Starting phenix.real_space_refine on Fri Feb 14 14:31:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wsr_37822/02_2025/8wsr_37822.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wsr_37822/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wsr_37822/02_2025/8wsr_37822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wsr_37822/02_2025/8wsr_37822.map" model { file = "/net/cci-nas-00/data/ceres_data/8wsr_37822/02_2025/8wsr_37822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wsr_37822/02_2025/8wsr_37822.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.06, per 1000 atoms: 0.63 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: 1.58 Conformation dependent library (CDL) restraints added in 958.9 milliseconds 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: 0.74 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: 1.89 Time building geometry restraints manager: 1.86 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.560 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:13.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.580 ------------------------------------------------------------------------------- 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 6655 Z= 0.334 Angle : 0.822 11.615 9051 Z= 0.497 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 : 6.73 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (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 TRP 0.016 0.001 TRP A 478 HIS 0.006 0.001 HIS A 374 PHE 0.017 0.001 PHE A 308 TYR 0.020 0.002 TYR A 183 ARG 0.007 0.001 ARG A 582 *********************** 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 : 0.634 Fit side-chains revert: symmetry clash 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: 1.3311 time to fit residues: 222.4251 Evaluate side-chains 140 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 65 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 86 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100312 restraints weight = 9650.219| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.25 r_work: 0.3074 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6655 Z= 0.223 Angle : 0.576 8.846 9051 Z= 0.302 Chirality : 0.044 0.204 969 Planarity : 0.005 0.058 1164 Dihedral : 6.758 55.184 1012 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.47 % Allowed : 22.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.29), residues: 785 helix: 1.36 (0.27), residues: 385 sheet: 1.22 (0.68), residues: 44 loop : -1.28 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 PHE 0.011 0.001 PHE A 308 TYR 0.017 0.001 TYR A 50 ARG 0.006 0.001 ARG A 582 *********************** 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 167 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 THR cc_start: 0.8730 (t) cc_final: 0.8383 (p) REVERT: A 184 VAL cc_start: 0.8339 (t) cc_final: 0.8058 (t) REVERT: A 257 SER cc_start: 0.9000 (t) cc_final: 0.8698 (p) REVERT: A 270 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8276 (tpp) REVERT: A 360 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8454 (ptm) REVERT: A 430 GLU cc_start: 0.8017 (mp0) cc_final: 0.7806 (mp0) REVERT: A 435 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7598 (mm-30) REVERT: A 574 VAL cc_start: 0.8855 (m) cc_final: 0.8574 (t) REVERT: A 600 LYS cc_start: 0.8563 (mtmt) cc_final: 0.8077 (mtmt) outliers start: 24 outliers final: 10 residues processed: 156 average time/residue: 1.1428 time to fit residues: 187.2007 Evaluate side-chains 146 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 156 LEU 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 360 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 0.3980 chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 134 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097931 restraints weight = 9581.439| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.21 r_work: 0.3030 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6655 Z= 0.337 Angle : 0.586 7.671 9051 Z= 0.309 Chirality : 0.046 0.377 969 Planarity : 0.005 0.055 1164 Dihedral : 6.298 59.350 1007 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.34 % Allowed : 22.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.29), residues: 785 helix: 1.47 (0.27), residues: 385 sheet: 1.17 (0.67), residues: 44 loop : -1.35 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 478 HIS 0.007 0.001 HIS A 374 PHE 0.018 0.001 PHE A 308 TYR 0.018 0.002 TYR A 385 ARG 0.006 0.001 ARG C 445 *********************** 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 175 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: C 489 VAL cc_start: 0.8772 (p) cc_final: 0.8524 (t) REVERT: A 129 THR cc_start: 0.8833 (t) cc_final: 0.8559 (p) REVERT: A 227 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: A 257 SER cc_start: 0.8998 (t) cc_final: 0.8705 (p) REVERT: A 430 GLU cc_start: 0.7983 (mp0) cc_final: 0.7734 (mp0) REVERT: A 435 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7509 (mm-30) REVERT: A 574 VAL cc_start: 0.8960 (m) cc_final: 0.8666 (t) REVERT: A 600 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8146 (mtmt) outliers start: 30 outliers final: 15 residues processed: 161 average time/residue: 1.2107 time to fit residues: 204.6970 Evaluate side-chains 151 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 446 SER Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 74 LYS 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 