Starting phenix.real_space_refine on Wed Feb 4 09:08:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ykj_73047/02_2026/9ykj_73047.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ykj_73047/02_2026/9ykj_73047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ykj_73047/02_2026/9ykj_73047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ykj_73047/02_2026/9ykj_73047.map" model { file = "/net/cci-nas-00/data/ceres_data/9ykj_73047/02_2026/9ykj_73047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ykj_73047/02_2026/9ykj_73047.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 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 P 4 5.49 5 S 44 5.16 5 C 6036 2.51 5 N 1659 2.21 5 O 1804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9547 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5417 Classifications: {'peptide': 686} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 655} Chain breaks: 6 Chain: "B" Number of atoms: 4076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4076 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 22, 'TRANS': 496} Chain breaks: 5 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.01, per 1000 atoms: 0.21 Number of scatterers: 9547 At special positions: 0 Unit cell: (74.26, 84.6, 159.8, 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) S 44 16.00 P 4 15.00 O 1804 8.00 N 1659 7.00 C 6036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 343.3 milliseconds 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 6 sheets defined 58.6% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 21 through 26 Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 71 through 86 Processing helix chain 'A' and resid 99 through 106 removed outlier: 4.615A pdb=" N GLN A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 163 through 173 removed outlier: 3.561A pdb=" N ILE A 171 " --> pdb=" O CYS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 183 through 193 removed outlier: 3.907A pdb=" N HIS A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 199 removed outlier: 3.592A pdb=" N GLU A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 211 removed outlier: 3.822A pdb=" N ASP A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.929A pdb=" N LEU A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 252 " --> pdb=" O TRP A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 252' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.604A pdb=" N ALA A 285 " --> pdb=" O TYR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 299 No H-bonds generated for 'chain 'A' and resid 297 through 299' Processing helix chain 'A' and resid 300 through 306 removed outlier: 3.564A pdb=" N GLY A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 314 removed outlier: 3.754A pdb=" N ILE A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 336 through 339 Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 365 through 368 Processing helix chain 'A' and resid 369 through 376 Processing helix chain 'A' and resid 384 through 395 removed outlier: 4.118A pdb=" N ALA A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 393 " --> pdb=" O VAL A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 430 through 440 removed outlier: 3.701A pdb=" N LEU A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 458 removed outlier: 3.895A pdb=" N SER A 453 " --> pdb=" O ARG A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 478 through 483 removed outlier: 4.208A pdb=" N ARG A 483 " --> pdb=" O VAL A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 491 removed outlier: 3.753A pdb=" N LEU A 491 " --> pdb=" O ARG A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 515 Processing helix chain 'A' and resid 518 through 532 Processing helix chain 'A' and resid 534 through 545 Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 554 through 573 Processing helix chain 'A' and resid 575 through 590 Processing helix chain 'A' and resid 593 through 609 removed outlier: 4.141A pdb=" N GLY A 598 " --> pdb=" O PRO A 594 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TRP A 599 " --> pdb=" O ASP A 595 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 607 " --> pdb=" O GLU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 627 Processing helix chain 'A' and resid 664 through 675 Processing helix chain 'A' and resid 682 through 697 removed outlier: 4.727A pdb=" N ALA A 694 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE A 695 " --> pdb=" O ASN A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 744 through 758 removed outlier: 4.143A pdb=" N ASN A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 71 through 83 Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.505A pdb=" N ASP B 169 " --> pdb=" O HIS B 165 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 193 removed outlier: 3.711A pdb=" N ALA B 188 " --> pdb=" O PRO B 184 