Starting phenix.real_space_refine on Tue May 13 21:27:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8poe_17789/05_2025/8poe_17789.cif Found real_map, /net/cci-nas-00/data/ceres_data/8poe_17789/05_2025/8poe_17789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8poe_17789/05_2025/8poe_17789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8poe_17789/05_2025/8poe_17789.map" model { file = "/net/cci-nas-00/data/ceres_data/8poe_17789/05_2025/8poe_17789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8poe_17789/05_2025/8poe_17789.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 7185 2.51 5 N 1929 2.21 5 O 1803 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10947 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3649 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 25, 'TRANS': 431} Chain breaks: 4 Chain: "B" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3649 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 25, 'TRANS': 431} Chain breaks: 4 Chain: "C" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3649 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 25, 'TRANS': 431} Chain breaks: 4 Time building chain proxies: 7.34, per 1000 atoms: 0.67 Number of scatterers: 10947 At special positions: 0 Unit cell: (130.68, 131.76, 89.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1803 8.00 N 1929 7.00 C 7185 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 1.5 seconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2604 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 3 sheets defined 78.3% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 191 through 205 removed outlier: 3.822A pdb=" N PHE A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 236 removed outlier: 3.867A pdb=" N VAL A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 243 removed outlier: 3.570A pdb=" N ALA A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 265 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 279 through 318 removed outlier: 3.651A pdb=" N ASP A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 329 through 342 Processing helix chain 'A' and resid 353 through 375 removed outlier: 3.681A pdb=" N ILE A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TYR A 364 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N THR A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 405 Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 427 through 470 Proline residue: A 451 - end of helix removed outlier: 3.630A pdb=" N LEU A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 removed outlier: 4.252A pdb=" N LEU A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 Processing helix chain 'A' and resid 495 through 517 removed outlier: 4.871A pdb=" N ARG A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Proline residue: A 509 - end of helix removed outlier: 3.578A pdb=" N ALA A 517 " --> pdb=" O PHE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 548 removed outlier: 3.933A pdb=" N TYR A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 576 removed outlier: 3.676A pdb=" N ALA A 561 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 598 removed outlier: 3.920A pdb=" N HIS A 596 " --> pdb=" O THR A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 620 Processing helix chain 'A' and resid 622 through 645 Proline residue: A 634 - end of helix Proline residue: A 638 - end of helix removed outlier: 3.874A pdb=" N LEU A 641 " --> pdb=" O THR A 637 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 659 Processing helix chain 'B' and resid 192 through 205 removed outlier: 3.782A pdb=" N PHE B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 235 Processing helix chain 'B' and resid 237 through 243 removed outlier: 3.619A pdb=" N LEU B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 279 through 318 removed outlier: 3.603A pdb=" N ASP B 308 " --> pdb=" O PHE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 324 Processing helix chain 'B' and resid 329 through 342 Processing helix chain 'B' and resid 353 through 374 removed outlier: 3.572A pdb=" N ILE B 361 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N TYR B 364 " --> pdb=" O ARG B 360 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N THR B 365 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 405 Processing helix chain 'B' and resid 419 through 423 Processing helix chain 'B' and resid 427 through 470 