156 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 383 MET 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 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 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 = 0.3520 r_free = 0.3520 target = 0.121877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.099971 restraints weight = 9659.648| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.28 r_work: 0.3076 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6655 Z= 0.179 Angle : 0.502 5.512 9051 Z= 0.267 Chirality : 0.042 0.343 969 Planarity : 0.004 0.052 1164 Dihedral : 6.192 58.251 1007 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.89 % Allowed : 23.27 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.29), residues: 785 helix: 1.60 (0.27), residues: 386 sheet: 1.20 (0.67), residues: 44 loop : -1.19 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 PHE 0.009 0.001 PHE A 308 TYR 0.016 0.001 TYR A 50 ARG 0.006 0.000 ARG C 445 *********************** 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 150 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 420 VAL cc_start: 0.8168 (t) cc_final: 0.7885 (m) REVERT: A 129 THR cc_start: 0.8732 (t) cc_final: 0.8402 (p) REVERT: A 166 GLU cc_start: 0.8050 (tp30) cc_final: 0.7667 (mm-30) REVERT: A 171 GLU cc_start: 0.8161 (tt0) cc_final: 0.7929 (tm-30) REVERT: A 184 VAL cc_start: 0.8315 (t) cc_final: 0.8066 (t) REVERT: A 206 ASP cc_start: 0.8510 (t0) cc_final: 0.8220 (t0) REVERT: A 227 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: A 257 SER cc_start: 0.8982 (t) cc_final: 0.8688 (p) REVERT: A 430 GLU cc_start: 0.7959 (mp0) cc_final: 0.7682 (mp0) REVERT: A 435 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7472 (mm-30) REVERT: A 574 VAL cc_start: 0.8883 (m) cc_final: 0.8676 (t) REVERT: A 600 LYS cc_start: 0.8583 (mtmt) cc_final: 0.8075 (mtmt) outliers start: 20 outliers final: 10 residues processed: 144 average time/residue: 1.2879 time to fit residues: 194.0408 Evaluate side-chains 138 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 468 SER Chi-restraints excluded: chain A residue 52 THR 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 553 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 68 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 3 optimal weight: 0.0040 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 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 = 0.3507 r_free = 0.3507 target = 0.121248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.099553 restraints weight = 9600.051| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.25 r_work: 0.3067 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6655 Z= 0.211 Angle : 0.505 7.591 9051 Z= 0.268 Chirality : 0.043 0.362 969 Planarity : 0.004 0.051 1164 Dihedral : 5.695 53.066 1005 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.75 % Allowed : 23.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.30), residues: 785 helix: 1.62 (0.27), residues: 386 sheet: 1.26 (0.67), residues: 44 loop : -1.15 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.005 0.001 HIS A 374 PHE 0.013 0.001 PHE A 308 TYR 0.016 0.001 TYR A 202 ARG 0.004 0.000 ARG C 445 *********************** 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 155 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: C 489 VAL cc_start: 0.8773 (p) cc_final: 0.8515 (t) REVERT: A 129 THR cc_start: 0.8749 (t) cc_final: 0.8430 (p) REVERT: A 166 GLU cc_start: 0.8028 (tp30) cc_final: 0.7717 (mm-30) REVERT: A 171 GLU cc_start: 0.8199 (tt0) cc_final: 0.7884 (tm-30) REVERT: A 184 VAL cc_start: 0.8308 (t) cc_final: 0.8067 (t) REVERT: A 227 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: A 257 SER cc_start: 0.8980 (t) cc_final: 0.8689 (p) REVERT: A 430 GLU cc_start: 0.7941 (mp0) cc_final: 0.7675 (mp0) REVERT: A 435 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7502 (mm-30) REVERT: A 600 LYS cc_start: 0.8651 (mtmt) cc_final: 0.8181 (mtmt) outliers start: 19 outliers final: 13 residues processed: 148 average time/residue: 1.2395 time to fit residues: 192.2790 Evaluate side-chains 142 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 52 THR Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 125 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 69 optimal weight: 0.7980 chunk 39 optimal weight: 0.0470 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS 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 = 0.3521 r_free = 0.3521 target = 0.121820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.100205 restraints weight = 9435.873| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.22 r_work: 0.3079 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6655 Z= 0.203 Angle : 0.494 5.081 9051 Z= 0.263 Chirality : 0.042 0.333 969 Planarity : 0.004 0.051 1164 Dihedral : 5.556 52.908 1005 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.18 % Allowed : 24.