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS B 191 " --> pdb=" O HIS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 202 removed outlier: 3.849A pdb=" N LEU B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLN B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 275 through 283 removed outlier: 7.388A pdb=" N SER B 281 " --> pdb=" O ASP B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 299 No H-bonds generated for 'chain 'B' and resid 297 through 299' Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 308 through 313 removed outlier: 4.280A pdb=" N ILE B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 Processing helix chain 'B' and resid 336 through 340 Processing helix chain 'B' and resid 341 through 349 removed outlier: 3.719A pdb=" N VAL B 345 " --> pdb=" O ARG B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'B' and resid 384 through 394 removed outlier: 3.842A pdb=" N ALA B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 431 through 440 removed outlier: 4.022A pdb=" N GLU B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 457 removed outlier: 3.855A pdb=" N SER B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'B' and resid 484 through 491 Processing helix chain 'B' and resid 492 through 515 Processing helix chain 'B' and resid 518 through 532 Processing helix chain 'B' and resid 534 through 545 removed outlier: 3.700A pdb=" N PHE B 540 " --> pdb=" O GLY B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 548 No H-bonds generated for 'chain 'B' and resid 546 through 548' Processing helix chain 'B' and resid 554 through 573 removed outlier: 3.741A pdb=" N GLU B 559 " --> pdb=" O LYS B 555 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 589 Processing helix chain 'B' and resid 595 through 609 removed outlier: 4.768A pdb=" N LEU B 601 " --> pdb=" O ARG B 597 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 602 " --> pdb=" O GLY B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 625 removed outlier: 3.816A pdb=" N ALA B 616 " --> pdb=" O ASN B 612 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG B 625 " --> pdb=" O VAL B 621 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95 removed outlier: 3.576A pdb=" N THR A 135 " --> pdb=" O TYR A 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 180 removed outlier: 4.731A pdb=" N CYS A 260 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 401 through 404 removed outlier: 6.654A pdb=" N ILE A 359 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU A 403 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ALA A 361 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 420 " --> pdb=" O VAL A 472 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 700 through 702 removed outlier: 3.994A pdb=" N ALA A 700 " --> pdb=" O ALA A 717 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 63 through 66 removed outlier: 3.960A pdb=" N SER B 292 " --> pdb=" O ILE B 64 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 326 through 330 removed outlier: 6.157A pdb=" N GLU B 326 " --> pdb=" O SER B 469 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 471 " --> pdb=" O GLU B 326 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N MET B 328 " --> pdb=" O VAL B 471 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA B 473 " --> pdb=" O MET B 328 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU B 330 " --> pdb=" O ALA B 473 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE B 359 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N LEU B 403 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA B 361 " --> pdb=" O LEU B 403 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1164 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: 1.11 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2715 1.33 - 1.46: 1724 1.46 - 1.58: 5214 1.58 - 1.70: 6 1.70 - 1.82: 68 Bond restraints: 9727 Sorted by residual: bond pdb=" C ALA B 349 " pdb=" N PRO B 350 " ideal model delta sigma weight residual 1.332 1.389 -0.057 1.26e-02 6.30e+03 2.06e+01 bond pdb=" N ASN A 314 " pdb=" CA ASN A 314 " ideal model delta sigma weight residual 1.462 1.496 -0.034 9.90e-03 1.02e+04 1.21e+01 bond pdb=" C CYS B 95 " pdb=" N PRO B 96 " ideal model delta sigma weight residual 1.334 1.396 -0.062 2.34e-02 1.83e+03 7.06e+00 bond pdb=" N GLN A 544 " pdb=" CA GLN A 544 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.30e-02 5.92e+03 6.68e+00 bond pdb=" CB VAL B 479 " pdb=" CG1 VAL B 479 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.68e+00 ... (remaining 9722 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 12586 3.14 - 6.28: 487 6.28 - 9.42: 69 9.42 - 12.57: 13 12.57 - 15.71: 4 Bond angle restraints: 13159 Sorted by residual: angle pdb=" N ALA A 349 " pdb=" CA ALA A 349 " pdb=" C ALA A 349 " ideal model delta sigma weight residual 109.81 120.78 -10.97 2.21e+00 2.05e-01 2.46e+01 angle pdb=" CB ARG B 452 " pdb=" CG