Proline residue: B 451 - end of helix removed outlier: 3.627A pdb=" N LEU B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG B 470 " --> pdb=" O VAL B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 478 removed outlier: 4.285A pdb=" N LEU B 476 " --> pdb=" O GLU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 489 Processing helix chain 'B' and resid 495 through 517 removed outlier: 4.994A pdb=" N ARG B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Proline residue: B 509 - end of helix removed outlier: 3.648A pdb=" N ALA B 517 " --> pdb=" O PHE B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 548 removed outlier: 3.876A pdb=" N TYR B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 576 removed outlier: 3.643A pdb=" N ALA B 561 " --> pdb=" O HIS B 557 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR B 563 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA B 564 " --> pdb=" O THR B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 598 removed outlier: 4.092A pdb=" N HIS B 596 " --> pdb=" O THR B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 620 Processing helix chain 'B' and resid 622 through 645 Proline residue: B 634 - end of helix Proline residue: B 638 - end of helix removed outlier: 3.895A pdb=" N LEU B 641 " --> pdb=" O THR B 637 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE B 645 " --> pdb=" O LEU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 659 removed outlier: 3.527A pdb=" N ILE B 653 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 205 removed outlier: 3.796A pdb=" N PHE C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 235 Processing helix chain 'C' and resid 237 through 243 removed outlier: 3.625A pdb=" N LEU C 241 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 243 " --> pdb=" O ASN C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 265 Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 279 through 318 removed outlier: 3.512A pdb=" N LEU C 283 " --> pdb=" O PRO C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 324 Processing helix chain 'C' and resid 329 through 342 Processing helix chain 'C' and resid 353 through 374 removed outlier: 3.551A pdb=" N ILE C 361 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N TYR C 364 " --> pdb=" O ARG C 360 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N THR C 365 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 405 Processing helix chain 'C' and resid 419 through 424 Processing helix chain 'C' and resid 427 through 470 Proline residue: C 451 - end of helix removed outlier: 3.617A pdb=" N LEU C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 477 removed outlier: 4.197A pdb=" N LEU C 476 " --> pdb=" O GLU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 489 Processing helix chain 'C' and resid 495 through 517 removed outlier: 5.026A pdb=" N ARG C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Proline residue: C 509 - end of helix removed outlier: 3.526A pdb=" N ALA C 517 " --> pdb=" O PHE C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 548 removed outlier: 3.955A pdb=" N TYR C 548 " --> pdb=" O VAL C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 576 removed outlier: 3.739A pdb=" N ALA C 561 " --> pdb=" O HIS C 557 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR C 563 " --> pdb=" O LEU C 559 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA C 564 " --> pdb=" O THR C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 598 removed outlier: 3.977A pdb=" N HIS C 596 " --> pdb=" O THR C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 620 Processing helix chain 'C' and resid 622 through 645 Proline residue: C 634 - end of helix Proline residue: C 638 - end of helix removed outlier: 3.908A pdb=" N LEU C 641 " --> pdb=" O THR C 637 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE C 645 " --> pdb=" O LEU C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 659 removed outlier: 3.500A pdb=" N PHE C 659 " --> pdb=" O PHE C 655 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 660 through 663 Processing sheet with id=AA2, first strand: chain 'B' and resid 660 through 663 Processing sheet with id=AA3, first strand: chain 'C' and resid 660 through 663 741 hydrogen bonds defined for protein. 