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.30), residues: 785 helix: 1.58 (0.27), residues: 392 sheet: 1.46 (0.65), residues: 43 loop : -1.15 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 PHE 0.011 0.001 PHE A 308 TYR 0.017 0.001 TYR A 202 ARG 0.009 0.000 ARG C 445 *********************** 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 153 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: C 470 VAL cc_start: 0.8733 (t) cc_final: 0.8486 (p) REVERT: C 489 VAL cc_start: 0.8758 (p) cc_final: 0.8498 (t) REVERT: A 129 THR cc_start: 0.8758 (t) cc_final: 0.8441 (p) REVERT: A 166 GLU cc_start: 0.8047 (tp30) cc_final: 0.7737 (mm-30) REVERT: A 171 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7882 (tm-30) REVERT: A 184 VAL cc_start: 0.8302 (t) cc_final: 0.8074 (t) REVERT: A 227 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: A 257 SER cc_start: 0.8978 (t) cc_final: 0.8686 (p) REVERT: A 430 GLU cc_start: 0.7909 (mp0) cc_final: 0.7665 (mp0) REVERT: A 435 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7499 (mm-30) REVERT: A 600 LYS cc_start: 0.8656 (mtmt) cc_final: 0.8192 (mtmt) outliers start: 22 outliers final: 15 residues processed: 144 average time/residue: 1.2392 time to fit residues: 187.1344 Evaluate side-chains 146 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 52 THR 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 331 SER Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 553 LYS 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 57 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 45 optimal weight: 0.0370 chunk 40 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 73 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3557 r_free = 0.3557 target = 0.124396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.102730 restraints weight = 9470.576| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.24 r_work: 0.3122 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6655 Z= 0.147 Angle : 0.469 9.003 9051 Z= 0.247 Chirality : 0.040 0.279 969 Planarity : 0.004 0.050 1164 Dihedral : 5.353 53.514 1005 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.46 % Allowed : 24.71 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.30), residues: 785 helix: 1.68 (0.27), residues: 392 sheet: 1.43 (0.65), residues: 43 loop : -1.09 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 PHE 0.008 0.001 PHE C 387 TYR 0.018 0.001 TYR A 202 ARG 0.008 0.000 ARG C 445 *********************** 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 139 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: C 420 VAL cc_start: 0.8141 (t) cc_final: 0.7874 (m) REVERT: A 129 THR cc_start: 0.8655 (t) cc_final: 0.8309 (p) REVERT: A 171 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: A 206 ASP cc_start: 0.8552 (t0) cc_final: 0.8232 (t0) REVERT: A 227 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: A 401 HIS cc_start: 0.8131 (OUTLIER) cc_final: 0.7575 (m-70) REVERT: A 430 GLU cc_start: 0.7926 (mp0) cc_final: 0.7697 (mp0) REVERT: A 435 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7502 (mm-30) REVERT: A 600 LYS cc_start: 0.8626 (mtmt) cc_final: 0.8151 (mtmt) outliers start: 17 outliers final: 9 residues processed: 133 average time/residue: 1.2731 time to fit residues: 177.3078 Evaluate side-chains 133 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 74 LYS 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 382 ASP Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 0.0770 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN 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 = 0.3537 r_free = 0.3537 target = 0.123036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.101220 restraints weight = 9643.661| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.25 r_work: 0.3104 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6655 Z= 0.174 Angle : 0.478 4.885 9051 Z= 0.253 Chirality : 0.041 0.295 969 Planarity : 0.004 0.052 1164 Dihedral : 5.314 53.067 1005 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.31 % Allowed : 25.43 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.30), residues: 785 helix: 1.71 (0.27), residues: 392 sheet: 1.48 (0.65), residues: 43 loop : -1.07 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 165 HIS 0.005 0.001 HIS A 374 PHE 0.010 0.001 PHE A 308 TYR 0.018 0.001 TYR A 202 ARG 0.007 0.000 ARG C 445 *********************** 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 145 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: C 420 VAL cc_start: 0.8126 (t) cc_final: 0.7917 (p) REVERT: C 470 VAL cc_start: 0.8746 (t) cc_final: 0.8504 (p) REVERT: C 489 VAL cc_start: 0.8742 (p) cc_final: 0.8478 (t) REVERT: A 129 THR cc_start: 0.8708 (t) cc_final: 0.8381 (p) REVERT: A 171 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: A 206 ASP cc_start: 0.8570 (t0) cc_final: 0.8235 (t0) REVERT: A 227 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: A 401 HIS cc_start: 0.8196 (OUTLIER) cc_final: 0.7630 (m-70) REVERT: A 430 GLU cc_start: 0.7924 (mp0) cc_final: 0.7694 (mp0) REVERT: A 435 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7593 (mm-30) REVERT: A 600 LYS cc_start: 0.8651 (mtmt) cc_final: 0.8203 (mtmt) outliers start: 16 outliers final: 10 residues processed: 137 average time/residue: 1.2936 time to fit residues: 185.9063 Evaluate side-chains 141 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 468 SER Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 227 GLU 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 424 LEU Chi-restraints excluded: chain A residue 503 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 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 81 GLN 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 = 0.3538 r_free = 0.3538 target = 0.123262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.101422 restraints weight = 9632.739| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.26 