ARG B 452 " pdb=" CD ARG B 452 " ideal model delta sigma weight residual 111.30 122.69 -11.39 2.30e+00 1.89e-01 2.45e+01 angle pdb=" N GLN A 544 " pdb=" CA GLN A 544 " pdb=" C GLN A 544 " ideal model delta sigma weight residual 112.23 118.46 -6.23 1.26e+00 6.30e-01 2.45e+01 angle pdb=" CB ARG B 460 " pdb=" CG ARG B 460 " pdb=" CD ARG B 460 " ideal model delta sigma weight residual 111.30 122.10 -10.80 2.30e+00 1.89e-01 2.20e+01 angle pdb=" CB MET A 747 " pdb=" CG MET A 747 " pdb=" SD MET A 747 " ideal model delta sigma weight residual 112.70 126.66 -13.96 3.00e+00 1.11e-01 2.17e+01 ... (remaining 13154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.89: 5668 30.89 - 61.79: 215 61.79 - 92.68: 25 92.68 - 123.58: 2 123.58 - 154.47: 1 Dihedral angle restraints: 5911 sinusoidal: 2415 harmonic: 3496 Sorted by residual: dihedral pdb=" O1B ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PB ADP B 901 " pdb=" PA ADP B 901 " ideal model delta sinusoidal sigma weight residual 300.00 145.53 154.47 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" CA ILE A 64 " pdb=" C ILE A 64 " pdb=" N LYS A 65 " pdb=" CA LYS A 65 " ideal model delta harmonic sigma weight residual 180.00 150.50 29.50 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA GLN A 107 " pdb=" C GLN A 107 " pdb=" N ALA A 108 " pdb=" CA ALA A 108 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 5908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1259 0.104 - 0.207: 181 0.207 - 0.311: 18 0.311 - 0.415: 6 0.415 - 0.519: 2 Chirality restraints: 1466 Sorted by residual: chirality pdb=" CG LEU A 403 " pdb=" CB LEU A 403 " pdb=" CD1 LEU A 403 " pdb=" CD2 LEU A 403 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" CB ILE A 505 " pdb=" CA ILE A 505 " pdb=" CG1 ILE A 505 " pdb=" CG2 ILE A 505 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.13e+00 chirality pdb=" CB ILE A 410 " pdb=" CA ILE A 410 " pdb=" CG1 ILE A 410 " pdb=" CG2 ILE A 410 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.09e+00 ... (remaining 1463 not shown) Planarity restraints: 1692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 542 " -0.026 2.00e-02 2.50e+03 5.25e-02 2.75e+01 pdb=" C ALA A 542 " 0.091 2.00e-02 2.50e+03 pdb=" O ALA A 542 " -0.034 2.00e-02 2.50e+03 pdb=" N ASP A 543 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 754 " -0.029 2.00e-02 2.50e+03 3.86e-02 2.61e+01 pdb=" CG PHE A 754 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE A 754 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 754 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 PHE A 754 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 PHE A 754 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 754 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 248 " -0.038 2.00e-02 2.50e+03 2.74e-02 1.88e+01 pdb=" CG TRP A 248 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP A 248 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 248 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 248 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 248 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 248 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 248 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 248 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 248 " -0.018 2.00e-02 2.50e+03 ... (remaining 1689 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1779 2.78 - 3.31: 9882 3.31 - 3.84: 15843 3.84 - 4.37: 19531 4.37 - 4.90: 31404 Nonbonded interactions: 78439 Sorted by model distance: nonbonded pdb=" O SER A 493 " pdb=" OG1 THR A 497 " model vdw 2.254 3.040 nonbonded pdb=" OE2 GLU A 564 " pdb=" OH TYR A 600 " model vdw 2.264 3.040 nonbonded pdb=" N ASP B 484 " pdb=" OD1 ASP B 484 " model vdw 2.270 3.120 nonbonded pdb=" OE2 GLU B 564 " pdb=" OH TYR B 600 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASP A 169 " pdb=" NH2 ARG A 452 " model vdw 2.287 3.120 ... (remaining 78434 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.900 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.390 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5967 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 : 0.008 0.086 9727 Z= 0.359 Angle : 1.437 15.708 13159 Z= 0.773 Chirality : 0.077 0.519 1466 Planarity : 0.011 0.108 1692 Dihedral : 16.491 154.471 3647 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.63 % Favored : 91.52 % Rotamer: Outliers : 1.78 % Allowed : 13.68 % Favored : 84.54 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.23), residues: 1179 helix: -1.85 (0.17), residues: 556 sheet: -1.39 (0.51), residues: 89 loop : -1.14 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.004 ARG B 449 TYR 0.059 0.007 TYR A 607 PHE 0.081 0.005 PHE A 754 TRP 0.072 0.004 TRP A 248 HIS 0.021 0.003 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00785 ( 9727) covalent geometry : angle 1.43716 (13159) hydrogen bonds : bond 