Starting phenix.real_space_refine on Sat Aug 23 07:14:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lh2_23334/08_2025/7lh2_23334.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lh2_23334/08_2025/7lh2_23334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lh2_23334/08_2025/7lh2_23334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lh2_23334/08_2025/7lh2_23334.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lh2_23334/08_2025/7lh2_23334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lh2_23334/08_2025/7lh2_23334.map" } resolution = 3.43 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= 0.005 sd= 0.025 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 48 5.16 5 C 6930 2.51 5 N 1690 2.21 5 O 1860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 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: 10528 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5226 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 34, 'TRANS': 645} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5226 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 34, 'TRANS': 645} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'CLR': 1, 'SAL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'CLR': 1, 'SAL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.50, per 1000 atoms: 0.24 Number of scatterers: 10528 At special positions: 0 Unit cell: (102.16, 120.379, 113.872, 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 48 16.00 O 1860 8.00 N 1690 7.00 C 6930 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: 1.06 Conformation dependent library (CDL) restraints added in 431.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2512 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 5 sheets defined 69.6% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.592A pdb=" N LYS A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 48' Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 75 through 105 removed outlier: 5.451A pdb=" N LEU A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLY A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 109 through 115 removed outlier: 3.768A pdb=" N LEU A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 removed outlier: 3.664A pdb=" N PHE A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 152 Processing helix chain 'A' and resid 168 through 196 Processing helix chain 'A' and resid 197 through 205 removed outlier: 3.982A pdb=" N PHE A 200 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 202 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE A 203 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'A' and resid 258 through 282 Processing helix chain 'A' and resid 291 through 308 removed outlier: 3.614A pdb=" N PHE A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.845A pdb=" N TYR A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 366 removed outlier: 6.494A pdb=" N VAL A 341 " --> pdb=" O HIS A 337 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ASP A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 396 through 406 Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 436 through 448 removed outlier: 3.783A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 456 through 465 removed outlier: 3.549A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 481 Processing helix chain 'A' and resid 483 through 505 removed outlier: 3.866A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 560 removed outlier: 3.670A pdb=" N THR A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 579 Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 653 through 670 removed outlier: 3.747A pdb=" N VAL A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 690 Processing helix chain 'A' and resid 695 through 702 removed outlier: 3.928A pdb=" N GLU A 700 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 725 removed outlier: 4.045A pdb=" N SER A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 30 Processing helix chain 'B' and resid 43 through 48 removed outlier: 3.592A pdb=" N LYS B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 48' Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 75 through 105 removed outlier: 5.451A pdb=" N LEU B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLY B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) Proline residue: B 96 - end of helix Processing helix chain 'B' and resid 109 through 115 removed outlier: 3.769A pdb=" N LEU