2172 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: 3.10 Time building geometry restraints manager: 3.38 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: 3506 1.34 - 1.46: 2581 1.46 - 1.58: 5109 1.58 - 1.70: 0 1.70 - 1.82: 39 Bond restraints: 11235 Sorted by residual: bond pdb=" C LEU B 377 " pdb=" N PRO B 378 " ideal model delta sigma weight residual 1.332 1.350 -0.018 1.12e-02 7.97e+03 2.45e+00 bond pdb=" CG1 ILE B 225 " pdb=" CD1 ILE B 225 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.57e+00 bond pdb=" CG1 ILE C 225 " pdb=" CD1 ILE C 225 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.49e+00 bond pdb=" CG GLN A 221 " pdb=" CD GLN A 221 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.32e+00 bond pdb=" CA GLU C 273 " pdb=" CB GLU C 273 " ideal model delta sigma weight residual 1.528 1.545 -0.017 1.66e-02 3.63e+03 1.01e+00 ... (remaining 11230 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 14941 1.84 - 3.67: 291 3.67 - 5.51: 63 5.51 - 7.34: 10 7.34 - 9.18: 1 Bond angle restraints: 15306 Sorted by residual: angle pdb=" N GLU C 273 " pdb=" CA GLU C 273 " pdb=" CB GLU C 273 " ideal model delta sigma weight residual 110.28 116.14 -5.86 1.55e+00 4.16e-01 1.43e+01 angle pdb=" CA GLU C 273 " pdb=" CB GLU C 273 " pdb=" CG GLU C 273 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N GLU A 273 " pdb=" CA GLU A 273 " pdb=" CB GLU A 273 " ideal model delta sigma weight residual 110.12 115.10 -4.98 1.47e+00 4.63e-01 1.15e+01 angle pdb=" N GLU B 273 " pdb=" CA GLU B 273 " pdb=" CB GLU B 273 " ideal model delta sigma weight residual 110.12 114.94 -4.82 1.47e+00 4.63e-01 1.07e+01 angle pdb=" N GLN C 340 " pdb=" CA GLN C 340 " pdb=" CB GLN C 340 " ideal model delta sigma weight residual 110.28 115.36 -5.08 1.55e+00 4.16e-01 1.07e+01 ... (remaining 15301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 5959 17.71 - 35.43: 501 35.43 - 53.14: 113 53.14 - 70.85: 18 70.85 - 88.56: 9 Dihedral angle restraints: 6600 sinusoidal: 2598 harmonic: 4002 Sorted by residual: dihedral pdb=" CA ASP A 215 " pdb=" CB ASP A 215 " pdb=" CG ASP A 215 " pdb=" OD1 ASP A 215 " ideal model delta sinusoidal sigma weight residual -30.00 -87.13 57.13 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CB GLU C 417 " pdb=" CG GLU C 417 " pdb=" CD GLU C 417 " pdb=" OE1 GLU C 417 " ideal model delta sinusoidal sigma weight residual 0.00 -88.56 88.56 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA LEU C 376 " pdb=" C LEU C 376 " pdb=" N LEU C 377 " pdb=" CA LEU C 377 " ideal model delta harmonic sigma weight residual -180.00 -163.89 -16.11 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 6597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1114 0.032 - 0.064: 460 0.064 - 0.096: 122 0.096 - 0.128: 56 0.128 - 0.159: 9 Chirality restraints: 1761 Sorted by residual: chirality pdb=" CA ASN B 206 " pdb=" N ASN B 206 " pdb=" C ASN B 206 " pdb=" CB ASN B 206 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ASN A 206 " pdb=" N ASN A 206 " pdb=" C ASN A 206 " pdb=" CB ASN A 206 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CG LEU B 362 " pdb=" CB LEU B 362 " pdb=" CD1 LEU B 362 " pdb=" CD2 LEU B 362 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.15e-01 ... (remaining 1758 not shown) Planarity restraints: 1926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 533 " 0.021 2.00e-02 2.50e+03 1.86e-02 6.04e+00 pdb=" CG PHE B 533 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 533 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 533 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 533 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 533 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 533 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 508 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 509 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 509 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 509 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 533 " -0.018 2.00e-02 2.50e+03 1.22e-02 2.61e+00 pdb=" CG PHE A 533 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 533 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 533 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 533 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 533 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 533 " -0.009 2.00e-02 2.50e+03 ... (remaining 1923 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2471 2.79 - 3.32: 11000 3.32 - 3.85: 17505 3.85 - 4.37: 17764 4.37 - 4.90: 30949 Nonbonded interactions: 79689 Sorted by model