Starting phenix.real_space_refine on Sat Aug 23 06:32:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wsr_37822/08_2025/8wsr_37822.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wsr_37822/08_2025/8wsr_37822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wsr_37822/08_2025/8wsr_37822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wsr_37822/08_2025/8wsr_37822.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wsr_37822/08_2025/8wsr_37822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wsr_37822/08_2025/8wsr_37822.map" } resolution = 2.99 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= 0.003 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4891 atoms to isotropic. 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 37 5.16 5 C 4135 2.51 5 N 1065 2.21 5 O 1237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6475 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1514 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 12, 'TRANS': 180} Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 1.83, per 1000 atoms: 0.28 Number of scatterers: 6475 At special positions: 0 Unit cell: (75.9, 84.18, 120.75, 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 37 16.00 O 1237 8.00 N 1065 7.00 C 4135 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 901 " - " ASN A 103 " " NAG A 902 " - " ASN A 53 " " NAG A 903 " - " ASN A 90 " " NAG A 905 " - " ASN A 432 " " NAG A 906 " - " ASN A 322 " " NAG B 1 " - " ASN A 546 " Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 476.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 904 " pdb="ZN ZN A 904 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 904 " - pdb=" NE2 HIS A 378 " 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1486 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 6 sheets defined 59.4% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'C' and resid 324 through 329 Processing helix chain 'C' and resid 336 through 340 removed outlier: 3.518A pdb=" N TRP C 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.967A pdb=" N VAL C 354 " --> pdb=" O ASP C 351 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR C 356 " --> pdb=" O SER C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 376 removed outlier: 3.754A pdb=" N LEU C 374 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN C 375 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 397 Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 425 through 430 Processing helix chain 'C' and resid 488 through 492 removed outlier: 4.009A pdb=" N GLN C 492 " --> pdb=" O VAL C 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.896A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.771A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.758A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 88' Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.721A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.817A pdb=" N GLU A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.598A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 193 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 232 removed outlier: 4.121A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.535A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 282 removed outlier: 4.236A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.816A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.698A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.901A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.578A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.597A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.584A pdb=" N THR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.567A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 547 through 561 removed outlier: 3.802A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 560 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.838A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 removed outlier: 3.621A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Proline