0.16852 ( 421) hydrogen bonds : angle 7.76661 ( 1164) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 LYS cc_start: 0.7339 (mttt) cc_final: 0.6851 (mmtt) REVERT: A 448 MET cc_start: 0.7548 (mmm) cc_final: 0.7179 (mmm) REVERT: A 508 MET cc_start: 0.6574 (mmp) cc_final: 0.6188 (mmp) REVERT: A 571 TYR cc_start: 0.5506 (t80) cc_final: 0.5008 (t80) REVERT: A 699 PHE cc_start: 0.6258 (m-80) cc_final: 0.5739 (m-80) REVERT: A 714 ASN cc_start: 0.7137 (m110) cc_final: 0.6642 (t0) REVERT: A 747 MET cc_start: -0.2231 (tpp) cc_final: -0.2567 (mtt) REVERT: B 183 GLU cc_start: 0.1826 (OUTLIER) cc_final: 0.1126 (tt0) REVERT: B 378 LYS cc_start: 0.7590 (tptt) cc_final: 0.7342 (tttm) REVERT: B 390 SER cc_start: 0.6706 (t) cc_final: 0.6444 (p) REVERT: B 396 GLN cc_start: 0.7753 (tt0) cc_final: 0.7370 (tp40) REVERT: B 408 ASP cc_start: 0.6732 (OUTLIER) cc_final: 0.6326 (p0) REVERT: B 411 ASP cc_start: 0.6483 (m-30) cc_final: 0.6149 (p0) REVERT: B 435 TYR cc_start: 0.4733 (OUTLIER) cc_final: 0.3356 (t80) REVERT: B 453 SER cc_start: 0.7132 (m) cc_final: 0.6874 (p) REVERT: B 495 MET cc_start: 0.6431 (mmm) cc_final: 0.5807 (tmm) REVERT: B 545 MET cc_start: 0.2793 (mtp) cc_final: 0.2583 (mtp) REVERT: B 597 ARG cc_start: 0.7555 (mtt-85) cc_final: 0.7341 (mpp80) outliers start: 18 outliers final: 8 residues processed: 174 average time/residue: 0.0965 time to fit residues: 22.5462 Evaluate side-chains 139 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 435 TYR Chi-restraints excluded: chain B residue 484 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN A 306 GLN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.238434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.212098 restraints weight = 12415.049| |-----------------------------------------------------------------------------| r_work (start): 0.4752 rms_B_bonded: 2.72 r_work: 0.4558 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5828 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9727 Z= 0.155 Angle : 0.756 9.496 13159 Z= 0.378 Chirality : 0.045 0.147 1466 Planarity : 0.005 0.044 1692 Dihedral : 9.217 131.801 1350 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.16 % Favored : 95.76 % Rotamer: Outliers : 3.07 % Allowed : 12.78 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.24), residues: 1179 helix: -0.58 (0.20), residues: 595 sheet: -1.63 (0.47), residues: 98 loop : -0.74 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 256 TYR 0.024 0.002 TYR A 93 PHE 0.022 0.002 PHE B 99 TRP 0.013 0.002 TRP A 248 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9727) covalent geometry : angle 0.75602 (13159) hydrogen bonds : bond 0.04278 ( 421) hydrogen bonds : angle 5.52571 ( 1164) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 LYS cc_start: 0.7263 (mttt) cc_final: 0.6743 (mmtt) REVERT: A 448 MET cc_start: 0.7293 (mmm) cc_final: 0.7006 (mmm) REVERT: A 508 MET cc_start: 0.6622 (mmp) cc_final: 0.6074 (mmt) REVERT: A 709 LYS cc_start: 0.6774 (mmtt) cc_final: 0.6446 (mmtt) REVERT: A 714 ASN cc_start: 0.6990 (m110) cc_final: 0.6614 (t0) REVERT: B 99 PHE cc_start: 0.5262 (OUTLIER) cc_final: 0.4748 (p90) REVERT: B 163 ASP cc_start: 0.7059 (OUTLIER) cc_final: 0.6569 (m-30) REVERT: B 183 GLU cc_start: 0.1155 (OUTLIER) cc_final: 0.0822 (tt0) REVERT: B 334 MET cc_start: 0.4800 (tpp) cc_final: 0.4515 (ttp) REVERT: B 390 SER cc_start: 0.6896 (t) cc_final: 0.6646 (p) REVERT: B 396 GLN cc_start: 0.7647 (tt0) cc_final: 0.7404 (tp40) REVERT: B 435 TYR cc_start: 0.4737 (OUTLIER) cc_final: 0.3168 (t80) REVERT: B 495 MET cc_start: 0.6448 (mmm) cc_final: 0.5764 (tmm) REVERT: B 554 ASN cc_start: 0.3356 (m110) cc_final: 0.1543 (t0) outliers start: 31 outliers final: 13 residues processed: 169 average time/residue: 0.0745 time to fit residues: 17.5788 Evaluate side-chains 130 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 435 TYR Chi-restraints excluded: chain B residue 484 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.232826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.203540 restraints weight = 12404.554| |-----------------------------------------------------------------------------| r_work (start): 0.4679 rms_B_bonded: 3.75 r_work (final): 0.4679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5791 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9727 Z= 0.192 Angle : 0.764 8.578 13159 Z= 0.381 Chirality : 0.046 0.150 1466 Planarity : 0.005 0.055 1692 Dihedral : 8.840 121.739 1339 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.68 % Favored : 94.23 % Rotamer: Outliers : 3.27 % Allowed : 14.77 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.24), residues: 1179 helix: -0.35 (0.20), residues: 589 sheet: -1.89 (0.48), residues: 94 loop : -0.64 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 606 TYR 0.031 0.003 TYR B 93 PHE 0.018 0.002 PHE B 99 TRP 0.017 0.002 TRP A 753 HIS 0.006 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 