Starting phenix.real_space_refine on Sat Aug 23 08:56:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8poe_17789/08_2025/8poe_17789.cif Found real_map, /net/cci-nas-00/data/ceres_data/8poe_17789/08_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_17789/08_2025/8poe_17789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8poe_17789/08_2025/8poe_17789.map" model { file = "/net/cci-nas-00/data/ceres_data/8poe_17789/08_2025/8poe_17789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8poe_17789/08_2025/8poe_17789.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.79, per 1000 atoms: 0.25 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: 0.74 Conformation dependent library (CDL) restraints added in 415.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.40 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: 1.15 Time building geometry restraints manager: 0.97 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: 0.01 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: 2.410 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: 0.020 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.610 Find NCS groups from input model: 0.130 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.640 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.005 0.000 ARG A 470 TYR 0.012 0.001 TYR A 622 PHE 0.042 0.001 PHE B 533 TRP 0.008 0.001 TRP C 435 HIS 0.005 0.001 HIS B 497 Details of bonding type rmsd covalent geometry : bond 0.00270 (11235) covalent geometry : angle 0.63745 (15306) hydrogen bonds : bond 0.12644 ( 741) hydrogen bonds : angle 5.14771 ( 2172) *********************** 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 : 0.247 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: 0.0875 time to fit residues: 35.6751 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 : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.4069 r_free = 0.4069 target = 0.185468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.152762 restraints weight = 17825.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.155548 restraints weight = 13732.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.157499 restraints weight = 11279.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.158907 restraints weight = 9780.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.159897 restraints weight = 8824.251| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.0997 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= 0.153 Angle : 0.587 5.774 15306 Z= 0.302 Chirality : 0.041 0.163 1761 Planarity : 0.005 0.041 1926 Dihedral : 3.708 17.767 1515 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.26 % Allowed : 6.16 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.23), residues: 1341 helix: 1.53 (0.16), residues: 987 sheet: None (None), residues: 0 loop : -1.10 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 363 TYR 0.016 0.002 TYR C 622 PHE 0.030 0.001 PHE B 533 TRP 0.012 0.001 TRP B 329 HIS 0.004 0.001 HIS B 497 Details of bonding type rmsd covalent geometry : bond 0.00334 (11235) covalent geometry : angle 0.58733 (15306) hydrogen bonds : bond 0.04757 ( 741) hydrogen bonds : angle 4.34773 ( 2172) *********************** 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 291 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 288 time to evaluate : 0.430 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 447 LEU cc_start: 0.8680 (tp) cc_final: 0.8447 (tp) REVERT: A 548 TYR cc_start: 0.7632 (t80) cc_final: 0.7350 (t80) REVERT: A 562 MET cc_start: 0.7987 (mmm) cc_final: 0.7699 (mmt) REVERT: A 630 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7609 (mm-30) REVERT: A 669 ILE cc_start: 0.7997 (mt) cc_final: 0.7723 (mt) REVERT: B 362 LEU cc_start: 0.8756 (mm) cc_final: 0.8379 (mm) REVERT: B 494 GLU cc_start: 0.8400 (tp30) cc_final: 0.7742 (tp30) REVERT: B 621 GLN cc_start: 0.8510 (mm110) cc_final: 0.8261 (mm110) REVERT: C 356 ASP cc_start: 0.7722 (m-30) cc_final: 0.7380 (m-30) REVERT: C 630 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8420 (mm-30) REVERT: C 669 ILE cc_start: 0.7767 (mt) cc_final: 0.7459 (mt) outliers start: 3 outliers final: 1 residues processed: 289 average time/residue: 0.0834 time to fit residues: 34.4132 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 : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN A 491 HIS A 598 HIS B 491 HIS ** B 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.177103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.150118 restraints weight = 18321.