B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 127 removed outlier: 3.665A pdb=" N PHE B 125 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 152 Processing helix chain 'B' and resid 168 through 196 Processing helix chain 'B' and resid 197 through 205 removed outlier: 3.982A pdb=" N PHE B 200 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 202 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE B 203 " --> pdb=" O PHE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 225 Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'B' and resid 241 through 253 Processing helix chain 'B' and resid 254 through 257 Processing helix chain 'B' and resid 258 through 282 Processing helix chain 'B' and resid 291 through 308 removed outlier: 3.614A pdb=" N PHE B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.846A pdb=" N TYR B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 366 removed outlier: 6.493A pdb=" N VAL B 341 " --> pdb=" O HIS B 337 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ASP B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 396 through 406 Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 436 through 448 removed outlier: 3.783A pdb=" N LEU B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 456 through 465 removed outlier: 3.548A pdb=" N PHE B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 481 Processing helix chain 'B' and resid 483 through 505 removed outlier: 3.866A pdb=" N LEU B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 560 removed outlier: 3.670A pdb=" N THR B 560 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 579 Processing helix chain 'B' and resid 626 through 631 Processing helix chain 'B' and resid 653 through 670 removed outlier: 3.747A pdb=" N VAL B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 690 Processing helix chain 'B' and resid 695 through 702 removed outlier: 3.928A pdb=" N GLU B 700 " --> pdb=" O ALA B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 725 removed outlier: 4.044A pdb=" N SER B 725 " --> pdb=" O GLU B 721 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 135 removed outlier: 3.587A pdb=" N SER A 394 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.891A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N LYS A 513 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ILE A 535 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS A 536 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASP A 645 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE A 538 " --> pdb=" O ASP A 645 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL A 642 " --> pdb=" O TYR A 675 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALA A 677 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU A 644 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 134 through 135 removed outlier: 3.588A pdb=" N SER B 394 " --> pdb=" O GLY B 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.891A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N LYS B 513 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ILE B 535 " --> pdb=" O LYS B 513 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LYS B 536 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASP B 645 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE B 538 " --> pdb=" O ASP B 645 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL B 642 " --> pdb=" O TYR B 675 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALA B 677 " --> pdb=" O VAL B 642 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU B 644 " --> pdb=" O ALA B 677 " (cutoff:3.500A) 646 hydrogen bonds defined for protein. 1878 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: 1.77 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3242 1.34 - 1.46: 2346 1.46 - 1.58: 5104 1.58 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 10770 Sorted by residual: bond pdb=" C1 SAL A 801 " pdb=" C2 SAL A 801 " ideal model delta sigma weight residual 1.409 1.484 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C1 SAL B 801 " pdb=" C2 SAL B 801 " ideal model delta sigma weight residual 1.409 1.484 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" N VAL B 402 " pdb=" CA VAL B 402 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.49e+00 bond pdb=" N SER B 398 " pdb=" CA SER B 398 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.19e-02 7.06e+03 6.66e+00 bond pdb=" N GLN B 403 " pdb=" CA GLN B 403 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.83e+00 ... (remaining 10765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 14416 1.90 - 3.80: 198 3.80 - 5.70: 36 5.70 - 7.59: 2 7.59 - 9.49: 2 Bond angle restraints: 14654 Sorted by residual: angle pdb=" O VAL B 402 " pdb=" C VAL B 402 " pdb=" N GLN B 403 " ideal model delta sigma weight residual 121.87 124.67 -2.80 9.70e-01 1.06e+00 8.32e+00 angle pdb=" CA LEU A 448 " pdb=" CB LEU A 448 " pdb=" CG LEU A 448 " ideal model delta sigma weight residual 116.30 125.79 -9.49 3.50e+00 8.16e-02 7.36e+00 angle pdb=" CA LEU B 448 " pdb=" CB LEU B 448 " pdb=" CG LEU B 448 " ideal model delta sigma weight residual 116.30 125.74 -9.44 3.50e+00 8.16e-02 7.27e+00 angle pdb=" CA SER B 398 " pdb=" C SER B 398 " pdb=" O SER B 398 " ideal model delta sigma weight residual 120.82 118.04 2.78 1.05e+00 9.07e-01 7.00e+00 angle pdb=" CA ARG B 399 " pdb=" C ARG B 399 " pdb=" O ARG B 399 " ideal model delta sigma weight residual 120.55 117.84 2.71 1.06e+00 8.90e-01 6.52e+00 ... (remaining 14649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 5809 16.06 - 32.13: 527 32.13 - 48.19: 100 48.19 - 64.25: 22 64.25 - 80.32: 12 Dihedral angle restraints: 6470 sinusoidal: 2546 harmonic: 3924 Sorted by residual: dihedral pdb=" CA PHE A 23 " pdb=" C PHE A 23 " pdb=" N SER A 24 " pdb=" CA SER A 24 " ideal model delta harmonic sigma weight residual 180.00 160.58 19.42 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA PHE B 23 " pdb=" C PHE B 23 " pdb=" N SER B 24 " pdb=" CA SER B 24 " ideal model delta harmonic sigma weight residual 180.00 160.58 19.42 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ASP B 686 " pdb=" CB ASP B 686 " pdb=" CG ASP B 686 " pdb=" OD1 ASP B 686 " ideal model delta sinusoidal sigma weight residual -30.00 -87.57 57.57 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 6467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1174 0.039 - 0.077: 427 0.077 - 0.116: 123 0.116 - 0.154: 16 0.154 - 0.193: 4 Chirality restraints: 1744 Sorted by residual: chirality pdb=" CG LEU A 193 " pdb=" CB LEU A 193 " pdb=" CD1 LEU A 193 " pdb=" CD2 LEU A 193 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CG LEU B 193 " pdb=" CB LEU B 193 " pdb=" CD1 LEU B 193 " pdb=" CD2 LEU B 193 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CA VAL B 402 " pdb=" N VAL B 402 " pdb=" C VAL B 402 " pdb=" CB VAL B 402 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.28e-01 ... (remaining 1741 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 633 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO B 634 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 634 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 634 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 633 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO A 634 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 634 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 634 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 198 " 0.015 2.00e-02 2.50e+03 1.47e-02 3.78e+00 pdb=" CG PHE B 198 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 198 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 198 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 198 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 198 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 198 " 0.000 2.00e-02 2.50e+03 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 64 2.60 - 3.18: 9454 3.18 - 3.75: 16149 3.75 - 4.33: 21547 4.33 - 4.90: 36174 Nonbonded interactions: 83388 Sorted by model distance: nonbonded pdb=" OG SER A 398 " pdb=" O2' SAL A 801 " model vdw 2.030 3.040 nonbonded pdb=" OG SER B 86 " pdb=" O GLN B 403 " model vdw 2.164 3.040 nonbonded pdb=" OD2 ASP A 83 " pdb=" OG1 THR A 410 " model vdw 2.223 3.040 nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 410 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR B 503 " pdb=" OH TYR B 545 " model vdw 2.226 3.040 ... (remaining 83383 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.600 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 0.075 10770 Z= 0.155 Angle : 0.558 9.493 14654 Z= 0.304 Chirality : 0.043 0.193 1744 Planarity : 0.004 0.053 1812 Dihedral : 13.017 80.315 3958 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.18 % Allowed : 0.53 % Favored : 99.29 % 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: 0.96 (0.24), residues: 1352 helix: 1.34 (0.18), residues: 894 sheet: 1.90 (0.69), residues: 52 loop : -1.07 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 