distance: nonbonded pdb=" NH1 ARG B 363 " pdb=" OD1 ASP B 668 " model vdw 2.265 3.120 nonbonded pdb=" NH1 ARG C 363 " pdb=" OD1 ASP C 668 " model vdw 2.273 3.120 nonbonded pdb=" OD1 ASN C 399 " pdb=" ND2 ASN C 446 " model vdw 2.287 3.120 nonbonded pdb=" O ARG B 276 " pdb=" NH1 ARG B 276 " model vdw 2.289 3.120 nonbonded pdb=" N GLU A 354 " pdb=" OE1 GLU A 354 " model vdw 2.297 3.120 ... (remaining 79684 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 group one per residue 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.100 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11235 Z= 0.137 Angle : 0.637 9.178 15306 Z= 0.331 Chirality : 0.040 0.159 1761 Planarity : 0.004 0.041 1926 Dihedral : 14.198 88.563 3996 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.24), residues: 1341 helix: 1.65 (0.17), residues: 957 sheet: None (None), residues: 0 loop : -0.67 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 435 HIS 0.005 0.001 HIS B 497 PHE 0.042 0.001 PHE B 533 TYR 0.012 0.001 TYR A 622 ARG 0.005 0.000 ARG A 470 Details of bonding type rmsd hydrogen bonds : bond 0.12644 ( 741) hydrogen bonds : angle 5.14771 ( 2172) covalent geometry : bond 0.00270 (11235) covalent geometry : angle 0.63745 (15306) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 TYR cc_start: 0.7571 (t80) cc_final: 0.7234 (t80) REVERT: A 562 MET cc_start: 0.7838 (mmm) cc_final: 0.7518 (mmt) REVERT: A 630 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7851 (mm-30) REVERT: A 669 ILE cc_start: 0.7986 (mt) cc_final: 0.7783 (mt) REVERT: B 219 LEU cc_start: 0.9006 (mt) cc_final: 0.8785 (mt) REVERT: B 494 GLU cc_start: 0.8289 (tp30) cc_final: 0.8000 (tp30) REVERT: B 669 ILE cc_start: 0.8167 (mt) cc_final: 0.7950 (mt) REVERT: C 356 ASP cc_start: 0.7617 (m-30) cc_final: 0.7280 (m-30) REVERT: C 669 ILE cc_start: 0.7701 (mt) cc_final: 0.7387 (mt) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.2233 time to fit residues: 89.7332 Evaluate side-chains 210 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 69 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN A 446 ASN B 491 HIS ** B 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN C 446 ASN ** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.184655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.153382 restraints weight = 18021.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.155591 restraints weight = 14586.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.156957 restraints weight = 12456.692| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11235 Z= 0.151 Angle : 0.592 6.011 15306 Z= 0.303 Chirality : 0.041 0.165 1761 Planarity : 0.005 0.041 1926 Dihedral : 3.740 18.074 1515 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.26 % Allowed : 6.68 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.23), residues: 1341 helix: 1.50 (0.16), residues: 987 sheet: None (None), residues: 0 loop : -1.11 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 329 HIS 0.004 0.001 HIS B 497 PHE 0.030 0.001 PHE B 533 TYR 0.015 0.002 TYR B 599 ARG 0.007 0.001 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.04696 ( 741) hydrogen bonds : angle 4.28381 ( 2172) covalent geometry : bond 0.00327 (11235) covalent geometry : angle 0.59169 (15306) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 287 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 LEU cc_start: 0.8755 (tp) cc_final: 0.8520 (tp) REVERT: A 548 TYR cc_start: 0.7647 (t80) cc_final: 0.7357 (t80) REVERT: A 630 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7626 (mm-30) REVERT: A 669 ILE cc_start: 0.8020 (mt) cc_final: 0.7723 (mt) REVERT: B 362 LEU cc_start: 0.8790 (mm) cc_final: 0.8405 (mm) REVERT: C 356 ASP cc_start: 0.7771 (m-30) cc_final: 0.7476 (m-30) REVERT: C 630 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8440 (mm-30) REVERT: C 669 ILE cc_start: 0.7634 (mt) cc_final: 0.7327 (mt) outliers start: 3 outliers final: 1 residues processed: 288 average time/residue: 0.2218 time to fit residues: 90.0654 Evaluate side-chains 208 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 56 optimal weight: 0.1980 chunk 115 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN A 598 HIS B 491 HIS B 530 GLN C 399 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.188287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.156328 restraints weight = 17429.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.159026 restraints weight = 13568.