9727) covalent geometry : angle 0.76424 (13159) hydrogen bonds : bond 0.04236 ( 421) hydrogen bonds : angle 5.46682 ( 1164) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.4450 (OUTLIER) cc_final: 0.4184 (tt) REVERT: A 368 ARG cc_start: 0.5672 (OUTLIER) cc_final: 0.3587 (mmt-90) REVERT: A 394 LYS cc_start: 0.7129 (mttt) cc_final: 0.6654 (mmtt) REVERT: A 448 MET cc_start: 0.7404 (mmm) cc_final: 0.7071 (mmm) REVERT: B 99 PHE cc_start: 0.5559 (OUTLIER) cc_final: 0.5199 (p90) REVERT: B 163 ASP cc_start: 0.6574 (OUTLIER) cc_final: 0.6041 (m-30) REVERT: B 183 GLU cc_start: 0.1900 (OUTLIER) cc_final: 0.1544 (tt0) REVERT: B 334 MET cc_start: 0.4689 (tpp) cc_final: 0.4404 (ttp) REVERT: B 390 SER cc_start: 0.6646 (t) cc_final: 0.6444 (p) REVERT: B 435 TYR cc_start: 0.4905 (OUTLIER) cc_final: 0.3052 (t80) outliers start: 33 outliers final: 15 residues processed: 157 average time/residue: 0.0863 time to fit residues: 19.1075 Evaluate side-chains 138 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 435 TYR Chi-restraints excluded: chain B residue 484 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 38 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 22 optimal weight: 0.0470 chunk 113 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 GLN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.231846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.201844 restraints weight = 12494.672| |-----------------------------------------------------------------------------| r_work (start): 0.4633 rms_B_bonded: 3.69 r_work: 0.4401 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.4401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5943 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9727 Z= 0.147 Angle : 0.701 8.143 13159 Z= 0.344 Chirality : 0.044 0.141 1466 Planarity : 0.005 0.055 1692 Dihedral : 8.313 112.964 1339 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.73 % Favored : 96.18 % Rotamer: Outliers : 2.87 % Allowed : 17.44 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.25), residues: 1179 helix: -0.13 (0.21), residues: 597 sheet: -1.93 (0.49), residues: 85 loop : -0.47 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 613 TYR 0.023 0.002 TYR B 93 PHE 0.017 0.002 PHE B 99 TRP 0.019 0.002 TRP A 753 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9727) covalent geometry : angle 0.70084 (13159) hydrogen bonds : bond 0.03657 ( 421) hydrogen bonds : angle 5.15904 ( 1164) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 LYS cc_start: 0.7093 (mttt) cc_final: 0.6574 (mmtt) REVERT: A 448 MET cc_start: 0.7461 (mmm) cc_final: 0.7254 (mmm) REVERT: A 528 ASN cc_start: 0.4760 (m110) cc_final: 0.4528 (p0) REVERT: B 68 THR cc_start: 0.6043 (m) cc_final: 0.5667 (p) REVERT: B 99 PHE cc_start: 0.5297 (OUTLIER) cc_final: 0.4968 (p90) REVERT: B 183 GLU cc_start: 0.1129 (OUTLIER) cc_final: 0.0900 (tt0) REVERT: B 334 MET cc_start: 0.4990 (tpp) cc_final: 0.4563 (ttp) REVERT: B 390 SER cc_start: 0.6878 (t) cc_final: 0.6529 (p) REVERT: B 495 MET cc_start: 0.6225 (mmm) cc_final: 0.5669 (tmm) outliers start: 29 outliers final: 17 residues processed: 159 average time/residue: 0.0828 time to fit residues: 18.1402 Evaluate side-chains 139 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 484 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 67 optimal weight: 0.0010 chunk 29 optimal weight: 0.9980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 GLN B 336 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.234679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.206382 restraints weight = 12369.907| |-----------------------------------------------------------------------------| r_work (start): 0.4669 rms_B_bonded: 2.86 r_work: 0.4479 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5831 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9727 Z= 0.128 Angle : 0.666 7.680 13159 Z= 0.326 Chirality : 0.043 0.135 1466 Planarity : 0.004 0.055 1692 Dihedral : 7.916 109.292 1337 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.97 % Allowed : 18.14 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.25), residues: 1179 helix: 0.06 (0.21), residues: 601 sheet: -1.70 (0.49), residues: 92 loop : -0.43 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 613 TYR 0.020 0.002 TYR A 435 PHE 0.014 0.001 PHE B 99 TRP 0.021 0.002 TRP A 753 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9727) covalent geometry : angle 0.66586 (13159) hydrogen bonds : bond 0.03459 ( 421) hydrogen bonds : angle 4.91236 ( 1164) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 LYS cc_start: 0.7021 (mttt) cc_final: 0.6511 (mmtt) REVERT: A 448 MET cc_start: 0.7422 (mmm) cc_final: 0.7118 (mmm) REVERT: A 714 ASN cc_start: 0.7049 (m110) cc_final: 0.6048 (t0) REVERT: A 761 MET cc_start: 0.3420 (tpt) cc_final: 0.2901 (tpt) REVERT: B 68 THR cc_start: 0.6134 (m) cc_final: 0.5356 (p) REVERT: B 99 PHE cc_start: 0.5295 (OUTLIER) cc_final: 0.5066 (p90) REVERT: B 163 ASP cc_start: 0.6705 (OUTLIER) cc_final: 0.6328 (m-30) REVERT: B 183 GLU cc_start: 0.1247 (OUTLIER) cc_final: 0.0586 (tt0) REVERT: B 334 MET cc_start: 0.4800 (tpp) cc_final: 0.4421 (ttt) REVERT: B 390 SER cc_start: 0.6945 (t) cc_final: 0.6548 (p) REVERT: B 449 ARG cc_start: 0.6893 (tmm-80) cc_final: 0.6605 (mtt-85) REVERT: B 495 MET cc_start: 0.6215 (mmm) cc_final: 0.5667 (mmm) outliers start: 30 outliers final: 15 residues processed: 164 average time/residue: 0.0917 time to fit residues: 20.5171 Evaluate side-chains 150 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 391 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 56 optimal weight: 10.0000 chunk 40 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN A 528 ASN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.233429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.205588 restraints weight = 12040.717| |-----------------------------------------------------------------------------| r_work (start): 0.4671 rms_B_bonded: 3.17 r_work: 0.4446 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5867 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9727 Z= 0.134 Angle : 0.674 9.466 13159 Z= 0.329 Chirality : 0.043 0.152 1466 Planarity : 0.005 0.055 1692 Dihedral : 7.687 104.468 1334 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.57 % Allowed : 19.03 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.25), residues: 1179 helix: 0.15 (0.21), residues: 598 sheet: -1.72 (0.50), residues: 82 loop : -0.47 (0.30), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 256 TYR 0.021 0.002 TYR A 93 PHE 0.012 0.001 PHE B 99 TRP 0.020 0.002 TRP A 753 HIS 0.004 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9727) covalent geometry : angle 0.67353 (13159) hydrogen bonds : bond 0.03312 ( 421) hydrogen bonds : angle 4.83860 ( 1164) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7048 (p0) cc_final: 0.6296 (t0) REVERT: A 394 LYS cc_start: 0.7116 (mttt) cc_final: 0.6580 (mmtt) REVERT: A 448 MET cc_start: 0.7387 (mmm) cc_final: 0.7115 (mmm) REVERT: A 500 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6838 (tt0) REVERT: A 610 ASP cc_start: 0.4446 (t0) cc_final: 0.4163 (m-30) REVERT: A 747 MET cc_start: -0.1331 (mmm) cc_final: -0.1823 (mmt) REVERT: A 761 MET cc_start: 0.3740 (tpt) cc_final: 0.3045 (tpt) REVERT: B 163 ASP cc_start: 0.6697 (OUTLIER) cc_final: 0.6310 (m-30) REVERT: B 183 GLU cc_start: 0.1416 (OUTLIER) cc_final: 0.0770 (tt0) REVERT: B 334 MET cc_start: 0.4715 (tpp) cc_final: 0.4350 (ttt) REVERT: B 390 SER cc_start: 0.6908 (t) cc_final: 0.6476 (p) REVERT: B 495 MET cc_start: 0.6032 (mmm) cc_final: 0.5553 (mmm) outliers start: 36 outliers final: 21 residues processed: 164 average time/residue: 0.0872 time to fit residues: 20.2597 Evaluate side-chains 153 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 787 MET Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 453 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 56 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 58 optimal weight: 0.0470 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 0.0570 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 456 GLN A 584 GLN B 81 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4997 r_free = 0.4997 target = 0.243189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.215652 restraints weight = 12458.699| |-----------------------------------------------------------------------------| r_work (start): 0.4782 rms_B_bonded: 2.86 r_work: 0.4591 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.4591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9727 Z= 0.116 Angle : 0.650 8.719 13159 Z= 0.315 Chirality : 0.042 0.155 1466 Planarity : 0.005 0.055 1692 Dihedral : 7.249 100.695 1332 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.37 % Allowed : 19.43 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.25), residues: 1179 helix: 0.34 (0.21), residues: 598 sheet: -1.62 (0.46), residues: 104 loop : -0.22 (0.31), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 613 TYR 0.020 0.002 TYR A 435 PHE 0.010 0.001 PHE A 422 TRP 0.023 0.002 TRP A 753 HIS 0.007 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9727) covalent geometry : angle 0.65042 (13159) hydrogen bonds : bond 0.03138 ( 421) hydrogen bonds : angle 4.68885 ( 1164) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 LYS cc_start: 0.7164 (mttt) cc_final: 0.6608 (mmtt) REVERT: A 448 MET cc_start: 0.7348 (mmm) cc_final: 0.7132 (mmm) REVERT: A 500 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6741 (tt0) REVERT: A 610 ASP cc_start: 0.4247 (t0) cc_final: 0.3999 (m-30) REVERT: A 761 MET cc_start: 0.3758 (tpt) cc_final: 0.3159 (tpt) REVERT: B 163 ASP cc_start: 0.6399 (OUTLIER) cc_final: 0.6034 (m-30) REVERT: B 183 GLU cc_start: 0.1722 (OUTLIER) cc_final: 