572 TYR 0.014 0.001 TYR B 237 PHE 0.034 0.001 PHE B 198 TRP 0.004 0.001 TRP B 472 HIS 0.002 0.001 HIS A 25 Details of bonding type rmsd covalent geometry : bond 0.00299 (10770) covalent geometry : angle 0.55807 (14654) hydrogen bonds : bond 0.15501 ( 646) hydrogen bonds : angle 5.43705 ( 1878) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 0.342 Fit side-chains REVERT: A 545 TYR cc_start: 0.8268 (p90) cc_final: 0.7954 (p90) outliers start: 2 outliers final: 2 residues processed: 146 average time/residue: 0.0789 time to fit residues: 17.6415 Evaluate side-chains 105 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain B residue 453 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.137354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.109930 restraints weight = 16447.182| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.26 r_work: 0.3316 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10770 Z= 0.161 Angle : 0.567 11.001 14654 Z= 0.283 Chirality : 0.044 0.143 1744 Planarity : 0.004 0.050 1812 Dihedral : 5.043 44.177 1594 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.23 % Allowed : 7.76 % Favored : 91.01 % 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: 1.19 (0.24), residues: 1352 helix: 1.55 (0.18), residues: 896 sheet: 2.01 (0.70), residues: 52 loop : -1.10 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 576 TYR 0.013 0.001 TYR A 237 PHE 0.023 0.001 PHE A 198 TRP 0.007 0.001 TRP A 699 HIS 0.007 0.001 HIS A 704 Details of bonding type rmsd covalent geometry : bond 0.00378 (10770) covalent geometry : angle 0.56663 (14654) hydrogen bonds : bond 0.04364 ( 646) hydrogen bonds : angle 4.27603 ( 1878) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.384 Fit side-chains REVERT: A 198 PHE cc_start: 0.7698 (t80) cc_final: 0.7482 (t80) REVERT: B 198 PHE cc_start: 0.7230 (t80) cc_final: 0.6783 (t80) outliers start: 14 outliers final: 13 residues processed: 127 average time/residue: 0.0817 time to fit residues: 15.6938 Evaluate side-chains 118 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 453 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 75 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 122 optimal weight: 0.6980 chunk 129 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.135124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.108811 restraints weight = 16608.506| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.09 r_work: 0.3301 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10770 Z= 0.191 Angle : 0.575 9.430 14654 Z= 0.288 Chirality : 0.044 0.136 1744 Planarity : 0.004 0.055 1812 Dihedral : 4.547 37.648 1594 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.03 % Allowed : 11.20 % Favored : 86.77 % 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: 1.27 (0.24), residues: 1352 helix: 1.59 (0.18), residues: 886 sheet: 1.84 (0.69), residues: 52 loop : -0.90 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 572 TYR 0.016 0.001 TYR B 545 PHE 0.016 0.002 PHE A 198 TRP 0.008 0.001 TRP B 70 HIS 0.005 0.001 HIS A 704 Details of bonding type rmsd covalent geometry : bond 0.00460 (10770) covalent geometry : angle 0.57498 (14654) hydrogen bonds : bond 0.04353 ( 646) hydrogen bonds : angle 4.17997 ( 1878) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.344 Fit side-chains REVERT: A 227 LYS cc_start: 0.7810 (ptmt) cc_final: 0.7485 (ptpt) REVERT: B 198 PHE cc_start: 0.7397 (t80) cc_final: 0.6938 (t80) REVERT: B 227 LYS cc_start: 0.7802 (ptmt) cc_final: 0.7485 (ptpt) REVERT: B 452 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.8001 (m-10) outliers start: 23 outliers final: 14 residues processed: 132 average time/residue: 0.0769 time to fit residues: 15.2078 Evaluate side-chains 117 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 452 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 71 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.136174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.110283 restraints weight = 16560.395| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.10 r_work: 0.3305 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10770 Z= 0.152 Angle : 0.540 8.623 14654 Z= 0.269 Chirality : 0.043 0.129 1744 Planarity : 0.004 0.056 1812 Dihedral : 4.295 33.747 1588 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.76 % Allowed : 13.49 % Favored : 84.74 % 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: 1.39 (0.24), residues: 1352 helix: 1.70 (0.18), residues: 882 sheet: 1.69 (0.69), residues: 52 loop : -0.87 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 572 TYR 0.013 0.001 TYR A 545 PHE 0.011 0.001 PHE B 391 TRP 0.009 0.001 TRP B 70 HIS 0.004 0.001 HIS A 704 Details of bonding type rmsd covalent geometry : bond 0.00361 (10770) covalent geometry : angle 0.53969 (14654) hydrogen bonds : bond 0.03998 ( 646) hydrogen bonds : angle 4.08181 ( 1878) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 227 LYS cc_start: 0.7797 (ptmt) cc_final: 0.7452 (ptpt) REVERT: A 694 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6697 (mp0) REVERT: B 198 PHE cc_start: 0.7385 (t80) cc_final: 0.6892 (t80) REVERT: B 227 LYS cc_start: 0.7785 (ptmt) cc_final: 0.7459 (ptpt) REVERT: B 237 TYR cc_start: 0.7673 (m-10) cc_final: 0.7455 (m-10) REVERT: B 694 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7008 (mp0) outliers start: 20 outliers final: 16 residues processed: 127 average time/residue: 0.0764 time to fit residues: 14.9581 Evaluate side-chains 122 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 424 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 101 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 chunk 35 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.138935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.113281 restraints weight = 16466.987| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.08 r_work: 0.3368 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10770 Z= 0.141 Angle : 0.538 8.998 14654 Z= 0.264 Chirality : 0.043 0.126 1744 Planarity : 0.004 0.056 1812 Dihedral : 4.227 38.987 1588 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.03 % Allowed : 14.46 % Favored : 83.51 % 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: 1.49 (0.24), residues: 1352 helix: 1.79 (0.18), residues: 882 sheet: 1.63 (0.69), residues: 52 loop : -0.83 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 572 TYR 0.012 0.001 TYR B 62 PHE 0.011 0.001 PHE B 391 TRP 0.010 0.001 TRP B 70 HIS 0.003 0.001 HIS A 704 Details of bonding type rmsd covalent geometry : bond 0.00332 (10770) covalent geometry : angle 0.53827 (14654) hydrogen bonds : bond 0.03840 ( 646) hydrogen bonds : angle 4.01437 ( 1878) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.345 Fit side-chains REVERT: A 227 LYS cc_start: 0.7827 (ptmt) cc_final: 0.7485 (ptpt) REVERT: A 694 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6875 (mp0) REVERT: B 70 TRP cc_start: 0.7952 (p-90) cc_final: 0.7743 (p-90) REVERT: B 198 PHE cc_start: 0.7423 (t80) cc_final: 0.6906 (t80) REVERT: B 227 LYS cc_start: 0.7797 (ptmt) cc_final: 0.7478 (ptpt) REVERT: B 694 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6763 (mp0) outliers start: 23 outliers final: 18 residues processed: 128 average time/residue: 0.0790 time to fit residues: 15.3953 Evaluate side-chains 128 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 452 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.0570 chunk 51 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 70 optimal weight: 20.0000 chunk 21 optimal weight: 0.6980 chunk 90 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.143081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.114600 restraints weight = 16440.725| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.42 r_work: 0.3438 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10770 Z= 0.097 Angle : 0.509 8.251 14654 Z= 0.246 Chirality : 0.041 0.127 1744 Planarity : 0.004 0.055 1812 Dihedral : 4.151 43.196 1588 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.03 % Allowed : 14.73 % Favored : 83.25 % 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: 1.75 (0.24), residues: 1352 helix: 1.92 (0.18), residues: 892 sheet: 1.90 (0.69), residues: 52 loop : -0.64 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 572 TYR 0.009 0.001 TYR B 237 PHE 0.011 0.001 PHE B 269 TRP 0.011 0.001 TRP A 70 HIS 0.001 0.001 HIS B 707 Details of bonding type rmsd covalent geometry : bond 0.00199 (10770) covalent geometry : angle 0.50891 (14654) hydrogen bonds : bond 0.03229 ( 646) hydrogen bonds : angle 3.84656 ( 1878) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.363 Fit side-chains REVERT: A 70 TRP cc_start: 0.7917 (p-90) cc_final: 0.7676 (p-90) REVERT: A 198 PHE cc_start: 0.7618 (t80) cc_final: 0.7395 (t80) REVERT: A 227 LYS cc_start: 0.7725 (ptmt) cc_final: 0.7341 (ptpp) REVERT: A 694 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6546 (mp0) REVERT: B 