residue: A 590 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 341 through 344 removed outlier: 3.667A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN C 381 " --> pdb=" O GLU C 502 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.177A pdb=" N CYS C 348 " --> pdb=" O CYS C 511 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 510 " --> pdb=" O PHE C 379 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AA4, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA5, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.346A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 350 301 hydrogen bonds defined for protein. 840 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: 1.09 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2062 1.34 - 1.46: 1722 1.46 - 1.59: 2813 1.59 - 1.71: 0 1.71 - 1.84: 58 Bond restraints: 6655 Sorted by residual: bond pdb=" N PRO A 135 " pdb=" CD PRO A 135 " ideal model delta sigma weight residual 1.473 1.393 0.080 1.40e-02 5.10e+03 3.24e+01 bond pdb=" CA TYR A 83 " pdb=" C TYR A 83 " ideal model delta sigma weight residual 1.524 1.588 -0.064 1.26e-02 6.30e+03 2.58e+01 bond pdb=" C TYR A 83 " pdb=" N PRO A 84 " ideal model delta sigma weight residual 1.332 1.388 -0.057 1.30e-02 5.92e+03 1.90e+01 bond pdb=" CA ASN A 322 " pdb=" C ASN A 322 " ideal model delta sigma weight residual 1.528 1.480 0.049 1.28e-02 6.10e+03 1.46e+01 bond pdb=" C ILE A 468 " pdb=" N PRO A 469 " ideal model delta sigma weight residual 1.330 1.372 -0.042 1.25e-02 6.40e+03 1.14e+01 ... (remaining 6650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 8824 2.32 - 4.65: 190 4.65 - 6.97: 28 6.97 - 9.29: 3 9.29 - 11.62: 6 Bond angle restraints: 9051 Sorted by residual: angle pdb=" N GLY C 463 " pdb=" CA GLY C 463 " pdb=" C GLY C 463 " ideal model delta sigma weight residual 112.37 100.84 11.53 1.40e+00 5.10e-01 6.78e+01 angle pdb=" N TYR C 460 " pdb=" CA TYR C 460 " pdb=" C TYR C 460 " ideal model delta sigma weight residual 111.24 122.11 -10.87 1.38e+00 5.25e-01 6.20e+01 angle pdb=" N ILE C 459 " pdb=" CA ILE C 459 " pdb=" C ILE C 459 " ideal model delta sigma weight residual 112.17 118.43 -6.26 9.50e-01 1.11e+00 4.35e+01 angle pdb=" C ILE A 468 " pdb=" N PRO A 469 " pdb=" CA PRO A 469 " ideal model delta sigma weight residual 120.21 114.43 5.78 9.60e-01 1.09e+00 3.63e+01 angle pdb=" N GLU A 402 " pdb=" CA GLU A 402 " pdb=" C GLU A 402 " ideal model delta sigma weight residual 111.82 118.50 -6.68 1.16e+00 7.43e-01 3.32e+01 ... (remaining 9046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3438 17.86 - 35.73: 415 35.73 - 53.59: 126 53.59 - 71.46: 30 71.46 - 89.32: 11 Dihedral angle restraints: 4020 sinusoidal: 1704 harmonic: 2316 Sorted by residual: dihedral pdb=" CB CYS C 323 " pdb=" SG CYS C 323 " pdb=" SG CYS C 348 " pdb=" CB CYS C 348 " ideal model delta sinusoidal sigma weight residual -86.00 -174.14 88.14 1 1.00e+01 1.00e-02 9.29e+01 dihedral pdb=" N TYR C 460 " pdb=" C TYR C 460 " pdb=" CA TYR C 460 " pdb=" CB TYR C 460 " ideal model delta harmonic sigma weight residual 122.80 142.12 -19.32 0 2.50e+00 1.60e-01 5.97e+01 dihedral pdb=" C TYR C 460 " pdb=" N TYR C 460 " pdb=" CA TYR C 460 " pdb=" CB TYR C 460 " ideal model delta harmonic sigma weight residual -122.60 -139.37 16.77 0 2.50e+00 1.60e-01 4.50e+01 ... (remaining 4017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.172: 950 0.172 - 0.343: 16 0.343 - 0.515: 2 0.515 - 0.686: 0 0.686 - 0.858: 1 Chirality restraints: 969 Sorted by residual: chirality pdb=" CA TYR C 460 " pdb=" N TYR C 460 " pdb=" C TYR C 460 " pdb=" CB TYR C 460 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.84e+01 chirality pdb=" CA GLU A 402 " pdb=" N GLU A 402 " pdb=" C GLU A 402 " pdb=" CB GLU A 402 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 966 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 901 " -0.356 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG A 901 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG A 901 " -0.139 2.00e-02 2.50e+03 pdb=" N2 NAG A 901 " 0.543 