r_work: 0.3094 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6655 Z= 0.182 Angle : 0.496 9.975 9051 Z= 0.259 Chirality : 0.041 0.298 969 Planarity : 0.004 0.052 1164 Dihedral : 5.302 53.172 1005 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.32 % Allowed : 24.42 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.30), residues: 785 helix: 1.72 (0.27), residues: 392 sheet: 1.56 (0.65), residues: 43 loop : -1.08 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.005 0.001 HIS A 374 PHE 0.010 0.001 PHE A 308 TYR 0.018 0.001 TYR A 202 ARG 0.007 0.000 ARG C 445 *********************** 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 154 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: C 470 VAL cc_start: 0.8749 (t) cc_final: 0.8513 (p) REVERT: C 489 VAL cc_start: 0.8752 (p) cc_final: 0.8488 (t) REVERT: A 129 THR cc_start: 0.8723 (t) cc_final: 0.8433 (p) REVERT: A 171 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7874 (tm-30) REVERT: A 184 VAL cc_start: 0.8311 (t) cc_final: 0.8011 (t) REVERT: A 206 ASP cc_start: 0.8582 (t0) cc_final: 0.8266 (t0) REVERT: A 227 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: A 257 SER cc_start: 0.8983 (t) cc_final: 0.8694 (p) REVERT: A 401 HIS cc_start: 0.8220 (OUTLIER) cc_final: 0.7638 (m-70) REVERT: A 406 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8145 (mm-30) REVERT: A 430 GLU cc_start: 0.7941 (mp0) cc_final: 0.7680 (mp0) REVERT: A 435 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7540 (mm-30) REVERT: A 600 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8225 (mtmt) outliers start: 23 outliers final: 13 residues processed: 144 average time/residue: 1.2639 time to fit residues: 190.8683 Evaluate side-chains 143 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 52 THR Chi-restraints excluded: chain A residue 74 LYS 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 382 ASP Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 553 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 0.0270 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.123371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.101448 restraints weight = 9655.881| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.26 r_work: 0.3099 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6655 Z= 0.175 Angle : 0.492 6.537 9051 Z= 0.258 Chirality : 0.042 0.296 969 Planarity : 0.004 0.052 1164 Dihedral : 5.419 53.241 1005 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.46 % Allowed : 25.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.30), residues: 785 helix: 1.75 (0.27), residues: 392 sheet: 1.59 (0.65), residues: 43 loop : -1.05 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.005 0.001 HIS A 374 PHE 0.009 0.001 PHE A 308 TYR 0.019 0.001 TYR A 202 ARG 0.006 0.000 ARG C 445 ********************** 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 146 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: C 420 VAL cc_start: 0.8120 (t) cc_final: 0.7905 (p) REVERT: C 470 VAL cc_start: 0.8773 (t) cc_final: 0.8540 (p) REVERT: C 489 VAL cc_start: 0.8756 (p) cc_final: 0.8490 (t) REVERT: A 62 MET cc_start: 0.8177 (ttp) cc_final: 0.7954 (ttt) REVERT: A 129 THR cc_start: 0.8730 (t) cc_final: 0.8451 (p) REVERT: A 171 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: A 184 VAL cc_start: 0.8298 (t) cc_final: 0.7992 (t) REVERT: A 206 ASP cc_start: 0.8587 (t0) cc_final: 0.8274 (t0) REVERT: A 401 HIS cc_start: 0.8221 (OUTLIER) cc_final: 0.7650 (m-70) REVERT: A 406 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8157 (mm-30) REVERT: A 430 GLU cc_start: 0.7916 (mp0) cc_final: 0.7665 (mp0) REVERT: A 435 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7554 (mm-30) REVERT: A 600 LYS cc_start: 0.8664 (mtmt) cc_final: 0.8208 (mtmt) outliers start: 17 outliers final: 12 residues processed: 139 average time/residue: 1.2361 time to fit residues: 180.2263 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 : 0.673 ------------------------------------------------------------------------------- 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 151 ILE Chi-restraints excluded: chain A residue 171 GLU 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 424 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 553 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 chunk 36 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 76 optimal weight: 0.1980 chunk 42 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 14 optimal weight: 0.0270 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.125918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.103943 restraints weight = 9797.924| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.28 r_work: 0.3134 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6655 Z= 0.144 Angle : 0.480 9.631 9051 Z= 0.250 Chirality : 0.040 0.264 969 Planarity : 0.004 0.051 1164 Dihedral : 5.304 53.392 1005 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.31 % Allowed : 26.16 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.30), residues: 785 helix: 1.79 (0.27), residues: 392 sheet: 1.59 (0.65), residues: 43 loop : -0.94 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 PHE 0.006 0.001 PHE A 308 TYR 0.019 0.001 TYR A 202 ARG 0.006 0.000 ARG C 445 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5056.03 seconds wall clock time: 89 minutes 41.92 seconds (5381.92 seconds total)