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.148324 restraints weight = 17062.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.149354 restraints weight = 16465.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.149810 restraints weight = 16269.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.150174 restraints weight = 13539.880| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 11235 Z= 0.259 Angle : 0.771 8.076 15306 Z= 0.400 Chirality : 0.047 0.237 1761 Planarity : 0.006 0.057 1926 Dihedral : 4.290 24.126 1515 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.80 % Favored : 96.12 % Rotamer: Outliers : 0.26 % Allowed : 6.16 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.23), residues: 1341 helix: 0.97 (0.16), residues: 1002 sheet: None (None), residues: 0 loop : -1.45 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 274 TYR 0.050 0.004 TYR C 313 PHE 0.035 0.003 PHE B 533 TRP 0.016 0.002 TRP A 644 HIS 0.010 0.002 HIS B 491 Details of bonding type rmsd covalent geometry : bond 0.00584 (11235) covalent geometry : angle 0.77083 (15306) hydrogen bonds : bond 0.05838 ( 741) hydrogen bonds : angle 4.70448 ( 2172) *********************** 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 292 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 289 time to evaluate : 0.359 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: 0.8068 (t) cc_final: 0.7854 (m) REVERT: A 356 ASP cc_start: 0.8562 (m-30) cc_final: 0.8354 (m-30) REVERT: A 659 PHE cc_start: 0.7456 (m-80) cc_final: 0.7198 (m-80) REVERT: A 669 ILE cc_start: 0.8164 (mt) cc_final: 0.7844 (mt) REVERT: B 356 ASP cc_start: 0.8485 (m-30) cc_final: 0.8088 (m-30) REVERT: B 470 ARG cc_start: 0.7477 (tmm160) cc_final: 0.7197 (tmm160) REVERT: B 594 LEU cc_start: 0.7539 (mm) cc_final: 0.6941 (tt) REVERT: C 235 CYS cc_start: 0.8066 (t) cc_final: 0.7489 (m) REVERT: C 423 LYS cc_start: 0.7254 (tppp) cc_final: 0.7046 (tppp) REVERT: C 630 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8255 (mm-30) REVERT: C 669 ILE cc_start: 0.7794 (mt) cc_final: 0.7561 (mt) outliers start: 3 outliers final: 1 residues processed: 291 average time/residue: 0.0975 time to fit residues: 39.4537 Evaluate side-chains 214 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 95 optimal weight: 0.0980 chunk 12 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 HIS A 491 HIS A 598 HIS A 657 HIS B 295 GLN B 333 GLN B 530 GLN B 658 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.181001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.144448 restraints weight = 18305.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.147711 restraints weight = 13240.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.149654 restraints weight = 10557.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.151623 restraints weight = 9069.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.152628 restraints weight = 8052.587| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 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 0.063 11235 Z= 0.131 Angle : 0.588 6.423 15306 Z= 0.302 Chirality : 0.040 0.160 1761 Planarity : 0.004 0.044 1926 Dihedral : 3.979 18.256 1515 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.02 % Rotamer: Outliers : 0.09 % Allowed : 3.34 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.23), residues: 1341 helix: 1.20 (0.16), residues: 966 sheet: None (None), residues: 0 loop : -1.09 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 437 TYR 0.023 0.002 TYR B 306 PHE 0.036 0.001 PHE B 533 TRP 0.009 0.001 TRP B 329 HIS 0.003 0.001 HIS A 491 Details of bonding type rmsd covalent geometry : bond 0.00268 (11235) covalent geometry : angle 0.58840 (15306) hydrogen bonds : bond 0.04826 ( 741) hydrogen bonds : angle 4.28501 ( 2172) *********************** 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 288 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 287 time to evaluate : 0.256 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: symmetry clash REVERT: A 235 CYS cc_start: 0.7835 (t) cc_final: 0.7618 (m) REVERT: A 494 GLU cc_start: 0.8361 (tp30) cc_final: 0.7815 (tp30) REVERT: A 548 TYR cc_start: 0.7596 (t80) cc_final: 0.7383 (t80) REVERT: A 669 ILE cc_start: 0.8111 (mt) cc_final: 