2.00e-02 2.50e+03 pdb=" O7 NAG A 901 " -0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 906 " 0.263 2.00e-02 2.50e+03 2.25e-01 6.33e+02 pdb=" C7 NAG A 906 " -0.064 2.00e-02 2.50e+03 pdb=" C8 NAG A 906 " 0.165 2.00e-02 2.50e+03 pdb=" N2 NAG A 906 " -0.390 2.00e-02 2.50e+03 pdb=" O7 NAG A 906 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 78 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" C THR A 78 " 0.052 2.00e-02 2.50e+03 pdb=" O THR A 78 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU A 79 " -0.017 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.88: 4 1.88 - 2.63: 59 2.63 - 3.39: 8244 3.39 - 4.14: 13890 4.14 - 4.90: 26230 Nonbonded interactions: 48427 Sorted by model distance: nonbonded pdb=" ND2 ASN A 137 " pdb=" OE2 GLU A 140 " model vdw 1.124 3.120 nonbonded pdb=" O PRO A 135 " pdb=" OD1 ASP A 136 " model vdw 1.291 3.040 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 904 " model vdw 1.453 2.230 nonbonded pdb=" ND2 ASN A 137 " pdb=" CD GLU A 140 " model vdw 1.735 3.350 nonbonded pdb=" OD1 ASN A 134 " pdb=" CD PRO A 135 " model vdw 2.046 3.440 ... (remaining 48422 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.580 Find NCS groups from input model: 0.030 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:9.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 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 : 0.005 0.080 6671 Z= 0.280 Angle : 0.839 11.615 9086 Z= 0.500 Chirality : 0.063 0.858 969 Planarity : 0.012 0.305 1164 Dihedral : 17.386 89.319 2513 Min Nonbonded Distance : 1.124 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.45 % Allowed : 22.83 % Favored : 75.72 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: -0.22 (0.29), residues: 785 helix: 0.66 (0.28), residues: 383 sheet: 1.16 (0.68), residues: 44 loop : -1.20 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 582 TYR 0.020 0.002 TYR A 183 PHE 0.017 0.001 PHE A 308 TRP 0.016 0.001 TRP A 478 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 6655) covalent geometry : angle 0.82163 ( 9051) SS BOND : bond 0.00388 ( 7) SS BOND : angle 1.00353 ( 14) hydrogen bonds : bond 0.18605 ( 301) hydrogen bonds : angle 6.51435 ( 840) metal coordination : bond 0.00503 ( 2) link_BETA1-4 : bond 0.00200 ( 1) link_BETA1-4 : angle 1.19021 ( 3) link_NAG-ASN : bond 0.00692 ( 6) link_NAG-ASN : angle 3.81410 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.190 Fit side-chains REVERT: A 129 THR cc_start: 0.8785 (t) cc_final: 0.8570 (p) outliers start: 10 outliers final: 6 residues processed: 160 average time/residue: 0.5652 time to fit residues: 94.2548 Evaluate side-chains 139 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 391 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 40.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0010 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 396 GLN C 437 ASN C 492 GLN A 34 HIS A 42 GLN A 102 GLN A 121 ASN A 194 ASN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN A 340 GLN A 531 GLN A 535 HIS A 601 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.123470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101563 restraints weight = 9745.348| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.28 r_work: 0.3089 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6671 Z= 0.131 Angle : 0.574 7.491 9086 Z= 0.296 Chirality : 0.043 0.281 969 Planarity : 0.005 0.057 1164 Dihedral : 6.706 54.683 1012 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.18 % Allowed : 23.12 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: 0.32 (0.29), residues: 785 helix: 1.34 (0.27), residues: 388 sheet: 1.23 (0.68), residues: 44 loop : -1.24 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 582 TYR 0.018 0.001 TYR A 50 PHE 0.008 0.001 PHE A 308 TRP 0.010 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6655) covalent geometry : angle 0.56197 ( 9051) SS BOND : bond 0.00260 ( 7) SS BOND : angle 0.66908 ( 14) hydrogen bonds : bond 0.05878 ( 301) hydrogen bonds : angle 4.40976 ( 840) metal