Starting phenix.real_space_refine on Mon Jun 9 10:04:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lh2_23334/06_2025/7lh2_23334.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lh2_23334/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7lh2_23334/06_2025/7lh2_23334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lh2_23334/06_2025/7lh2_23334.map" model { file = "/net/cci-nas-00/data/ceres_data/7lh2_23334/06_2025/7lh2_23334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lh2_23334/06_2025/7lh2_23334.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG: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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG: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: 7.22, per 1000 atoms: 0.69 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: 2.61 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.28 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: 3.62 Time building geometry restraints manager: 3.07 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: 0.05 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.860 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.790 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (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 TRP 0.004 0.001 TRP B 472 HIS 0.002 0.001 HIS A 25 PHE 0.034 0.001 PHE B 198 TYR 0.014 0.001 TYR B 237 ARG 0.008 0.001 ARG B 572 Details of bonding type rmsd hydrogen bonds : bond 0.15501 ( 646) hydrogen bonds : angle 5.43705 ( 1878) covalent geometry : bond 0.00299 (10770) covalent geometry : angle 0.55807 (14654) *********************** 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 : 1.049 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: 0.1963 time to fit residues: 44.2046 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 : 1.034 ------------------------------------------------------------------------------- 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 114 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 0.2980 chunk 35 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3884 r_free = 0.3884 target = 0.140280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.114676 restraints weight = 16162.512| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.11 r_work: 0.3369 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10770 Z= 0.121 Angle : 0.533 11.041 14654 Z= 0.263 Chirality : 0.042 0.128 1744 Planarity : 0.004 0.050 1812 Dihedral : 4.935 42.852 1594 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.15 % Allowed : 7.67 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.24), residues: 1352 helix: 1.60 (0.18), residues: 896 sheet: 2.11 (0.70), residues: 52 loop : -1.03 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 699 HIS 0.006 0.001 HIS A 704 PHE 0.021 0.001 PHE A 198 TYR 0.012 0.001 TYR A 237 ARG 0.004 0.000 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 646) hydrogen bonds : angle 4.24127 ( 1878) covalent geometry : bond 0.00259 (10770) covalent geometry : angle 0.53339 (14654) *********************** 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 138 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 2.182 Fit side-chains REVERT: A 198 PHE cc_start: 0.7746 (t80) cc_final: 0.7500 (t80) REVERT: A 545 TYR cc_start: 0.8586 (p90) cc_final: 0.8144 (p90) REVERT: A 575 MET cc_start: 0.7645 (tmm) cc_final: 0.7444 (tmm) REVERT: B 198 PHE cc_start: 0.7324 (t80) cc_final: 0.6891 (t80) outliers start: 13 outliers final: 10 residues processed: 132 average time/residue: 0.2866 time to fit residues: 57.0086 Evaluate side-chains 116 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 1.303 ------------------------------------------------------------------------------- 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 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 424 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 90 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 107 optimal weight: 0.0000 chunk 8 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.142378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.116637 restraints weight = 16292.346| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.10 r_work: 0.3412 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1340 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 : 0.507 10.083 14654 Z= 0.246 Chirality : 0.041 0.128 1744 Planarity : 0.004 0.054 1812 Dihedral : 4.260 38.984 1588 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.94 % Allowed : 7.94 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.24), residues: 1352 helix: 1.82 (0.18), residues: 888 sheet: 2.24 (0.70), residues: 52 loop : -0.80 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 70 HIS 0.003 0.000 HIS A 704 PHE 0.014 0.001 PHE A 198 TYR 0.013 0.001 TYR A 578 ARG 0.004 0.000 ARG B 572 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 646) hydrogen bonds : angle 3.99486 ( 1878) covalent geometry : bond 0.00191 (10770) covalent geometry : angle 0.50665 (14654) *********************** 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 144 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.671 Fit side-chains REVERT: A 545 TYR cc_start: 0.8543 (p90) cc_final: 0.8191 (p90) REVERT: A 575 MET cc_start: 0.7753 (tmm) cc_final: 0.7470 (tmm) REVERT: B 198 PHE cc_start: 0.7242 (t80) cc_final: 0.6802 (t80) REVERT: B 228 TYR cc_start: 0.7772 (m-80) cc_final: 0.7562 (m-80) REVERT: B 