0.7686 (mt) REVERT: B 263 ASP cc_start: 0.8787 (m-30) cc_final: 0.8537 (m-30) REVERT: B 356 ASP cc_start: 0.8510 (m-30) cc_final: 0.8168 (m-30) REVERT: B 362 LEU cc_start: 0.8828 (mm) cc_final: 0.8503 (mm) REVERT: B 659 PHE cc_start: 0.8003 (m-80) cc_final: 0.7669 (m-80) REVERT: C 393 SER cc_start: 0.8790 (t) cc_final: 0.8576 (t) REVERT: C 423 LYS cc_start: 0.7273 (tppp) cc_final: 0.7019 (tppp) REVERT: C 630 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8365 (mm-30) outliers start: 1 outliers final: 1 residues processed: 288 average time/residue: 0.0859 time to fit residues: 34.4426 Evaluate side-chains 213 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 30 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 82 optimal weight: 0.0670 chunk 0 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 HIS B 491 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.181741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.144899 restraints weight = 18050.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.148212 restraints weight = 13073.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.150563 restraints weight = 10425.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.152258 restraints weight = 8868.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.153292 restraints weight = 7907.256| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11235 Z= 0.127 Angle : 0.571 6.322 15306 Z= 0.290 Chirality : 0.039 0.161 1761 Planarity : 0.004 0.042 1926 Dihedral : 3.816 17.358 1515 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.02 % Rotamer: Outliers : 0.09 % Allowed : 2.81 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.23), residues: 1341 helix: 1.33 (0.16), residues: 966 sheet: None (None), residues: 0 loop : -1.03 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 479 TYR 0.019 0.001 TYR C 313 PHE 0.034 0.001 PHE B 533 TRP 0.017 0.001 TRP A 644 HIS 0.002 0.001 HIS B 557 Details of bonding type rmsd covalent geometry : bond 0.00259 (11235) covalent geometry : angle 0.57052 (15306) hydrogen bonds : bond 0.04497 ( 741) hydrogen bonds : angle 4.18037 ( 2172) *********************** 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 280 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 279 time to evaluate : 0.247 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 235 CYS cc_start: 0.7843 (t) cc_final: 0.7627 (m) REVERT: A 494 GLU cc_start: 0.8286 (tp30) cc_final: 0.7699 (tp30) REVERT: A 548 TYR cc_start: 0.7608 (t80) cc_final: 0.7407 (t80) REVERT: A 630 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7446 (mm-30) REVERT: A 669 ILE cc_start: 0.8033 (mt) cc_final: 0.7580 (mt) REVERT: B 263 ASP cc_start: 0.8783 (m-30) cc_final: 0.8528 (m-30) REVERT: B 356 ASP cc_start: 0.8456 (m-30) cc_final: 0.8148 (m-30) REVERT: B 362 LEU cc_start: 0.8820 (mm) cc_final: 0.8476 (mm) REVERT: B 426 ASP cc_start: 0.8978 (p0) cc_final: 0.8764 (p0) REVERT: C 356 ASP cc_start: 0.7650 (m-30) cc_final: 0.7364 (m-30) REVERT: C 423 LYS cc_start: 0.7272 (tppp) cc_final: 0.6985 (tppp) REVERT: C 630 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8342 (mm-30) outliers start: 1 outliers final: 0 residues processed: 280 average time/residue: 0.0828 time to fit residues: 32.4925 Evaluate side-chains 212 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 4 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 HIS B 295 GLN B 658 HIS C 295 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.176656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.139028 restraints weight = 18953.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.142117 restraints weight = 14041.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.144279 restraints weight = 11328.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.145800 restraints weight = 9759.