coordination : bond 0.00120 ( 2) link_BETA1-4 : bond 0.00528 ( 1) link_BETA1-4 : angle 0.91042 ( 3) link_NAG-ASN : bond 0.00644 ( 6) link_NAG-ASN : angle 2.66610 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 129 THR cc_start: 0.8684 (t) cc_final: 0.8313 (p) REVERT: A 184 VAL cc_start: 0.8322 (t) cc_final: 0.8046 (t) REVERT: A 270 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8241 (tpp) REVERT: A 316 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8530 (p) REVERT: A 430 GLU cc_start: 0.8012 (mp0) cc_final: 0.7801 (mp0) REVERT: A 435 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7576 (mm-30) REVERT: A 574 VAL cc_start: 0.8808 (m) cc_final: 0.8529 (t) REVERT: A 600 LYS cc_start: 0.8551 (mtmt) cc_final: 0.8066 (mtmt) outliers start: 22 outliers final: 5 residues processed: 152 average time/residue: 0.5402 time to fit residues: 86.1266 Evaluate side-chains 138 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 401 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 66 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 86 GLN A 134 ASN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN A 601 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.120918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.099171 restraints weight = 9554.747| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.22 r_work: 0.3043 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6671 Z= 0.194 Angle : 0.580 8.754 9086 Z= 0.300 Chirality : 0.045 0.363 969 Planarity : 0.004 0.054 1164 Dihedral : 6.044 52.996 1005 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.32 % Allowed : 22.54 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: 0.38 (0.29), residues: 785 helix: 1.52 (0.27), residues: 385 sheet: 1.18 (0.67), residues: 44 loop : -1.36 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 445 TYR 0.016 0.002 TYR A 385 PHE 0.017 0.001 PHE A 308 TRP 0.011 0.001 TRP A 477 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 6655) covalent geometry : angle 0.56866 ( 9051) SS BOND : bond 0.00246 ( 7) SS BOND : angle 0.85082 ( 14) hydrogen bonds : bond 0.07135 ( 301) hydrogen bonds : angle 4.29824 ( 840) metal coordination : bond 0.00535 ( 2) link_BETA1-4 : bond 0.00016 ( 1) link_BETA1-4 : angle 1.10468 ( 3) link_NAG-ASN : bond 0.00322 ( 6) link_NAG-ASN : angle 2.52385 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.225 Fit side-chains REVERT: C 489 VAL cc_start: 0.8744 (p) cc_final: 0.8491 (t) REVERT: A 129 THR cc_start: 0.8795 (t) cc_final: 0.8500 (p) REVERT: A 154 ASN cc_start: 0.8954 (m-40) cc_final: 0.8744 (m-40) REVERT: A 184 VAL cc_start: 0.8379 (t) cc_final: 0.8111 (t) REVERT: A 227 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: A 257 SER cc_start: 0.8998 (t) cc_final: 0.8705 (p) REVERT: A 430 GLU cc_start: 0.7977 (mp0) cc_final: 0.7721 (mp0) REVERT: A 435 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7506 (mm-30) REVERT: A 574 VAL cc_start: 0.8934 (m) cc_final: 0.8649 (t) REVERT: A 600 LYS cc_start: 0.8608 (mtmt) cc_final: 0.8107 (mtmt) outliers start: 23 outliers final: 9 residues processed: 156 average time/residue: 0.5304 time to fit residues: 86.5162 Evaluate side-chains 144 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN A 531 GLN A 601 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.121780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.099981 restraints weight = 9581.965| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.24 r_work: 0.3056 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6671 Z= 0.152 Angle : 0.535 7.157 9086 Z= 0.279 Chirality : 0.043 0.347 969 Planarity : 0.004 0.052 1164 Dihedral : 6.010 58.841 1005 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.03 % Allowed : 22.54 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: 0.51 (0.29), residues: 785 helix: 1.63 (0.27), residues: 384 sheet: 1.21 (0.67), residues: 44 loop : -1.28 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 445 TYR 0.015 0.001 TYR A 50 PHE 0.012 0.001 PHE A 308 TRP 0.009 