0.1033 (tt0) REVERT: B 334 MET cc_start: 0.4540 (tpp) cc_final: 0.4235 (ttt) REVERT: B 390 SER cc_start: 0.6888 (t) cc_final: 0.6467 (p) REVERT: B 495 MET cc_start: 0.5902 (mmm) cc_final: 0.5475 (tmm) REVERT: B 540 PHE cc_start: 0.5049 (t80) cc_final: 0.4849 (m-10) REVERT: B 554 ASN cc_start: 0.2486 (m110) cc_final: 0.0963 (t0) outliers start: 34 outliers final: 19 residues processed: 164 average time/residue: 0.0816 time to fit residues: 19.0379 Evaluate side-chains 149 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 613 ARG Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 453 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 69 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 GLN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 HIS B 529 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.238411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.210061 restraints weight = 12543.884| |-----------------------------------------------------------------------------| r_work (start): 0.4741 rms_B_bonded: 3.16 r_work: 0.4528 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5915 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9727 Z= 0.149 Angle : 0.707 12.172 13159 Z= 0.340 Chirality : 0.045 0.185 1466 Planarity : 0.005 0.055 1692 Dihedral : 7.303 90.666 1332 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.97 % Allowed : 20.91 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.25), residues: 1179 helix: 0.34 (0.21), residues: 597 sheet: -1.57 (0.48), residues: 98 loop : -0.40 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 676 TYR 0.021 0.002 TYR B 93 PHE 0.011 0.001 PHE A 422 TRP 0.024 0.002 TRP A 753 HIS 0.006 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9727) covalent geometry : angle 0.70700 (13159) hydrogen bonds : bond 0.03329 ( 421) hydrogen bonds : angle 4.72936 ( 1164) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.5841 (mmp) cc_final: 0.5606 (mmt) REVERT: A 394 LYS cc_start: 0.7164 (mttt) cc_final: 0.6609 (mmtt) REVERT: A 448 MET cc_start: 0.7495 (mmm) cc_final: 0.7226 (mmm) REVERT: A 599 TRP cc_start: 0.7651 (t-100) cc_final: 0.7050 (t60) REVERT: A 709 LYS cc_start: 0.6906 (mmtt) cc_final: 0.6640 (mmtm) REVERT: A 747 MET cc_start: -0.1593 (mmm) cc_final: -0.2158 (mmt) REVERT: A 761 MET cc_start: 0.3612 (tpt) cc_final: 0.3064 (tpt) REVERT: B 81 GLN cc_start: 0.4633 (OUTLIER) cc_final: 0.3168 (tp-100) REVERT: B 163 ASP cc_start: 0.6562 (OUTLIER) cc_final: 0.6156 (m-30) REVERT: B 183 GLU cc_start: 0.1666 (OUTLIER) cc_final: 0.0938 (tt0) REVERT: B 334 MET cc_start: 0.4654 (tpp) cc_final: 0.4365 (ttp) REVERT: B 390 SER cc_start: 0.6936 (t) cc_final: 0.6474 (p) REVERT: B 495 MET cc_start: 0.5970 (mmm) cc_final: 0.5512 (mmm) outliers start: 30 outliers final: 22 residues processed: 150 average time/residue: 0.0859 time to fit residues: 18.1513 Evaluate side-chains 147 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 613 ARG Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 787 MET Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 453 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 112 optimal weight: 0.1980 chunk 63 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN B 336 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.239964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.212100 restraints weight = 12496.303| |-----------------------------------------------------------------------------| r_work (start): 0.4753 rms_B_bonded: 2.73 r_work: 0.4563 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5879 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9727 Z= 0.149 Angle : 0.710 11.524 13159 Z= 0.346 Chirality : 0.044 0.164 1466 Planarity : 0.005 0.056 1692 Dihedral : 7.208 87.579 1332 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.17 % Allowed : 21.31 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.25), residues: 1179 helix: 0.24 (0.21), residues: 598 sheet: -1.64 (0.47), residues: 98 loop : -0.49 (0.31), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 256 TYR 0.024 0.002 TYR A 571 PHE 0.011 0.001 PHE A 422 TRP 0.027 0.002 TRP A 753 HIS 0.005 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9727) covalent geometry : angle 0.71020 (13159) hydrogen bonds : bond 0.03348 ( 421) hydrogen bonds : angle 4.76190 ( 1164) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.5732 (mmp) cc_final: 0.5522 (mmt) REVERT: A 394 LYS cc_start: 0.7221 (mttt) cc_final: 0.6651 (mmtt) REVERT: A 599 TRP cc_start: 0.7641 (t-100) cc_final: 0.7023 (t60) REVERT: A 709 LYS cc_start: 0.7025 (mmtt) cc_final: 0.6687 (mmtm) REVERT: A 747 MET cc_start: -0.1786 (mmm) cc_final: -0.2329 (mmt) REVERT: A 761 MET cc_start: 0.3756 (tpt) cc_final: 0.3235 (tpt) REVERT: B 81 GLN cc_start: 0.4704 (OUTLIER) cc_final: 0.3262 (tp-100) REVERT: B 163 ASP cc_start: 0.6668 (OUTLIER) cc_final: 0.6265 (m-30) REVERT: B 183 GLU cc_start: 0.1395 (OUTLIER) cc_final: 0.0742 (tt0) REVERT: B 334 MET cc_start: 0.4598 (tpp) cc_final: 0.4332 (ttp) REVERT: B 390 SER cc_start: 0.6961 (t) cc_final: 0.6516 (p) REVERT: B 495 MET cc_start: 0.6160 (mmm) cc_final: 0.5681 (mmm) REVERT: B 540 PHE cc_start: 0.4950 (t80) cc_final: 0.4713 (m-10) REVERT: B 554 ASN cc_start: 0.2582 (m110) cc_final: 0.0913 (t0) outliers start: 32 outliers final: 24 residues processed: 146 average time/residue: 0.0975 time to fit residues: 19.5872 Evaluate side-chains 147 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 613 ARG Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 787 MET Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 453 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 61 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 78 optimal weight: 0.4980 chunk 88 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN B 336 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.235180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.207124 restraints weight = 12315.919| |-----------------------------------------------------------------------------| r_work (start): 0.4682 rms_B_bonded: 2.63 r_work: 0.4507 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5824 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9727 Z= 0.139 Angle : 0.709 11.608 13159 Z= 0.343 Chirality : 0.044 0.162 1466 Planarity : 0.005 0.055 1692 Dihedral : 7.003 85.547 1332 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.68 % Allowed : 21.80 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.25), residues: 1179 helix: 0.35 (0.22), residues: 593 sheet: -1.64 (0.48), residues: 98 loop : -0.49 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 36 TYR 0.023 0.002 TYR A 571 PHE 0.010 0.001 PHE A 422 TRP 0.031 0.002 TRP A 753 HIS 0.005 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9727) covalent geometry : angle 0.70899 (13159) hydrogen bonds : bond 0.03211 ( 421) hydrogen bonds : angle 4.75083 ( 1164) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.6759 (p0) cc_final: 0.6098 (t0) REVERT: A 105 CYS cc_start: 0.4796 (OUTLIER) cc_final: 0.2891 (p) REVERT: A 225 MET cc_start: 0.5715 (mmp) cc_final: 0.5379 (mmt) REVERT: A 228 GLU cc_start: 0.5846 (pm20) cc_final: 0.5398 (pm20) REVERT: A 335 MET cc_start: 0.3441 (mtt) cc_final: 0.2873 (mtm) REVERT: A 394 LYS cc_start: 0.7176 (mttt) cc_final: 0.6569 (mmtt) REVERT: A 495 MET cc_start: 0.5970 (tpt) cc_final: 0.5353 (tpt) REVERT: A 599 TRP cc_start: 0.7635 (t-100) cc_final: 0.7016 (t60) REVERT: A 632 LYS cc_start: 0.6876 (tttt) cc_final: 0.6653 (tmtt) REVERT: A 709 LYS cc_start: 0.7019 (mmtt) cc_final: 0.6708 (mmtm) REVERT: B 81 GLN cc_start: 0.4829 (OUTLIER) cc_final: 0.3375 (tp-100) REVERT: B 163 ASP cc_start: 0.6639 (OUTLIER) cc_final: 0.6230 (m-30) REVERT: B 183 GLU cc_start: 0.1726 (OUTLIER) cc_final: 0.1060 (tt0) REVERT: B 390 SER cc_start: 0.6917 (t) cc_final: 0.6466 (p) REVERT: B 495 MET cc_start: 0.6141 (mmm) cc_final: 0.5686 (mmm) REVERT: B 554 ASN cc_start: 0.2455 (m110) cc_final: 0.0928 (t0) REVERT: B 600 TYR cc_start: 0.8157 (m-80) cc_final: 0.7925 (m-80) outliers start: 27 outliers final: 22 residues processed: 146 average time/residue: 0.0869 time to fit residues: 17.7625 Evaluate side-chains 150 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 613 ARG Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 787 MET Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 391 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 4 optimal weight: 0.5980 chunk 70 optimal weight: 0.2980 chunk 57 optimal weight: 20.0000 chunk 21 optimal weight: 0.0980 chunk 46 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 79 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.238769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.210006 restraints weight = 12345.359| |-----------------------------------------------------------------------------| r_work (start): 0.4698 rms_B_bonded: 2.91 r_work: 0.4523 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5744 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9727 Z= 0.122 Angle : 0.691 12.071 13159 Z= 0.333 Chirality : 0.043 0.159 1466 Planarity : 0.005 0.055 1692 Dihedral : 6.554 78.878 1332 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.38 % Allowed : 21.90 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.25), residues: 1179 helix: 0.48 (0.22), residues: 591 sheet: -1.54 (0.48), residues: 98 loop : -0.37 (0.31), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 36 TYR 0.021 0.002 TYR A 571 PHE 0.012 0.001 PHE A 422 TRP 0.031 0.002 TRP A 753 HIS 0.005 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9727) covalent geometry : angle 0.69120 (13159) hydrogen bonds : bond 0.03102 ( 421) hydrogen bonds : angle 4.65597 ( 1164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1908.04 seconds wall clock time: 33 minutes 27.91 seconds (2007.91 seconds total)