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.146828 restraints weight = 8788.778| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11235 Z= 0.189 Angle : 0.659 6.501 15306 Z= 0.341 Chirality : 0.042 0.164 1761 Planarity : 0.005 0.043 1926 Dihedral : 3.998 20.503 1515 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.88 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.23), residues: 1341 helix: 1.19 (0.16), residues: 966 sheet: None (None), residues: 0 loop : -1.04 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 274 TYR 0.039 0.003 TYR C 313 PHE 0.037 0.002 PHE B 533 TRP 0.010 0.001 TRP B 385 HIS 0.005 0.001 HIS B 596 Details of bonding type rmsd covalent geometry : bond 0.00425 (11235) covalent geometry : angle 0.65941 (15306) hydrogen bonds : bond 0.04981 ( 741) hydrogen bonds : angle 4.45505 ( 2172) *********************** 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 283 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 ASP cc_start: 0.8608 (m-30) cc_final: 0.8397 (m-30) REVERT: A 548 TYR cc_start: 0.7745 (t80) cc_final: 0.7489 (t80) REVERT: A 630 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7273 (mm-30) REVERT: A 669 ILE cc_start: 0.8056 (mt) cc_final: 0.7673 (mt) REVERT: B 263 ASP cc_start: 0.8838 (m-30) cc_final: 0.8620 (m-30) REVERT: B 356 ASP cc_start: 0.8534 (m-30) cc_final: 0.8085 (m-30) REVERT: B 470 ARG cc_start: 0.7444 (tmm160) cc_final: 0.7180 (tmm160) REVERT: B 659 PHE cc_start: 0.7979 (m-80) cc_final: 0.7653 (m-80) REVERT: C 423 LYS cc_start: 0.7428 (tppp) cc_final: 0.7074 (tppp) REVERT: C 426 ASP cc_start: 0.8987 (p0) cc_final: 0.8775 (p0) REVERT: C 630 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8145 (mm-30) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.0934 time to fit residues: 37.2552 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 : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 10 optimal weight: 0.0870 chunk 65 optimal weight: 0.0010 chunk 113 optimal weight: 2.9990 chunk 107 optimal weight: 0.0270 chunk 91 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 chunk 4 optimal weight: 3.9990 overall best weight: 0.2020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 HIS A 497 HIS A 598 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.184156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.147485 restraints weight = 18252.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.150797 restraints weight = 13418.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.153072 restraints weight = 10760.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.154707 restraints weight = 9234.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.155414 restraints weight = 8278.200| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11235 Z= 0.126 Angle : 0.584 6.578 15306 Z= 0.295 Chirality : 0.039 0.153 1761 Planarity : 0.004 0.044 1926 Dihedral : 3.871 16.894 1515 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.09 % Allowed : 2.29 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.23), residues: 1341 helix: 1.40 (0.17), residues: 963 sheet: None (None), residues: 0 loop : -1.02 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 234 TYR 0.025 0.002 TYR B 306 PHE 0.035 0.001 PHE B 533 TRP 0.025 0.001 TRP A 644 HIS 0.003 0.001 HIS B 557 Details of bonding type rmsd covalent geometry : bond 0.00246 (11235) covalent geometry : angle 0.58437 (15306) hydrogen bonds : bond 0.04332 ( 741) hydrogen bonds : angle 4.20417 ( 2172) *********************** 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 280 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 279 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 HIS cc_start: 0.8186 (OUTLIER) cc_final: 0.7850 (m-70) REVERT: A 494 GLU cc_start: 0.8165 (tp30) cc_final: 0.7374 (tp30) REVERT: A 573 ARG cc_start: 0.8789 (mmm160) cc_final: 0.8436 (mmm160) REVERT: A 630 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7222 (mm-30) REVERT: A 669 ILE cc_start: 0.8095 (mt) cc_final: 0.7710 (mt) REVERT: B 263 ASP cc_start: 0.8773 (m-30) cc_final: 0.8526 (m-30) REVERT: B 362 LEU cc_start: 0.8805 (mm) cc_final: 0.8433 (mm) REVERT: C 356 ASP cc_start: 0.7746 (m-30) cc_final: 0.7398 (m-30) REVERT: C 423 LYS cc_start: 0.7398 (tppp) cc_final: 0.7024 (tppt) REVERT: C 630 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8295 (mm-30) outliers start: 1 outliers final: 0 residues processed: 280 average time/residue: 0.0978 time to fit residues: 38.6039 Evaluate side-chains 213 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.0470 chunk 51 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 119 optimal weight: 0.0980 chunk 126 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.186994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.154949 restraints weight = 17969.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.157486 restraints weight = 13961.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.159361 restraints weight = 11624.