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6655) covalent geometry : angle 0.52423 ( 9051) SS BOND : bond 0.00326 ( 7) SS BOND : angle 0.88143 ( 14) hydrogen bonds : bond 0.06270 ( 301) hydrogen bonds : angle 4.19668 ( 840) metal coordination : bond 0.00388 ( 2) link_BETA1-4 : bond 0.00318 ( 1) link_BETA1-4 : angle 1.10667 ( 3) link_NAG-ASN : bond 0.00278 ( 6) link_NAG-ASN : angle 2.38655 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.234 Fit side-chains REVERT: C 489 VAL cc_start: 0.8767 (p) cc_final: 0.8512 (t) REVERT: A 81 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7735 (mp-120) REVERT: A 129 THR cc_start: 0.8770 (t) cc_final: 0.8461 (p) REVERT: A 166 GLU cc_start: 0.8032 (tp30) cc_final: 0.7666 (mm-30) REVERT: A 171 GLU cc_start: 0.8161 (tt0) cc_final: 0.7931 (tm-30) REVERT: A 184 VAL cc_start: 0.8340 (t) cc_final: 0.8096 (t) REVERT: A 227 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: A 257 SER cc_start: 0.8984 (t) cc_final: 0.8691 (p) REVERT: A 430 GLU cc_start: 0.7930 (mp0) cc_final: 0.7658 (mp0) REVERT: A 435 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7454 (mm-30) REVERT: A 574 VAL cc_start: 0.8920 (m) cc_final: 0.8695 (t) REVERT: A 600 LYS cc_start: 0.8623 (mtmt) cc_final: 0.8100 (mtmt) outliers start: 21 outliers final: 12 residues processed: 145 average time/residue: 0.5160 time to fit residues: 78.4111 Evaluate side-chains 146 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 67 optimal weight: 0.4980 chunk 2 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN A 601 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.101031 restraints weight = 9587.412| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.26 r_work: 0.3090 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6671 Z= 0.119 Angle : 0.498 5.201 9086 Z= 0.262 Chirality : 0.041 0.298 969 Planarity : 0.004 0.051 1164 Dihedral : 5.663 53.418 1005 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.89 % Allowed : 23.55 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: 0.61 (0.30), residues: 785 helix: 1.64 (0.27), residues: 387 sheet: 1.25 (0.67), residues: 44 loop : -1.16 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 445 TYR 0.015 0.001 TYR A 50 PHE 0.010 0.001 PHE A 308 TRP 0.008 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6655) covalent geometry : angle 0.48751 ( 9051) SS BOND : bond 0.00341 ( 7) SS BOND : angle 0.73332 ( 14) hydrogen bonds : bond 0.05422 ( 301) hydrogen bonds : angle 4.10517 ( 840) metal coordination : bond 0.00241 ( 2) link_BETA1-4 : bond 0.00300 ( 1) link_BETA1-4 : angle 1.07610 ( 3) link_NAG-ASN : bond 0.00289 ( 6) link_NAG-ASN : angle 2.20673 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: C 420 VAL cc_start: 0.8149 (t) cc_final: 0.7939 (p) REVERT: C 489 VAL cc_start: 0.8754 (p) cc_final: 0.8489 (t) REVERT: A 129 THR cc_start: 0.8716 (t) cc_final: 0.8389 (p) REVERT: A 166 GLU cc_start: 0.8009 (tp30) cc_final: 0.7700 (mm-30) REVERT: A 171 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: A 184 VAL cc_start: 0.8299 (t) cc_final: 0.8064 (t) REVERT: A 227 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: A 257 SER cc_start: 0.8988 (t) cc_final: 0.8694 (p) REVERT: A 430 GLU cc_start: 0.7921 (mp0) cc_final: 0.7661 (mp0) REVERT: A 435 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7469 (mm-30) REVERT: A 600 LYS cc_start: 0.8615 (mtmt) cc_final: 0.8156 (mtmt) outliers start: 20 outliers final: 11 residues processed: 141 average time/residue: 0.5129 time to fit residues: 75.7024 Evaluate side-chains 140 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 0.0020 chunk 17 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN A 601 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.123368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101329 restraints weight = 9640.529| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.28 r_work: 0.3100 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6671 Z= 0.115 Angle : 0.499 8.677 9086 Z= 0.258 Chirality : 0.041 0.266 969 Planarity : 0.004 0.050 1164 