545 TYR cc_start: 0.8646 (p90) cc_final: 0.8392 (p90) REVERT: B 694 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6712 (mp0) outliers start: 22 outliers final: 15 residues processed: 138 average time/residue: 0.1993 time to fit residues: 44.2876 Evaluate side-chains 129 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 390 THR 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 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 453 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 64 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 112 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.136032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.110160 restraints weight = 16483.313| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.10 r_work: 0.3314 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1560 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= 0.190 Angle : 0.572 8.107 14654 Z= 0.285 Chirality : 0.044 0.137 1744 Planarity : 0.004 0.056 1812 Dihedral : 4.246 34.587 1588 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.12 % Allowed : 11.29 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.24), residues: 1352 helix: 1.70 (0.18), residues: 886 sheet: 1.92 (0.68), residues: 52 loop : -0.84 (0.33), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 70 HIS 0.004 0.001 HIS A 704 PHE 0.016 0.002 PHE A 111 TYR 0.018 0.002 TYR B 228 ARG 0.004 0.001 ARG A 576 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 646) hydrogen bonds : angle 4.08965 ( 1878) covalent geometry : bond 0.00462 (10770) covalent geometry : angle 0.57233 (14654) *********************** 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 138 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 575 MET cc_start: 0.7869 (tmm) cc_final: 0.7524 (tmm) REVERT: B 198 PHE cc_start: 0.7350 (t80) cc_final: 0.6888 (t80) REVERT: B 227 LYS cc_start: 0.7784 (ptmt) cc_final: 0.7421 (ptpp) outliers start: 24 outliers final: 19 residues processed: 136 average time/residue: 0.1911 time to fit residues: 39.4418 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 : 1.145 ------------------------------------------------------------------------------- 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 178 VAL 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 452 PHE Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain B residue 104 LEU 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 452 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 38 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 26 optimal weight: 30.0000 chunk 51 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 125 optimal weight: 0.5980 chunk 94 optimal weight: 30.0000 chunk 76 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.137873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.110250 restraints weight = 16382.630| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.38 r_work: 0.3320 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10770 Z= 0.128 Angle : 0.521 9.276 14654 Z= 0.257 Chirality : 0.042 0.125 1744 Planarity : 0.004 0.057 1812 Dihedral : 4.058 31.108 1588 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.85 % Allowed : 12.26 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.24), residues: 1352 helix: 1.80 (0.18), residues: 886 sheet: 1.89 (0.69), residues: 52 loop : -0.82 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 70 HIS 0.003 0.001 HIS A 704 PHE 0.018 0.001 PHE A 198 TYR 0.011 0.001 TYR B 578 ARG 0.004 0.000 ARG B 572 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 646) hydrogen bonds : angle 3.97502 ( 1878) covalent geometry : bond 0.00298 (10770) covalent geometry : angle 0.52056 (14654) *********************** 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 136 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.114 Fit side-chains REVERT: A 227 LYS cc_start: 0.7818 (ptmt) cc_final: 0.7503 (ptpt) REVERT: A 575 MET cc_start: 0.7809 (tmm) cc_final: 0.7437 (tmm) REVERT: A 694 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6523 (mp0) REVERT: B 70 TRP cc_start: 0.7863 (p-90) cc_final: 0.7662 (p-90) REVERT: B 198 PHE cc_start: 0.7252 (t80) cc_final: 0.6771 (t80) REVERT: B 227 LYS cc_start: 0.7787 (ptmt) cc_final: 0.7535 (ptpt) REVERT: B 694 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6743 (mp0) outliers start: 21 outliers final: 16 residues processed: 134 average time/residue: 0.1917 time to fit residues: 39.0618 Evaluate side-chains 124 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 398 SER 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 398 SER 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 83 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 26 optimal weight: 30.0000 chunk 71 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.140357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.114513 restraints weight = 16476.128| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.07 r_work: 0.3405 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1765 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= 0.139 Angle : 0.534 8.268 14654 Z= 0.262 Chirality : 0.043 0.161 1744 Planarity : 0.004 0.056 1812 Dihedral : 4.122 41.297 1588 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.68 % Allowed : 13.40 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.24), residues: 1352 helix: 1.83 (0.18), residues: 886 sheet: 1.84 (0.69), residues: 52 loop : -0.84 