6507 Z= 0.162 Angle : 0.554 11.664 8837 Z= 0.278 Chirality : 0.041 0.195 921 Planarity : 0.004 0.042 1137 Dihedral : 5.374 43.241 859 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.92 % Allowed : 16.21 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.95 (0.30), residues: 774 helix: -0.48 (0.26), residues: 391 sheet: -0.67 (0.83), residues: 41 loop : -0.62 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 168 HIS 0.005 0.001 HIS B 417 PHE 0.008 0.001 PHE A 420 TYR 0.011 0.001 TYR B 385 ARG 0.010 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 128 time to evaluate : 0.762 Fit side-chains REVERT: A 401 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8752 (mm) REVERT: A 415 LYS cc_start: 0.8043 (tppt) cc_final: 0.7785 (tppt) REVERT: A 446 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8056 (mtp85) REVERT: A 460 VAL cc_start: 0.7810 (t) cc_final: 0.7599 (p) REVERT: A 471 SER cc_start: 0.8214 (t) cc_final: 0.7727 (p) REVERT: A 478 TYR cc_start: 0.6786 (OUTLIER) cc_final: 0.6048 (m-80) REVERT: B 74 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7086 (mm-30) REVERT: B 94 LYS cc_start: 0.8377 (tttt) cc_final: 0.7914 (ttmt) REVERT: B 141 CYS cc_start: 0.5390 (OUTLIER) cc_final: 0.5073 (t) REVERT: B 366 MET cc_start: 0.6827 (mmm) cc_final: 0.6616 (tpt) REVERT: B 483 LYS cc_start: 0.7649 (mttp) cc_final: 0.7424 (mttp) REVERT: B 518 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.6866 (ppt90) REVERT: B 601 ASN cc_start: 0.7896 (m-40) cc_final: 0.7657 (t0) outliers start: 34 outliers final: 19 residues processed: 148 average time/residue: 0.1837 time to fit residues: 35.8932 Evaluate side-chains 143 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 0.0970 chunk 18 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 277 ASN B 535 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6507 Z= 0.198 Angle : 0.577 12.662 8837 Z= 0.285 Chirality : 0.042 0.191 921 Planarity : 0.004 0.043 1137 Dihedral : 5.037 43.127 856 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.92 % Allowed : 16.79 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.71 (0.31), residues: 774 helix: -0.27 (0.27), residues: 390 sheet: -0.53 (0.85), residues: 40 loop : -0.53 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 168 HIS 0.003 0.001 HIS B 417 PHE 0.029 0.001 PHE B 525 TYR 0.014 0.001 TYR B 385 ARG 0.012 0.001 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 121 time to evaluate : 0.805 Fit side-chains REVERT: A 401 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8773 (mm) REVERT: A 415 LYS cc_start: 0.8041 (tppt) cc_final: 0.7761 (tppt) REVERT: A 446 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7963 (mtp85) REVERT: A 478 TYR cc_start: 0.6779 (OUTLIER) cc_final: 0.6002 (m-80) REVERT: B 74 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7076 (mm-30) REVERT: B 94 LYS cc_start: 0.8423 (tttt) cc_final: 0.7923 (ttmt) REVERT: B 219 ARG cc_start: 0.7744 (mtm-85) cc_final: 0.7387 (mtm-85) REVERT: B 483 LYS cc_start: 0.7705 (mttp) cc_final: 0.7484 (mttp) REVERT: B 518 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.6843 (ppt90) REVERT: B 601 ASN cc_start: 0.7906 (m-40) cc_final: 0.7680 (t0) outliers start: 34 outliers final: 25 residues processed: 140 average time/residue: 0.1993 time to fit residues: 36.4614 Evaluate side-chains 148 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 118 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 TYR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 0.0670 chunk 46 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 277 ASN B 535 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 6507 Z= 0.201 Angle : 0.581 13.538 8837 Z= 0.290 Chirality : 0.042 0.190 921 Planarity : 0.004 0.050 1137 Dihedral : 5.003 43.158 856 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 5.79 % Allowed : 16.50 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.60 (0.31), residues: 774 helix: -0.19 (0.27), residues: 391 sheet: -0.45 (0.83), residues: 40 loop : -0.46 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 168 HIS 0.003 0.001 HIS B 417 PHE 0.015 0.001 PHE B 525 TYR 0.013 0.001 TYR B 385 ARG 0.012 0.000 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 121 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 401 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8748 (mm) REVERT: A 415 LYS cc_start: 0.8048 (tppt) cc_final: 0.7540 (tppt) REVERT: A 446 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8025 (mtp85) REVERT: A 478 TYR cc_start: 0.6763 (OUTLIER) cc_final: 0.5986 (m-80) REVERT: B 74 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7045 (mm-30) REVERT: B 94 LYS cc_start: 0.8414 (tttt) cc_final: 0.7901 (ttmt) REVERT: B 366 MET cc_start: 0.6860 (mmm) cc_final: 0.6586 (tpt) REVERT: B 408 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7007 (mpt) REVERT: B 483 LYS cc_start: 0.7726 (mttp) cc_final: 0.7502 (mttp) REVERT: B 518 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.6853 (ppt90) REVERT: B 601 ASN cc_start: 0.7907 (m-40) cc_final: 0.7675 (t0) outliers start: 40 outliers final: 28 residues processed: 143 average time/residue: 0.1927 time to fit residues: 36.0881 Evaluate side-chains 152 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 118 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 TYR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 277 ASN B 524 GLN B 535 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6507 Z= 0.206 Angle : 0.592 14.149 8837 Z= 0.294 Chirality : 0.042 0.186 921 Planarity : 0.004 0.052 1137 Dihedral : 4.953 43.031 856 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.35 % Allowed : 16.93 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.48 (0.31), residues: 774 helix: -0.07 (0.27), residues: 390 sheet: -0.40 (0.83), residues: 40 loop : -0.44 