Dihedral : 5.446 53.198 1005 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.31 % Allowed : 25.00 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: 0.64 (0.30), residues: 785 helix: 1.62 (0.27), residues: 393 sheet: 1.44 (0.66), residues: 43 loop : -1.15 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 445 TYR 0.015 0.001 TYR A 50 PHE 0.010 0.001 PHE A 308 TRP 0.009 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 6655) covalent geometry : angle 0.48988 ( 9051) SS BOND : bond 0.00298 ( 7) SS BOND : angle 0.76043 ( 14) hydrogen bonds : bond 0.05080 ( 301) hydrogen bonds : angle 4.02518 ( 840) metal coordination : bond 0.00208 ( 2) link_BETA1-4 : bond 0.00319 ( 1) link_BETA1-4 : angle 1.08527 ( 3) link_NAG-ASN : bond 0.00276 ( 6) link_NAG-ASN : angle 2.03814 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: C 420 VAL cc_start: 0.8159 (t) cc_final: 0.7946 (p) REVERT: C 489 VAL cc_start: 0.8759 (p) cc_final: 0.8487 (t) REVERT: A 129 THR cc_start: 0.8700 (t) cc_final: 0.8371 (p) REVERT: A 166 GLU cc_start: 0.8007 (tp30) cc_final: 0.7762 (mm-30) REVERT: A 171 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7878 (tm-30) REVERT: A 184 VAL cc_start: 0.8260 (t) cc_final: 0.8031 (t) REVERT: A 227 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: A 257 SER cc_start: 0.8974 (t) cc_final: 0.8678 (p) REVERT: A 401 HIS cc_start: 0.8216 (OUTLIER) cc_final: 0.7626 (m-70) REVERT: A 430 GLU cc_start: 0.7920 (mp0) cc_final: 0.7671 (mp0) REVERT: A 435 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7486 (mm-30) REVERT: A 600 LYS cc_start: 0.8626 (mtmt) cc_final: 0.8165 (mtmt) outliers start: 16 outliers final: 9 residues processed: 139 average time/residue: 0.5022 time to fit residues: 73.2536 Evaluate side-chains 137 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN A 601 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.121947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.100086 restraints weight = 9502.048| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.23 r_work: 0.3073 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6671 Z= 0.149 Angle : 0.507 4.940 9086 Z= 0.267 Chirality : 0.042 0.282 969 Planarity : 0.004 0.050 1164 Dihedral : 5.464 52.775 1005 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.03 % Allowed : 23.70 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: 0.63 (0.30), residues: 785 helix: 1.69 (0.27), residues: 387 sheet: 1.29 (0.66), residues: 44 loop : -1.19 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 445 TYR 0.013 0.001 TYR A 516 PHE 0.013 0.001 PHE A 308 TRP 0.009 0.001 TRP A 165 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6655) covalent geometry : angle 0.49706 ( 9051) SS BOND : bond 0.00301 ( 7) SS BOND : angle 0.80361 ( 14) hydrogen bonds : bond 0.05963 ( 301) hydrogen bonds : angle 4.05811 ( 840) metal coordination : bond 0.00367 ( 2) link_BETA1-4 : bond 0.00280 ( 1) link_BETA1-4 : angle 1.19396 ( 3) link_NAG-ASN : bond 0.00278 ( 6) link_NAG-ASN : angle 2.13639 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.192 Fit side-chains REVERT: C 470 VAL cc_start: 0.8732 (t) cc_final: 0.8490 (p) REVERT: C 489 VAL cc_start: 0.8767 (p) cc_final: 0.8505 (t) REVERT: A 129 THR cc_start: 0.8776 (t) cc_final: 0.8494 (p) REVERT: A 171 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: A 227 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: A 257 SER cc_start: 0.8975 (t) cc_final: 0.8680 (p) REVERT: A 430 GLU cc_start: 0.7937 (mp0) cc_final: 0.7703 (mp0) REVERT: A 435 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7494 (mm-30) REVERT: A 600 LYS cc_start: 0.8708 (mtmt) cc_final: 0.8237 (mtmt) outliers start: 21 outliers final: 12 residues processed: 142 average time/residue: 0.5108 time to fit residues: 75.9160 Evaluate side-chains 143 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN A 601 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.121725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100015 restraints weight = 9604.867| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.24 