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.160725 restraints weight = 10173.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.161655 restraints weight = 9255.824| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 11235 Z= 0.122 Angle : 0.586 6.483 15306 Z= 0.294 Chirality : 0.039 0.154 1761 Planarity : 0.004 0.055 1926 Dihedral : 3.809 18.293 1515 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.23), residues: 1341 helix: 1.46 (0.16), residues: 975 sheet: None (None), residues: 0 loop : -1.13 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 471 TYR 0.016 0.001 TYR C 599 PHE 0.033 0.001 PHE B 533 TRP 0.017 0.001 TRP C 416 HIS 0.006 0.001 HIS A 491 Details of bonding type rmsd covalent geometry : bond 0.00250 (11235) covalent geometry : angle 0.58631 (15306) hydrogen bonds : bond 0.04219 ( 741) hydrogen bonds : angle 4.16325 ( 2172) *********************** 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 274 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 GLU cc_start: 0.8090 (tp30) cc_final: 0.7462 (tp30) REVERT: A 498 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6997 (mt-10) REVERT: A 630 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7515 (mm-30) REVERT: A 669 ILE cc_start: 0.8122 (mt) cc_final: 0.7768 (mt) REVERT: B 263 ASP cc_start: 0.8727 (m-30) cc_final: 0.8486 (m-30) REVERT: B 337 LEU cc_start: 0.8773 (mt) cc_final: 0.7744 (mt) REVERT: B 356 ASP cc_start: 0.8433 (m-30) cc_final: 0.7943 (m-30) REVERT: B 362 LEU cc_start: 0.8752 (mm) cc_final: 0.8495 (mm) REVERT: B 470 ARG cc_start: 0.7418 (tmm160) cc_final: 0.7166 (tmm160) REVERT: C 356 ASP cc_start: 0.7906 (m-30) cc_final: 0.7595 (m-30) REVERT: C 423 LYS cc_start: 0.7292 (tppp) cc_final: 0.6856 (tppt) REVERT: C 630 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8238 (mm-30) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.1013 time to fit residues: 38.8232 Evaluate side-chains 206 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 92 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 63 optimal weight: 0.0670 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.0980 chunk 72 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.186678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.154332 restraints weight = 18128.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.156941 restraints weight = 14175.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.158510 restraints weight = 11855.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.159996 restraints weight = 10467.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.160763 restraints weight = 9537.950| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2714 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= 0.121 Angle : 0.591 11.245 15306 Z= 0.298 Chirality : 0.040 0.194 1761 Planarity : 0.004 0.043 1926 Dihedral : 3.743 17.482 1515 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.68 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.23), residues: 1341 helix: 1.54 (0.16), residues: 963 sheet: None (None), residues: 0 loop : -1.00 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 341 TYR 0.015 0.001 TYR C 313 PHE 0.032 0.001 PHE B 533 TRP 0.015 0.001 TRP C 416 HIS 0.003 0.001 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00252 (11235) covalent geometry : angle 0.59100 (15306) hydrogen bonds : bond 0.04148 ( 741) hydrogen bonds : angle 4.15519 ( 2172) *********************** 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 267 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.288 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 479 ARG cc_start: 0.5047 (mmm160) cc_final: 0.4795 (mmm160) REVERT: A 494 GLU cc_start: 0.8100 (tp30) cc_final: 0.7512 (tp30) REVERT: A 573 ARG cc_start: 0.8690 (mmm160) cc_final: 0.8357 (mmm160) REVERT: A 630 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7554 (mm-30) REVERT: A 669 ILE cc_start: 0.8117 (mt) cc_final: 0.7746 (mt) REVERT: B 263 ASP cc_start: 0.8778 (m-30) cc_final: 0.8517 (m-30) REVERT: B 356 ASP cc_start: 0.8437 (m-30) cc_final: 0.7955 (m-30) REVERT: B 362 LEU cc_start: 0.8780 (mm) cc_final: 0.8394 (mm) REVERT: B 562 MET cc_start: 0.8238 (ttm) cc_final: 0.7835 (tmm) REVERT: C 356 ASP cc_start: 0.7616 (m-30) cc_final: 0.7318 (m-30) REVERT: C 423 LYS cc_start: 0.7312 (tppp) cc_final: 0.7037 (tptm) REVERT: C 630 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8266 (mm-30) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.0881 time to fit residues: 33.3062 Evaluate side-chains 208 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 103 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.184877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.151914 restraints weight = 18749.