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 168 HIS 0.004 0.001 HIS B 417 PHE 0.038 0.001 PHE B 525 TYR 0.014 0.001 TYR B 385 ARG 0.012 0.001 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 120 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: A 401 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8748 (mm) REVERT: A 415 LYS cc_start: 0.8029 (tppt) cc_final: 0.7533 (tppt) REVERT: A 446 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8034 (mtp85) REVERT: A 478 TYR cc_start: 0.6538 (OUTLIER) cc_final: 0.5709 (m-80) REVERT: B 74 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7012 (mm-30) REVERT: B 94 LYS cc_start: 0.8411 (tttt) cc_final: 0.7890 (ttmt) REVERT: B 408 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.6999 (mpt) REVERT: B 483 LYS cc_start: 0.7752 (mttp) cc_final: 0.7513 (mttp) REVERT: B 518 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.6834 (ppt90) REVERT: B 601 ASN cc_start: 0.7897 (m-40) cc_final: 0.7678 (t0) outliers start: 37 outliers final: 26 residues processed: 139 average time/residue: 0.2041 time to fit residues: 36.7957 Evaluate side-chains 148 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 116 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 TYR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 0.9980 chunk 41 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 44 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 277 ASN B 524 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6507 Z= 0.190 Angle : 0.592 13.835 8837 Z= 0.293 Chirality : 0.042 0.183 921 Planarity : 0.004 0.057 1137 Dihedral : 4.836 43.109 855 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.63 % Allowed : 17.66 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.36 (0.31), residues: 774 helix: 0.07 (0.27), residues: 390 sheet: -0.38 (0.84), residues: 40 loop : -0.42 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 477 HIS 0.004 0.001 HIS B 417 PHE 0.041 0.001 PHE B 525 TYR 0.013 0.001 TYR B 385 ARG 0.013 0.001 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 119 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 401 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8755 (mm) REVERT: A 415 LYS cc_start: 0.8046 (tppt) cc_final: 0.7564 (tppt) REVERT: A 446 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.8045 (mtp85) REVERT: B 94 LYS cc_start: 0.8365 (tttt) cc_final: 0.7870 (ttmt) REVERT: B 408 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.6991 (mpt) REVERT: B 483 LYS cc_start: 0.7750 (mttp) cc_final: 0.7499 (mttp) REVERT: B 518 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.6814 (ppt90) REVERT: B 601 ASN cc_start: 0.7880 (m-40) cc_final: 0.7674 (t0) outliers start: 32 outliers final: 24 residues processed: 133 average time/residue: 0.2028 time to fit residues: 34.8771 Evaluate side-chains 144 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 116 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 TYR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 0.0980 chunk 48 optimal weight: 0.4980 chunk 65 optimal weight: 0.0170 chunk 18 optimal weight: 0.2980 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 ASN B 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6507 Z= 0.172 Angle : 0.595 13.693 8837 Z= 0.293 Chirality : 0.041 0.180 921 Planarity : 0.004 0.060 1137 Dihedral : 4.688 43.205 853 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.34 % Allowed : 18.09 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.24 (0.31), residues: 774 helix: 0.15 (0.27), residues: 391 sheet: -0.32 (0.86), residues: 40 loop : -0.34 (0.36), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 477 HIS 0.004 0.001 HIS B 417 PHE 0.045 0.001 PHE B 525 TYR 0.011 0.001 TYR B 194 ARG 0.014 0.001 ARG B 531 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 0.687 Fit side-chains REVERT: A 401 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8707 (mm) REVERT: A 415 LYS cc_start: 0.8042 (tppt) cc_final: 0.7570 (tppt) REVERT: A 446 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8025 (mtp85) REVERT: B 94 LYS cc_start: 0.8322 (tttt) cc_final: 0.7816 (ttmt) REVERT: B 408 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.6873 (mpt) REVERT: B 483 LYS cc_start: 0.7724 (mttp) cc_final: 0.7475 (mttp) REVERT: B 518 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.6806 (ppt90) outliers start: 30 outliers final: 23 residues processed: 127 average time/residue: 0.1891 time to fit residues: 31.2817 Evaluate side-chains 140 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 TYR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.0030 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 7 optimal weight: 0.0370 chunk 11 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 44 optimal weight: 0.1980 overall best weight: 0.3268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 277 ASN B 524 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.183562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.149642 restraints weight = 7875.816| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.30 r_work: 0.3687 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6507 Z= 0.163 Angle : 0.581 13.487 8837 Z= 0.286 Chirality : 0.041 0.211 921 Planarity : 0.004 0.057 1137 Dihedral : 4.594 43.479 853 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.20 % Allowed : 17.95 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.09 (0.31), residues: 774 helix: 0.28 (0.27), residues: 396 sheet: -0.14 (0.88), residues: 40 loop : -0.30 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 461 HIS 0.004 0.001 HIS B 417 PHE 0.042 0.001 PHE B 525 TYR 0.011 0.001 TYR B 194 ARG 0.014 0.001 ARG B 531 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2036.38 seconds wall clock time: 36 minutes 30.85 seconds (2190.85 seconds total)