r_work: 0.3064 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6671 Z= 0.148 Angle : 0.523 9.425 9086 Z= 0.272 Chirality : 0.042 0.293 969 Planarity : 0.004 0.050 1164 Dihedral : 5.491 53.116 1005 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.75 % Allowed : 24.28 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: 0.60 (0.30), residues: 785 helix: 1.60 (0.27), residues: 393 sheet: 1.50 (0.65), residues: 43 loop : -1.21 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 445 TYR 0.013 0.001 TYR A 516 PHE 0.012 0.001 PHE A 308 TRP 0.009 0.001 TRP A 165 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6655) covalent geometry : angle 0.51330 ( 9051) SS BOND : bond 0.00367 ( 7) SS BOND : angle 0.83902 ( 14) hydrogen bonds : bond 0.05927 ( 301) hydrogen bonds : angle 4.06457 ( 840) metal coordination : bond 0.00373 ( 2) link_BETA1-4 : bond 0.00267 ( 1) link_BETA1-4 : angle 1.19915 ( 3) link_NAG-ASN : bond 0.00281 ( 6) link_NAG-ASN : angle 2.16818 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.263 Fit side-chains REVERT: C 470 VAL cc_start: 0.8743 (t) cc_final: 0.8502 (p) REVERT: C 489 VAL cc_start: 0.8766 (p) cc_final: 0.8502 (t) REVERT: A 129 THR cc_start: 0.8765 (t) cc_final: 0.8496 (p) REVERT: A 171 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: A 227 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: A 257 SER cc_start: 0.8978 (t) cc_final: 0.8689 (p) REVERT: A 269 ASP cc_start: 0.8417 (t0) cc_final: 0.8146 (m-30) REVERT: A 430 GLU cc_start: 0.7923 (mp0) cc_final: 0.7692 (mp0) REVERT: A 435 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7486 (mm-30) REVERT: A 600 LYS cc_start: 0.8725 (mtmt) cc_final: 0.8248 (mtmt) outliers start: 19 outliers final: 13 residues processed: 138 average time/residue: 0.5702 time to fit residues: 82.4112 Evaluate side-chains 143 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 56 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.122777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.101017 restraints weight = 9611.243| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.24 r_work: 0.3088 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6671 Z= 0.126 Angle : 0.501 4.905 9086 Z= 0.263 Chirality : 0.041 0.284 969 Planarity : 0.004 0.050 1164 Dihedral : 5.455 53.205 1005 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.31 % Allowed : 25.14 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: 0.66 (0.30), residues: 785 helix: 1.65 (0.27), residues: 393 sheet: 1.51 (0.65), residues: 43 loop : -1.18 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 445 TYR 0.013 0.001 TYR A 183 PHE 0.010 0.001 PHE A 308 TRP 0.009 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6655) covalent geometry : angle 0.49236 ( 9051) SS BOND : bond 0.00335 ( 7) SS BOND : angle 0.78922 ( 14) hydrogen bonds : bond 0.05348 ( 301) hydrogen bonds : angle 4.02687 ( 840) metal coordination : bond 0.00259 ( 2) link_BETA1-4 : bond 0.00355 ( 1) link_BETA1-4 : angle 1.17170 ( 3) link_NAG-ASN : bond 0.00293 ( 6) link_NAG-ASN : angle 2.07856 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: C 420 VAL cc_start: 0.8141 (t) cc_final: 0.7929 (p) REVERT: C 470 VAL cc_start: 0.8733 (t) cc_final: 0.8499 (p) REVERT: C 489 VAL cc_start: 0.8756 (p) cc_final: 0.8492 (t) REVERT: A 129 THR cc_start: 0.8739 (t) cc_final: 0.8464 (p) REVERT: A 171 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7814 (tm-30) REVERT: A 184 VAL cc_start: 0.8362 (t) cc_final: 0.8044 (t) REVERT: A 227 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: A 257 SER cc_start: 0.8975 (t) cc_final: 0.8686 (p) REVERT: A 269 ASP cc_start: 0.8388 (t0) cc_final: 0.8141 (m-30) REVERT: A 401 HIS cc_start: 0.8257 (OUTLIER) cc_final: 0.7690 (m-70) REVERT: A 430 GLU cc_start: 0.7921 (mp0) cc_final: 0.7675 (mp0) REVERT: A 435 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7506 (mm-30) REVERT: A 600 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8256 (mtmt) outliers start: 16 outliers final: 12 residues