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.154419 restraints weight = 14673.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.156269 restraints weight = 12315.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.157131 restraints weight = 10831.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.158304 restraints weight = 10019.619| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11235 Z= 0.134 Angle : 0.605 6.832 15306 Z= 0.307 Chirality : 0.041 0.156 1761 Planarity : 0.004 0.055 1926 Dihedral : 3.793 18.216 1515 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.98 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.23), residues: 1341 helix: 1.53 (0.17), residues: 963 sheet: None (None), residues: 0 loop : -1.02 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 274 TYR 0.021 0.002 TYR C 313 PHE 0.034 0.001 PHE B 533 TRP 0.030 0.001 TRP A 644 HIS 0.003 0.001 HIS A 491 Details of bonding type rmsd covalent geometry : bond 0.00293 (11235) covalent geometry : angle 0.60473 (15306) hydrogen bonds : bond 0.04275 ( 741) hydrogen bonds : angle 4.22378 ( 2172) ********************** 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 277 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.385 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: 0.8671 (m-30) cc_final: 0.8468 (m-30) REVERT: A 426 ASP cc_start: 0.8746 (p0) cc_final: 0.8427 (p0) REVERT: A 479 ARG cc_start: 0.5020 (mmm160) cc_final: 0.4677 (mmm160) REVERT: A 494 GLU cc_start: 0.8112 (tp30) cc_final: 0.7474 (tp30) REVERT: A 573 ARG cc_start: 0.8722 (mmm160) cc_final: 0.8318 (mmm160) REVERT: A 630 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7508 (mm-30) REVERT: A 669 ILE cc_start: 0.8118 (mt) cc_final: 0.7742 (mt) REVERT: B 263 ASP cc_start: 0.8802 (m-30) cc_final: 0.8552 (m-30) REVERT: B 356 ASP cc_start: 0.8454 (m-30) cc_final: 0.7984 (m-30) REVERT: B 470 ARG cc_start: 0.7455 (tmm160) cc_final: 0.7220 (tmm160) REVERT: B 562 MET cc_start: 0.8263 (ttm) cc_final: 0.7737 (tmm) REVERT: C 356 ASP cc_start: 0.7850 (m-30) cc_final: 0.7568 (m-30) REVERT: C 393 SER cc_start: 0.8673 (t) cc_final: 0.8469 (t) REVERT: C 423 LYS cc_start: 0.7378 (tppp) cc_final: 0.7120 (tptm) REVERT: C 630 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8250 (mm-30) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.0995 time to fit residues: 38.4074 Evaluate side-chains 209 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 115 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 74 optimal weight: 0.0470 chunk 112 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 82 optimal weight: 0.0670 chunk 59 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 overall best weight: 0.3416 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.187489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.154578 restraints weight = 18375.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.157329 restraints weight = 14232.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.159235 restraints weight = 11786.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.160463 restraints weight = 10298.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.161138 restraints weight = 9389.453| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 11235 Z= 0.116 Angle : 0.578 6.600 15306 Z= 0.288 Chirality : 0.039 0.152 1761 Planarity : 0.004 0.043 1926 Dihedral : 3.686 17.337 1515 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.23), residues: 1341 helix: 1.58 (0.17), residues: 966 sheet: None (None), residues: 0 loop : -0.99 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 470 TYR 0.025 0.001 TYR B 622 PHE 0.029 0.001 PHE B 533 TRP 0.015 0.001 TRP C 416 HIS 0.003 0.000 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00234 (11235) covalent geometry : angle 0.57838 (15306) hydrogen bonds : bond 0.03991 ( 741) hydrogen bonds : angle 4.09866 ( 2172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1654.95 seconds wall clock time: 29 minutes 14.89 seconds (1754.89 seconds total)