198 PHE cc_start: 0.7241 (t80) cc_final: 0.6691 (t80) REVERT: B 227 LYS cc_start: 0.7701 (ptmt) cc_final: 0.7309 (ptpp) REVERT: B 694 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6747 (mp0) outliers start: 23 outliers final: 18 residues processed: 137 average time/residue: 0.0820 time to fit residues: 17.1660 Evaluate side-chains 129 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 452 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 124 optimal weight: 30.0000 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.137894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.112324 restraints weight = 16691.701| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.05 r_work: 0.3386 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10770 Z= 0.225 Angle : 0.597 8.974 14654 Z= 0.298 Chirality : 0.044 0.140 1744 Planarity : 0.004 0.056 1812 Dihedral : 4.392 48.464 1588 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.68 % Allowed : 15.61 % Favored : 82.72 % 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: 1.47 (0.24), residues: 1352 helix: 1.79 (0.18), residues: 896 sheet: 1.63 (0.69), residues: 52 loop : -0.99 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 576 TYR 0.016 0.002 TYR B 545 PHE 0.015 0.002 PHE B 111 TRP 0.025 0.002 TRP B 70 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00549 (10770) covalent geometry : angle 0.59697 (14654) hydrogen bonds : bond 0.03984 ( 646) hydrogen bonds : angle 4.02525 ( 1878) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 198 PHE cc_start: 0.7728 (t80) cc_final: 0.7402 (t80) REVERT: A 227 LYS cc_start: 0.7868 (ptmt) cc_final: 0.7533 (ptpt) REVERT: B 70 TRP cc_start: 0.7913 (p-90) cc_final: 0.7513 (p-90) REVERT: B 198 PHE cc_start: 0.7441 (t80) cc_final: 0.6933 (t80) REVERT: B 227 LYS cc_start: 0.7838 (ptmt) cc_final: 0.7521 (ptpt) outliers start: 19 outliers final: 17 residues processed: 123 average time/residue: 0.0840 time to fit residues: 15.8072 Evaluate side-chains 120 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 452 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 25 optimal weight: 6.9990 chunk 29 optimal weight: 30.0000 chunk 71 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 chunk 0 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 126 optimal weight: 0.0470 overall best weight: 0.6684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.142818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.114494 restraints weight = 16317.225| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.37 r_work: 0.3437 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10770 Z= 0.099 Angle : 0.514 8.802 14654 Z= 0.252 Chirality : 0.041 0.127 1744 Planarity : 0.004 0.056 1812 Dihedral : 4.332 50.330 1588 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.85 % Allowed : 15.70 % Favored : 82.45 % 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: 1.83 (0.24), residues: 1352 helix: 2.01 (0.18), residues: 888 sheet: 1.87 (0.70), residues: 52 loop : -0.66 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 576 TYR 0.011 0.001 TYR A 237 PHE 0.012 0.001 PHE A 269 TRP 0.027 0.002 TRP B 70 HIS 0.002 0.001 HIS A 704 Details of bonding type rmsd covalent geometry : bond 0.00202 (10770) covalent geometry : angle 0.51395 (14654) hydrogen bonds : bond 0.03308 ( 646) hydrogen bonds : angle 3.83547 ( 1878) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 227 LYS cc_start: 0.7787 (ptmt) cc_final: 0.7395 (ptpp) REVERT: A 694 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6603 (mp0) REVERT: B 198 PHE cc_start: 0.7386 (t80) cc_final: 0.6827 (t80) REVERT: B 227 LYS cc_start: 0.7770 (ptmt) cc_final: 0.7371 (ptpp) REVERT: B 694 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6676 (mp0) outliers start: 21 outliers final: 17 residues processed: 129 average time/residue: 0.0890 time to fit residues: 17.5250 Evaluate side-chains 126 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 452 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 109 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 132 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 59 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.140680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.114797 restraints weight = 16566.760| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.08 r_work: 0.3411 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10770 Z= 0.130 Angle : 0.529 8.555 14654 Z= 0.261 Chirality : 0.042 