processed: 142 average time/residue: 0.5065 time to fit residues: 75.5810 Evaluate side-chains 144 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 71 optimal weight: 1.9990 chunk 3 optimal weight: 0.0020 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 0.0470 chunk 1 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.6888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.122811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.100732 restraints weight = 9622.437| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.25 r_work: 0.3096 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6671 Z= 0.121 Angle : 0.516 10.962 9086 Z= 0.265 Chirality : 0.041 0.273 969 Planarity : 0.004 0.052 1164 Dihedral : 5.356 53.261 1005 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.46 % Allowed : 25.58 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: 0.71 (0.30), residues: 785 helix: 1.69 (0.27), residues: 393 sheet: 1.52 (0.66), residues: 43 loop : -1.13 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 445 TYR 0.013 0.001 TYR A 516 PHE 0.009 0.001 PHE A 308 TRP 0.009 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6655) covalent geometry : angle 0.50833 ( 9051) SS BOND : bond 0.00310 ( 7) SS BOND : angle 0.73613 ( 14) hydrogen bonds : bond 0.05101 ( 301) hydrogen bonds : angle 3.99382 ( 840) metal coordination : bond 0.00223 ( 2) link_BETA1-4 : bond 0.00282 ( 1) link_BETA1-4 : angle 1.15479 ( 3) link_NAG-ASN : bond 0.00280 ( 6) link_NAG-ASN : angle 1.99780 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: C 420 VAL cc_start: 0.8138 (t) cc_final: 0.7922 (p) REVERT: C 470 VAL cc_start: 0.8743 (t) cc_final: 0.8512 (p) REVERT: C 489 VAL cc_start: 0.8750 (p) cc_final: 0.8487 (t) REVERT: A 129 THR cc_start: 0.8721 (t) cc_final: 0.8440 (p) REVERT: A 171 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7838 (tm-30) REVERT: A 184 VAL cc_start: 0.8331 (t) cc_final: 0.8039 (t) REVERT: A 227 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: A 257 SER cc_start: 0.8987 (t) cc_final: 0.8699 (p) REVERT: A 401 HIS cc_start: 0.8209 (OUTLIER) cc_final: 0.7616 (m-70) REVERT: A 406 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8143 (mm-30) REVERT: A 435 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7548 (mm-30) REVERT: A 600 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8250 (mtmt) outliers start: 17 outliers final: 13 residues processed: 141 average time/residue: 0.5858 time to fit residues: 86.6647 Evaluate side-chains 145 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 73 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 0.0970 chunk 18 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.0170 chunk 76 optimal weight: 0.9980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.125213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.103302 restraints weight = 9602.047| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.24 r_work: 0.3129 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6671 Z= 0.105 Angle : 0.484 5.528 9086 Z= 0.252 Chirality : 0.040 0.249 969 Planarity : 0.004 0.052 1164 Dihedral : 5.214 53.325 1005 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.02 % Allowed : 26.30 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: 0.83 (0.30), residues: 785 helix: 1.80 (0.27), residues: 392 sheet: 1.55 (0.66), residues: 43 loop : -1.07 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 445 TYR 0.013 0.001 TYR A 50 PHE 0.008 0.001 PHE A 308 TRP 0.010 0.001 TRP A 349 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 6655) covalent geometry : angle 0.47711 ( 9051) SS BOND : bond 0.00285 ( 7) SS BOND : angle 0.63858 ( 14) hydrogen bonds : bond 0.04390 ( 301) hydrogen bonds : angle 3.93719 ( 840) metal coordination : bond 0.00130 ( 2) link_BETA1-4 : bond 0.00366 ( 1) link_BETA1-4 : angle 1.09419 ( 3) link_NAG-ASN : bond 0.00271 ( 6) link_NAG-ASN : angle 1.82332 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2276.44 seconds wall clock time: 39 minutes 32.33 seconds (2372.33 seconds total)