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.160922 restraints weight = 11221.420| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11235 Z= 0.128 Angle : 0.572 5.801 15306 Z= 0.289 Chirality : 0.040 0.167 1761 Planarity : 0.004 0.040 1926 Dihedral : 3.682 16.429 1515 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.02 % Rotamer: Outliers : 0.18 % Allowed : 3.34 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.23), residues: 1341 helix: 1.56 (0.16), residues: 984 sheet: None (None), residues: 0 loop : -1.19 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 644 HIS 0.005 0.001 HIS B 203 PHE 0.031 0.001 PHE B 533 TYR 0.014 0.001 TYR C 313 ARG 0.003 0.000 ARG B 483 Details of bonding type rmsd hydrogen bonds : bond 0.04442 ( 741) hydrogen bonds : angle 4.18883 ( 2172) covalent geometry : bond 0.00265 (11235) covalent geometry : angle 0.57210 (15306) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 302 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 LEU cc_start: 0.8765 (tp) cc_final: 0.8545 (tp) REVERT: A 548 TYR cc_start: 0.7610 (t80) cc_final: 0.7394 (t80) REVERT: A 621 GLN cc_start: 0.8064 (mm110) cc_final: 0.7856 (mm-40) REVERT: A 630 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7689 (mm-30) REVERT: A 669 ILE cc_start: 0.7971 (mt) cc_final: 0.7671 (mt) REVERT: B 356 ASP cc_start: 0.8369 (m-30) cc_final: 0.7996 (m-30) REVERT: B 362 LEU cc_start: 0.8863 (mm) cc_final: 0.8428 (mm) REVERT: C 669 ILE cc_start: 0.7638 (mt) cc_final: 0.7366 (mt) outliers start: 2 outliers final: 0 residues processed: 302 average time/residue: 0.2493 time to fit residues: 104.3917 Evaluate side-chains 218 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 85 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 117 optimal weight: 0.0970 chunk 123 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.183872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.147299 restraints weight = 17880.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.150864 restraints weight = 12670.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.153363 restraints weight = 9945.347| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11235 Z= 0.118 Angle : 0.550 6.010 15306 Z= 0.276 Chirality : 0.039 0.160 1761 Planarity : 0.004 0.038 1926 Dihedral : 3.625 15.290 1515 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.09 % Allowed : 3.43 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.23), residues: 1341 helix: 1.56 (0.16), residues: 984 sheet: None (None), residues: 0 loop : -1.17 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 644 HIS 0.003 0.001 HIS C 557 PHE 0.031 0.001 PHE B 533 TYR 0.012 0.001 TYR B 200 ARG 0.003 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 741) hydrogen bonds : angle 4.12515 ( 2172) covalent geometry : bond 0.00238 (11235) covalent geometry : angle 0.55041 (15306) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 TYR cc_start: 0.7526 (t80) cc_final: 0.7257 (t80) REVERT: A 621 GLN cc_start: 0.8177 (mm110) cc_final: 0.7893 (mm-40) REVERT: A 630 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7707 (mm-30) REVERT: A 669 ILE cc_start: 0.7921 (mt) cc_final: 0.7611 (mt) REVERT: B 263 ASP cc_start: 0.8710 (m-30) cc_final: 0.8490 (m-30) REVERT: B 356 ASP cc_start: 0.8457 (m-30) cc_final: 0.8144 (m-30) REVERT: B 362 LEU cc_start: 0.8804 (mm) cc_final: 0.8449 (mm) REVERT: B 426 ASP cc_start: 0.8994 (p0) cc_final: 0.8777 (p0) REVERT: C 356 ASP cc_start: 0.7802 (m-30) cc_final: 0.7532 (m-30) REVERT: C 669 ILE cc_start: 0.7711 (mt) cc_final: 0.7443 (mt) outliers start: 1 outliers final: 0 residues processed: 300 average time/residue: 0.2250 time to fit residues: 94.2356 Evaluate side-chains 213 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 100 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 127 optimal weight: 0.0770 chunk 123 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 HIS B 333 GLN B 491 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.185593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.149714 restraints weight = 18304.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.153022 restraints weight = 13424.