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 70 HIS 0.003 0.001 HIS A 704 PHE 0.011 0.001 PHE B 391 TYR 0.013 0.001 TYR A 545 ARG 0.008 0.000 ARG A 572 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 646) hydrogen bonds : angle 3.96393 ( 1878) covalent geometry : bond 0.00328 (10770) covalent geometry : angle 0.53383 (14654) *********************** 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 130 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 1.278 Fit side-chains REVERT: A 70 TRP cc_start: 0.7945 (p-90) cc_final: 0.7702 (p-90) REVERT: A 227 LYS cc_start: 0.7865 (ptmt) cc_final: 0.7548 (ptpt) REVERT: A 575 MET cc_start: 0.7992 (tmm) cc_final: 0.7623 (tmm) REVERT: A 694 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6598 (mp0) REVERT: B 70 TRP cc_start: 0.7886 (p-90) cc_final: 0.7661 (p-90) REVERT: B 198 PHE cc_start: 0.7390 (t80) cc_final: 0.6915 (t80) REVERT: B 227 LYS cc_start: 0.7809 (ptmt) cc_final: 0.7547 (ptpt) REVERT: B 694 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6717 (mp0) outliers start: 19 outliers final: 18 residues processed: 126 average time/residue: 0.1981 time to fit residues: 38.2820 Evaluate side-chains 125 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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 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 398 SER 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 398 SER 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 93 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 overall best weight: 3.0784 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.140123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.114252 restraints weight = 16651.585| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.09 r_work: 0.3409 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10770 Z= 0.142 Angle : 0.531 9.057 14654 Z= 0.262 Chirality : 0.042 0.124 1744 Planarity : 0.004 0.057 1812 Dihedral : 4.204 46.418 1588 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.41 % Allowed : 13.93 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.24), residues: 1352 helix: 1.91 (0.18), residues: 884 sheet: 1.74 (0.68), residues: 52 loop : -0.78 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 70 HIS 0.002 0.001 HIS A 220 PHE 0.012 0.001 PHE A 198 TYR 0.012 0.001 TYR A 545 ARG 0.010 0.000 ARG B 572 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 646) hydrogen bonds : angle 3.94365 ( 1878) covalent geometry : bond 0.00336 (10770) covalent geometry : angle 0.53067 (14654) *********************** 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 130 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 1.353 Fit side-chains REVERT: A 70 TRP cc_start: 0.7951 (p-90) cc_final: 0.7698 (p-90) REVERT: A 198 PHE cc_start: 0.7782 (t80) cc_final: 0.7571 (t80) REVERT: A 227 LYS cc_start: 0.7867 (ptmt) cc_final: 0.7553 (ptpt) REVERT: A 575 MET cc_start: 0.8051 (tmm) cc_final: 0.7655 (tmm) REVERT: B 70 TRP cc_start: 0.7894 (p-90) cc_final: 0.7647 (p-90) REVERT: B 198 PHE cc_start: 0.7406 (t80) cc_final: 0.6908 (t80) REVERT: B 227 LYS cc_start: 0.7816 (ptmt) cc_final: 0.7572 (ptpt) outliers start: 16 outliers final: 16 residues processed: 127 average time/residue: 0.2826 time to fit residues: 54.1145 Evaluate side-chains 125 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 398 SER 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 398 SER 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 98 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 122 optimal weight: 0.0050 chunk 105 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.141454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.115740 restraints weight = 16375.515| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.07 r_work: 0.3456 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10770 Z= 0.113 Angle : 0.522 9.056 14654 Z= 0.253 Chirality : 0.042 0.124 1744 Planarity : 0.004 0.055 1812 Dihedral : 4.224 49.146 1588 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.59 % Allowed : 14.37 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.24), residues: 1352 helix: 1.97 (0.18), residues: 884 sheet: 1.87 (0.68), residues: 52 loop : -0.71 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 70 HIS 0.003 0.001 HIS B 704 PHE 0.009 0.001 PHE B 391 TYR 0.013 0.001 TYR A 237 ARG 0.009 0.000 ARG B 576 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 646) hydrogen bonds : angle 3.89067 ( 1878) covalent geometry : bond 0.00256 (10770) covalent geometry : angle 0.52222 (14654) *********************** 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 131 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.093 Fit side-chains REVERT: A 70 TRP cc_start: 0.7955 (p-90) cc_final: 0.7684 (p-90) REVERT: A 198 PHE cc_start: 0.7796 (t80) cc_final: 0.7471 (t80) REVERT: A 227 LYS cc_start: 0.7879 (ptmt) cc_final: 0.7503 (ptpp) REVERT: A 575 MET cc_start: 0.8106 (tmm) cc_final: 0.7698 (tmm) REVERT: A 694 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6581 (mp0) REVERT: B 70 TRP cc_start: 0.7880 (p-90) cc_final: 0.7637 (p-90) REVERT: B 198 PHE cc_start: 0.7372 (t80) cc_final: 0.6851 (t80) REVERT: B 227 LYS cc_start: 0.7833 (ptmt) cc_final: 0.7598 (ptpt) REVERT: B 694 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6660 (mp0) outliers start: 18 outliers final: 17 residues processed: 127 average time/residue: 0.1989 time to fit residues: 37.8802 