0.124 1744 Planarity : 0.004 0.056 1812 Dihedral : 4.381 52.356 1588 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.59 % Allowed : 15.26 % Favored : 83.16 % 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: 1.81 (0.24), residues: 1352 helix: 2.03 (0.18), residues: 886 sheet: 1.88 (0.70), residues: 52 loop : -0.74 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 576 TYR 0.012 0.001 TYR A 545 PHE 0.011 0.001 PHE B 111 TRP 0.031 0.002 TRP B 70 HIS 0.002 0.001 HIS A 704 Details of bonding type rmsd covalent geometry : bond 0.00307 (10770) covalent geometry : angle 0.52921 (14654) hydrogen bonds : bond 0.03476 ( 646) hydrogen bonds : angle 3.84110 ( 1878) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.329 Fit side-chains REVERT: A 70 TRP cc_start: 0.7935 (p-90) cc_final: 0.7710 (p-90) REVERT: A 227 LYS cc_start: 0.7883 (ptmt) cc_final: 0.7518 (ptpp) REVERT: A 694 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6756 (mp0) REVERT: B 198 PHE cc_start: 0.7384 (t80) cc_final: 0.6823 (t80) REVERT: B 227 LYS cc_start: 0.7890 (ptmt) cc_final: 0.7510 (ptpp) REVERT: B 694 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6889 (mp0) outliers start: 18 outliers final: 17 residues processed: 127 average time/residue: 0.0870 time to fit residues: 16.5693 Evaluate side-chains 126 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 452 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 126 optimal weight: 30.0000 chunk 53 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.141649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.113294 restraints weight = 16310.813| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.36 r_work: 0.3438 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10770 Z= 0.110 Angle : 0.538 10.218 14654 Z= 0.261 Chirality : 0.042 0.126 1744 Planarity : 0.004 0.056 1812 Dihedral : 4.389 54.175 1588 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.50 % Allowed : 15.96 % Favored : 82.54 % 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: 1.86 (0.24), residues: 1352 helix: 2.05 (0.18), residues: 886 sheet: 2.03 (0.71), residues: 52 loop : -0.68 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 576 TYR 0.015 0.001 TYR A 62 PHE 0.010 0.001 PHE B 269 TRP 0.034 0.002 TRP B 70 HIS 0.002 0.001 HIS A 704 Details of bonding type rmsd covalent geometry : bond 0.00249 (10770) covalent geometry : angle 0.53806 (14654) hydrogen bonds : bond 0.03335 ( 646) hydrogen bonds : angle 3.80773 ( 1878) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.407 Fit side-chains REVERT: A 70 TRP cc_start: 0.7880 (p-90) cc_final: 0.7671 (p-90) REVERT: A 227 LYS cc_start: 0.7841 (ptmt) cc_final: 0.7462 (ptpp) REVERT: A 694 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6553 (mp0) REVERT: B 198 PHE cc_start: 0.7400 (t80) cc_final: 0.6814 (t80) REVERT: B 227 LYS cc_start: 0.7820 (ptmt) cc_final: 0.7456 (ptpp) REVERT: B 694 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6910 (mp0) outliers start: 17 outliers final: 17 residues processed: 124 average time/residue: 0.0918 time to fit residues: 17.0091 Evaluate side-chains 125 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 486 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 11 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 117 optimal weight: 0.0980 chunk 55 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.143051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.117252 restraints weight = 16505.028| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.15 r_work: 0.3466 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10770 Z= 0.103 Angle : 0.519 9.676 14654 Z= 0.255 Chirality : 0.042 0.126 1744 Planarity : 0.004 0.055 1812 Dihedral : 4.374 56.215 1588 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.41 % Allowed : 16.23 % Favored : 82.36 % 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: 1.95 (0.24), residues: 1352 helix: 2.08 (0.18), residues: 888 sheet: 2.18 (0.72), residues: 52 loop : -0.59 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 576 TYR 0.010 0.001 TYR A 313 PHE 0.010 0.001 PHE B 269 TRP 0.034 0.002 TRP B 70 HIS 0.002 0.001 HIS A 704 Details of bonding type rmsd covalent geometry : bond 0.00229 (10770) covalent geometry : angle 0.51883 (14654) hydrogen bonds : bond 0.03187 ( 646) hydrogen bonds : angle 3.76532 ( 1878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2524.81 seconds wall clock time: 44 minutes 1.26 seconds (2641.26 seconds total)