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.155349 restraints weight = 10741.492| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11235 Z= 0.123 Angle : 0.565 6.263 15306 Z= 0.285 Chirality : 0.039 0.162 1761 Planarity : 0.004 0.038 1926 Dihedral : 3.617 15.123 1515 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.54 % Favored : 97.39 % Rotamer: Outliers : 0.09 % Allowed : 2.11 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.23), residues: 1341 helix: 1.56 (0.16), residues: 972 sheet: None (None), residues: 0 loop : -1.02 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 644 HIS 0.002 0.001 HIS C 358 PHE 0.032 0.001 PHE B 533 TYR 0.015 0.001 TYR C 313 ARG 0.003 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.04248 ( 741) hydrogen bonds : angle 4.08651 ( 2172) covalent geometry : bond 0.00258 (11235) covalent geometry : angle 0.56467 (15306) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 CYS cc_start: 0.7765 (t) cc_final: 0.7546 (m) REVERT: A 621 GLN cc_start: 0.8214 (mm110) cc_final: 0.7931 (mm-40) REVERT: A 630 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7747 (mm-30) REVERT: A 669 ILE cc_start: 0.8008 (mt) cc_final: 0.7641 (mt) REVERT: B 263 ASP cc_start: 0.8797 (m-30) cc_final: 0.8543 (m-30) REVERT: B 333 GLN cc_start: 0.6494 (mm-40) cc_final: 0.5751 (tp40) REVERT: B 356 ASP cc_start: 0.8465 (m-30) cc_final: 0.8121 (m-30) REVERT: B 362 LEU cc_start: 0.8857 (mm) cc_final: 0.8491 (mm) REVERT: B 659 PHE cc_start: 0.7914 (m-80) cc_final: 0.7653 (m-80) REVERT: C 356 ASP cc_start: 0.7753 (m-30) cc_final: 0.7483 (m-30) REVERT: C 669 ILE cc_start: 0.7784 (mt) cc_final: 0.7505 (mt) outliers start: 1 outliers final: 0 residues processed: 303 average time/residue: 0.2187 time to fit residues: 93.5756 Evaluate side-chains 225 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 111 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 117 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.181855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.145065 restraints weight = 18081.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.148411 restraints weight = 13038.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.150779 restraints weight = 10376.170| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11235 Z= 0.134 Angle : 0.586 6.856 15306 Z= 0.298 Chirality : 0.041 0.160 1761 Planarity : 0.004 0.040 1926 Dihedral : 3.641 15.873 1515 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.23), residues: 1341 helix: 1.49 (0.16), residues: 975 sheet: None (None), residues: 0 loop : -0.98 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 329 HIS 0.002 0.001 HIS C 491 PHE 0.033 0.002 PHE B 533 TYR 0.012 0.001 TYR A 367 ARG 0.005 0.000 ARG B 437 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 741) hydrogen bonds : angle 4.12950 ( 2172) covalent geometry : bond 0.00288 (11235) covalent geometry : angle 0.58640 (15306) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 TYR cc_start: 0.7486 (t80) cc_final: 0.7257 (t80) REVERT: A 621 GLN cc_start: 0.8306 (mm110) cc_final: 0.8028 (mm-40) REVERT: A 630 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7740 (mm-30) REVERT: A 669 ILE cc_start: 0.8037 (mt) cc_final: 0.7759 (mt) REVERT: B 263 ASP cc_start: 0.8794 (m-30) cc_final: 0.8540 (m-30) REVERT: B 333 GLN cc_start: 0.6558 (mm-40) cc_final: 0.6274 (mm110) REVERT: B 356 ASP cc_start: 0.8449 (m-30) cc_final: 0.8135 (m-30) REVERT: B 362 LEU cc_start: 0.8903 (mm) cc_final: 0.8534 (mm) REVERT: C 356 ASP cc_start: 0.7790 (m-30) cc_final: 0.7580 (m-30) REVERT: C 423 LYS cc_start: 0.7187 (tppt) cc_final: 0.6667 (tppp) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.2253 time to fit residues: 92.5181 Evaluate side-chains 213 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 82 optimal weight: 0.0370 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 31 optimal weight: 0.0570 chunk 63 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.189295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.157416 restraints weight = 18122.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.159782 restraints weight = 14434.