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 : 1.182 ------------------------------------------------------------------------------- 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 452 PHE 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 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 100 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.139920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.114029 restraints weight = 16723.651| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.10 r_work: 0.3400 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10770 Z= 0.157 Angle : 0.544 8.474 14654 Z= 0.269 Chirality : 0.043 0.128 1744 Planarity : 0.004 0.056 1812 Dihedral : 4.375 52.297 1588 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.85 % Allowed : 14.46 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.24), residues: 1352 helix: 1.94 (0.18), residues: 884 sheet: 1.82 (0.69), residues: 52 loop : -0.79 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 70 HIS 0.003 0.001 HIS B 704 PHE 0.012 0.001 PHE B 111 TYR 0.013 0.001 TYR A 545 ARG 0.008 0.000 ARG A 572 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 646) hydrogen bonds : angle 3.94200 ( 1878) covalent geometry : bond 0.00376 (10770) covalent geometry : angle 0.54386 (14654) *********************** 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 133 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.062 Fit side-chains REVERT: A 70 TRP cc_start: 0.7942 (p-90) cc_final: 0.7736 (p-90) REVERT: A 227 LYS cc_start: 0.7852 (ptmt) cc_final: 0.7500 (ptpt) REVERT: A 575 MET cc_start: 0.8145 (tmm) cc_final: 0.7720 (tmm) REVERT: A 694 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6808 (mp0) REVERT: B 70 TRP cc_start: 0.7899 (p-90) cc_final: 0.7661 (p-90) REVERT: B 198 PHE cc_start: 0.7430 (t80) cc_final: 0.6886 (t80) REVERT: B 227 LYS cc_start: 0.7791 (ptmt) cc_final: 0.7542 (ptpt) REVERT: B 694 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6866 (mp0) outliers start: 21 outliers final: 19 residues processed: 128 average time/residue: 0.2064 time to fit residues: 39.4689 Evaluate side-chains 127 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 266 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 722 GLN 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 132 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.141593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.115747 restraints weight = 16482.980| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.09 r_work: 0.3430 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10770 Z= 0.107 Angle : 0.527 10.769 14654 Z= 0.257 Chirality : 0.042 0.126 1744 Planarity : 0.004 0.056 1812 Dihedral : 4.357 54.070 1588 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.41 % Allowed : 15.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.24), residues: 1352 helix: 1.98 (0.18), residues: 886 sheet: 1.97 (0.69), residues: 52 loop : -0.69 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 70 HIS 0.002 0.001 HIS B 704 PHE 0.010 0.001 PHE B 269 TYR 0.010 0.001 TYR A 313 ARG 0.011 0.001 ARG A 576 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 646) hydrogen bonds : angle 3.86657 ( 1878) covalent geometry : bond 0.00239 (10770) covalent geometry : angle 0.52749 (14654) ********************** 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 130 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 1.275 Fit side-chains REVERT: A 227 LYS cc_start: 0.7862 (ptmt) cc_final: 0.7493 (ptpp) REVERT: A 575 MET cc_start: 0.8123 (tmm) cc_final: 0.7700 (tmm) REVERT: A 694 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6586 (mp0) REVERT: B 70 TRP cc_start: 0.7855 (p-90) cc_final: 0.7600 (p-90) REVERT: B 198 PHE cc_start: 0.7394 (t80) cc_final: 0.6850 (t80) REVERT: B 227 LYS cc_start: 0.7845 (ptmt) cc_final: 0.7608 (ptpt) REVERT: B 694 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6704 (mp0) outliers start: 16 outliers final: 16 residues processed: 125 average time/residue: 0.2541 time to fit residues: 48.3642 Evaluate side-chains 129 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 266 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 453 MET 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 53 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 89 optimal weight: 0.0980 chunk 80 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.141727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.116182 restraints weight = 16455.059| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.06 r_work: 0.3457 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10770 Z= 0.121 Angle : 0.535 10.340 14654 Z= 0.262 Chirality : 0.042 0.124 1744 Planarity : 0.004 0.055 1812 Dihedral : 4.374 55.381 1588 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.68 % Allowed : 15.34 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.24), residues: 1352 helix: 1.99 (0.18), residues: 886 sheet: 2.01 (0.70), residues: 52 loop : -0.69 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 70 HIS 0.002 0.001 HIS B 704 PHE 0.010 0.001 PHE B 111 TYR 0.010 0.001 TYR A 545 ARG 0.016 0.001 ARG A 576 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 646) hydrogen bonds : angle 3.85601 ( 1878) covalent geometry : bond 0.00281 (10770) covalent geometry : angle 0.53455 (14654) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6429.67 seconds wall clock time: 115 minutes 15.19 seconds (6915.19 seconds total)