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.161573 restraints weight = 12214.119| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11235 Z= 0.117 Angle : 0.562 6.436 15306 Z= 0.280 Chirality : 0.039 0.157 1761 Planarity : 0.004 0.038 1926 Dihedral : 3.640 15.279 1515 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.23), residues: 1341 helix: 1.58 (0.17), residues: 975 sheet: None (None), residues: 0 loop : -0.96 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 644 HIS 0.002 0.000 HIS C 491 PHE 0.033 0.001 PHE B 533 TYR 0.012 0.001 TYR C 313 ARG 0.005 0.000 ARG C 274 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 741) hydrogen bonds : angle 4.05927 ( 2172) covalent geometry : bond 0.00235 (11235) covalent geometry : angle 0.56208 (15306) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.8446 (tp30) cc_final: 0.8166 (tp30) REVERT: A 356 ASP cc_start: 0.8008 (m-30) cc_final: 0.7785 (m-30) REVERT: A 630 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7684 (mm-30) REVERT: A 669 ILE cc_start: 0.8095 (mt) cc_final: 0.7686 (mt) REVERT: B 263 ASP cc_start: 0.8737 (m-30) cc_final: 0.8501 (m-30) REVERT: B 356 ASP cc_start: 0.8352 (m-30) cc_final: 0.8037 (m-30) REVERT: B 362 LEU cc_start: 0.8828 (mm) cc_final: 0.8460 (mm) REVERT: B 393 SER cc_start: 0.8361 (t) cc_final: 0.8140 (t) REVERT: B 630 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7572 (mm-30) REVERT: B 659 PHE cc_start: 0.7565 (m-80) cc_final: 0.7292 (m-80) REVERT: C 356 ASP cc_start: 0.7749 (m-30) cc_final: 0.7495 (m-30) REVERT: C 423 LYS cc_start: 0.6997 (tppt) cc_final: 0.6438 (tppp) REVERT: C 669 ILE cc_start: 0.7940 (mt) cc_final: 0.7526 (mt) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.2280 time to fit residues: 93.3774 Evaluate side-chains 222 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 333 GLN B 658 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.187772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.155949 restraints weight = 17934.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.158327 restraints weight = 14393.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.159978 restraints weight = 12256.049| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11235 Z= 0.126 Angle : 0.579 6.748 15306 Z= 0.291 Chirality : 0.040 0.159 1761 Planarity : 0.004 0.038 1926 Dihedral : 3.631 15.438 1515 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.68 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.23), residues: 1341 helix: 1.60 (0.17), residues: 975 sheet: None (None), residues: 0 loop : -0.98 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 329 HIS 0.003 0.001 HIS B 491 PHE 0.033 0.001 PHE B 533 TYR 0.011 0.001 TYR C 622 ARG 0.004 0.000 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 741) hydrogen bonds : angle 4.09461 ( 2172) covalent geometry : bond 0.00265 (11235) covalent geometry : angle 0.57932 (15306) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 ASP cc_start: 0.8765 (p0) cc_final: 0.8484 (p0) REVERT: A 630 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7693 (mm-30) REVERT: A 669 ILE cc_start: 0.8101 (mt) cc_final: 0.7832 (mt) REVERT: B 263 ASP cc_start: 0.8776 (m-30) cc_final: 0.8543 (m-30) REVERT: B 356 ASP cc_start: 0.8422 (m-30) cc_final: 0.7932 (m-30) REVERT: B 362 LEU cc_start: 0.8805 (mm) cc_final: 0.8415 (mm) REVERT: B 393 SER cc_start: 0.8407 (t) cc_final: 0.8159 (t) REVERT: B 630 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7636 (mm-30) REVERT: B 659 PHE cc_start: 0.7755 (m-80) cc_final: 0.7433 (m-80) REVERT: C 356 ASP cc_start: 0.7836 (m-30) cc_final: 0.7365 (m-30) REVERT: C 423 LYS cc_start: 0.7042 (tppt) cc_final: 0.6491 (tppp) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.2096 time to fit residues: 85.5886 Evaluate side-chains 215 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 104 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.183083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.146074 restraints weight = 18294.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.149319 restraints weight = 13464.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.151580 restraints weight = 10807.494| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11235 Z= 0.126 Angle : 0.586 6.580 15306 Z= 0.296 Chirality : 0.040 0.157 1761 Planarity : 0.004 0.038 1926 Dihedral : 3.632 15.251 1515 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.76 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.23), residues: 1341 helix: 1.58 (0.17), residues: 972 sheet: None (None), residues: 0 loop : -1.04 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 644 HIS 0.002 0.000 HIS B 596 PHE 0.033 0.001 PHE B 533 TYR 0.017 0.002 TYR C 313 ARG 0.003 0.000 ARG A 234 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 741) hydrogen bonds : angle 4.16254 ( 2172) covalent geometry : bond 0.00267 (11235) covalent geometry : angle 0.58618 (15306) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.7779 (tpp-160) cc_final: 0.7567 (tpm170) REVERT: A 426 ASP cc_start: 0.8848 (p0) cc_final: 0.8592 (p0) REVERT: A 630 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7777 (mm-30) REVERT: A 669 ILE cc_start: 0.8078 (mt) cc_final: 0.7798 (mt) REVERT: B 263 ASP cc_start: 0.8813 (m-30) cc_final: 0.8562 (m-30) REVERT: B 356 ASP cc_start: 0.8452 (m-30) cc_final: 0.7978 (m-30) REVERT: B 362 LEU cc_start: 0.8854 (mm) cc_final: 0.8565 (mm) REVERT: B 393 SER cc_start: 0.8439 (t) cc_final: 0.8173 (t) REVERT: B 597 MET cc_start: 0.8129 (mmm) cc_final: 0.7557 (mmt) REVERT: B 630 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7724 (mm-30) REVERT: C 263 ASP cc_start: 0.8915 (m-30) cc_final: 0.8707 (m-30) REVERT: C 356 ASP cc_start: 0.7945 (m-30) cc_final: 0.7499 (m-30) REVERT: C 423 LYS cc_start: 0.7121 (tppt) cc_final: 0.6597 (tppp) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.2336 time to fit residues: 92.3481 Evaluate side-chains 218 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 62 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.186439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.154781 restraints weight = 17874.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.156991 restraints weight = 14404.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.158581 restraints weight = 12296.913| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11235 Z= 0.122 Angle : 0.582 6.641 15306 Z= 0.291 Chirality : 0.040 0.162 1761 Planarity : 0.004 0.043 1926 Dihedral : 3.615 16.000 1515 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.76 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.24), residues: 1341 helix: 1.64 (0.17), residues: 972 sheet: None (None), residues: 0 loop : -1.05 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 329 HIS 0.005 0.000 HIS C 491 PHE 0.030 0.001 PHE B 533 TYR 0.014 0.001 TYR B 367 ARG 0.008 0.000 ARG C 471 Details of bonding type rmsd hydrogen bonds : bond 0.04096 ( 741) hydrogen bonds : angle 4.12990 ( 2172) covalent geometry : bond 0.00257 (11235) covalent geometry : angle 0.58173 (15306) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ASP cc_start: 0.8652 (m-30) cc_final: 0.8445 (m-30) REVERT: A 426 ASP cc_start: 0.8757 (p0) cc_final: 0.8501 (p0) REVERT: A 573 ARG cc_start: 0.8687 (mmm160) cc_final: 0.8342 (mmm160) REVERT: A 630 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7679 (mm-30) REVERT: A 669 ILE cc_start: 0.8120 (mt) cc_final: 0.7857 (mt) REVERT: B 263 ASP cc_start: 0.8770 (m-30) cc_final: 0.8530 (m-30) REVERT: B 337 LEU cc_start: 0.8755 (mt) cc_final: 0.7731 (mt) REVERT: B 356 ASP cc_start: 0.8366 (m-30) cc_final: 0.7889 (m-30) REVERT: B 393 SER cc_start: 0.8412 (t) cc_final: 0.8175 (t) REVERT: B 431 LEU cc_start: 0.8770 (mt) cc_final: 0.8570 (mt) REVERT: B 597 MET cc_start: 0.8108 (mmm) cc_final: 0.7875 (mmt) REVERT: B 630 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7670 (mm-30) REVERT: C 356 ASP cc_start: 0.7944 (m-30) cc_final: 0.7429 (m-30) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.2386 time to fit residues: 95.8245 Evaluate side-chains 217 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 658 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.187251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.152256 restraints weight = 17802.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.155513 restraints weight = 13038.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.157830 restraints weight = 10430.345| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11235 Z= 0.123 Angle : 0.599 11.499 15306 Z= 0.300 Chirality : 0.040 0.157 1761 Planarity : 0.004 0.061 1926 Dihedral : 3.634 15.801 1515 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.83 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.23), residues: 1341 helix: 1.67 (0.17), residues: 972 sheet: None (None), residues: 0 loop : -1.04 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 644 HIS 0.003 0.000 HIS B 491 PHE 0.029 0.001 PHE B 533 TYR 0.020 0.001 TYR B 599 ARG 0.019 0.000 ARG B 341 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 741) hydrogen bonds : angle 4.14983 ( 2172) covalent geometry : bond 0.00261 (11235) covalent geometry : angle 0.59899 (15306) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3625.25 seconds wall clock time: 63 minutes 50.12 seconds (3830.12 seconds total)